1

The Ontology of Experiments

Barry Smith

httpontologybuffaloedusmith

2

Plan

1 The Experiment Ontology

2 The Ontology of Biomedical Investigations

3 Unit Ontology

4 Phenotype Ontology

5 Document Ontology

3

EXPO

The Ontology of Experiments

L Soldatova R KingDepartment of Computer Science

The University of Wales Aberystwyth

4

EXPO

controlled vocabularymeta-modeltheory of contentknowledge management10487081048708 knowledge systematization10487081048708 knowledge sharing10487081048708 knowledge treatment10487081048708 knowledge reusabilitydata integration

5

EXPO Formalisation of Science

The goal of science is to increase our knowledge of the natural world through the performance of experiments

This knowledge should ideally be expressed in a formal logical language

Formal languages promote semantic clarity which in turn supports the free exchange of scientific knowledge and simplifies scientific reasoning

6

7

8

9

Suggested Upper Merged Ontology

Adam Peaseapeasearticulatesoftwarecomhttpwwwarticulatesoftwarecom

10

SUMO top levelEntity

ndash Physical bull Object

ndash SelfConnectedObject raquo Substance raquo CorpuscularObject raquo Food

ndash Region ndash Collection ndash Agent

bull Process ndash Abstract

bull SetOrClass bull Relation bull Quantity

ndash Number ndash PhysicalQuantity

bull Attribute bull Proposition

2

Plan

1 The Experiment Ontology

2 The Ontology of Biomedical Investigations

3 Unit Ontology

4 Phenotype Ontology

5 Document Ontology

3

EXPO

The Ontology of Experiments

L Soldatova R KingDepartment of Computer Science

The University of Wales Aberystwyth

4

EXPO

controlled vocabularymeta-modeltheory of contentknowledge management10487081048708 knowledge systematization10487081048708 knowledge sharing10487081048708 knowledge treatment10487081048708 knowledge reusabilitydata integration

5

EXPO Formalisation of Science

The goal of science is to increase our knowledge of the natural world through the performance of experiments

This knowledge should ideally be expressed in a formal logical language

Formal languages promote semantic clarity which in turn supports the free exchange of scientific knowledge and simplifies scientific reasoning

6

7

8

9

Suggested Upper Merged Ontology

Adam Peaseapeasearticulatesoftwarecomhttpwwwarticulatesoftwarecom

10

SUMO top levelEntity

ndash Physical bull Object

ndash SelfConnectedObject raquo Substance raquo CorpuscularObject raquo Food

ndash Region ndash Collection ndash Agent

bull Process ndash Abstract

bull SetOrClass bull Relation bull Quantity

ndash Number ndash PhysicalQuantity

bull Attribute bull Proposition

3

EXPO

The Ontology of Experiments

L Soldatova R KingDepartment of Computer Science

The University of Wales Aberystwyth

4

EXPO

controlled vocabularymeta-modeltheory of contentknowledge management10487081048708 knowledge systematization10487081048708 knowledge sharing10487081048708 knowledge treatment10487081048708 knowledge reusabilitydata integration

5

EXPO Formalisation of Science

The goal of science is to increase our knowledge of the natural world through the performance of experiments

This knowledge should ideally be expressed in a formal logical language

Formal languages promote semantic clarity which in turn supports the free exchange of scientific knowledge and simplifies scientific reasoning

6

7

8

9

Suggested Upper Merged Ontology

Adam Peaseapeasearticulatesoftwarecomhttpwwwarticulatesoftwarecom

10

SUMO top levelEntity

ndash Physical bull Object

ndash SelfConnectedObject raquo Substance raquo CorpuscularObject raquo Food

ndash Region ndash Collection ndash Agent

bull Process ndash Abstract

bull SetOrClass bull Relation bull Quantity

ndash Number ndash PhysicalQuantity

bull Attribute bull Proposition

4

EXPO

controlled vocabularymeta-modeltheory of contentknowledge management10487081048708 knowledge systematization10487081048708 knowledge sharing10487081048708 knowledge treatment10487081048708 knowledge reusabilitydata integration

5

EXPO Formalisation of Science

The goal of science is to increase our knowledge of the natural world through the performance of experiments

This knowledge should ideally be expressed in a formal logical language

Formal languages promote semantic clarity which in turn supports the free exchange of scientific knowledge and simplifies scientific reasoning

6

7

8

9

Suggested Upper Merged Ontology

Adam Peaseapeasearticulatesoftwarecomhttpwwwarticulatesoftwarecom

10

SUMO top levelEntity

ndash Physical bull Object

ndash SelfConnectedObject raquo Substance raquo CorpuscularObject raquo Food

ndash Region ndash Collection ndash Agent

bull Process ndash Abstract

bull SetOrClass bull Relation bull Quantity

ndash Number ndash PhysicalQuantity

bull Attribute bull Proposition

5

EXPO Formalisation of Science

The goal of science is to increase our knowledge of the natural world through the performance of experiments

This knowledge should ideally be expressed in a formal logical language

Formal languages promote semantic clarity which in turn supports the free exchange of scientific knowledge and simplifies scientific reasoning

6

7

8

9

Suggested Upper Merged Ontology

Adam Peaseapeasearticulatesoftwarecomhttpwwwarticulatesoftwarecom

10

SUMO top levelEntity

ndash Physical bull Object

ndash SelfConnectedObject raquo Substance raquo CorpuscularObject raquo Food

ndash Region ndash Collection ndash Agent

bull Process ndash Abstract

bull SetOrClass bull Relation bull Quantity

ndash Number ndash PhysicalQuantity

bull Attribute bull Proposition

6

7

8

9

Suggested Upper Merged Ontology

Adam Peaseapeasearticulatesoftwarecomhttpwwwarticulatesoftwarecom

10

SUMO top levelEntity

ndash Physical bull Object

ndash SelfConnectedObject raquo Substance raquo CorpuscularObject raquo Food

ndash Region ndash Collection ndash Agent

bull Process ndash Abstract

bull SetOrClass bull Relation bull Quantity

ndash Number ndash PhysicalQuantity

bull Attribute bull Proposition

7

8

9

Suggested Upper Merged Ontology

Adam Peaseapeasearticulatesoftwarecomhttpwwwarticulatesoftwarecom

10

SUMO top levelEntity

ndash Physical bull Object

ndash SelfConnectedObject raquo Substance raquo CorpuscularObject raquo Food

ndash Region ndash Collection ndash Agent

bull Process ndash Abstract

bull SetOrClass bull Relation bull Quantity

ndash Number ndash PhysicalQuantity

bull Attribute bull Proposition

8

9

Suggested Upper Merged Ontology

Adam Peaseapeasearticulatesoftwarecomhttpwwwarticulatesoftwarecom

10

SUMO top levelEntity

ndash Physical bull Object

ndash SelfConnectedObject raquo Substance raquo CorpuscularObject raquo Food

ndash Region ndash Collection ndash Agent

bull Process ndash Abstract

bull SetOrClass bull Relation bull Quantity

ndash Number ndash PhysicalQuantity

bull Attribute bull Proposition

9

Suggested Upper Merged Ontology

Adam Peaseapeasearticulatesoftwarecomhttpwwwarticulatesoftwarecom

10

SUMO top levelEntity

ndash Physical bull Object

ndash SelfConnectedObject raquo Substance raquo CorpuscularObject raquo Food

ndash Region ndash Collection ndash Agent

bull Process ndash Abstract

bull SetOrClass bull Relation bull Quantity

ndash Number ndash PhysicalQuantity

bull Attribute bull Proposition

10

SUMO top levelEntity

ndash Physical bull Object

ndash SelfConnectedObject raquo Substance raquo CorpuscularObject raquo Food

ndash Region ndash Collection ndash Agent

bull Process ndash Abstract

bull SetOrClass bull Relation bull Quantity

ndash Number ndash PhysicalQuantity

bull Attribute bull Proposition

11

Suggested Upper Merged Ontology

1000 terms 4000 axioms 750 rules

Associated domain ontologies totalling 20000 terms and 60000 axioms

[includes ontology of boundaries from BS]

12

SUMO Structure

Structural Ontology

Base Ontology

SetClass Theory Numeric Temporal Mereotopology

Graph Measure Processes Objects

Qualities

13

SUMO+Domain OntologyStructuralOntology

BaseOntology

SetClassTheory

Numeric Temporal Mereotopology

Graph Measure Processes Objects

Qualities

SUMO

Mid-Level

Military

Geography

Elements

Terrorist Attack Types

Communications

People

TransnationalIssues Financial

Ontology

TerroristEconomy

NAICSTerroristAttacks

hellip

FranceAfghanistan

UnitedStates

DistributedComputing

BiologicalViruses

WMD

ECommerceServices

Government

Transportation

WorldAirports

Total Terms Total Axioms Rules

20399 67108 2500

14

entity physical object process dual object process intentional process intentional psychological process recreation or exercise organizational process guiding keeping maintaining repairing poking content development making constructing manufacture publication cooking searching social interaction maneuver motion internal change shape change abstract

12

SUMO Structure

Structural Ontology

Base Ontology

SetClass Theory Numeric Temporal Mereotopology

Graph Measure Processes Objects

Qualities

13

SUMO+Domain OntologyStructuralOntology

BaseOntology

SetClassTheory

Numeric Temporal Mereotopology

Graph Measure Processes Objects

Qualities

SUMO

Mid-Level

Military

Geography

Elements

Terrorist Attack Types

Communications

People

TransnationalIssues Financial

Ontology

TerroristEconomy

NAICSTerroristAttacks

hellip

FranceAfghanistan

UnitedStates

DistributedComputing

BiologicalViruses

WMD

ECommerceServices

Government

Transportation

WorldAirports

Total Terms Total Axioms Rules

20399 67108 2500

14

entity physical object process dual object process intentional process intentional psychological process recreation or exercise organizational process guiding keeping maintaining repairing poking content development making constructing manufacture publication cooking searching social interaction maneuver motion internal change shape change abstract

13

SUMO+Domain OntologyStructuralOntology

BaseOntology

SetClassTheory

Numeric Temporal Mereotopology

Graph Measure Processes Objects

Qualities

SUMO

Mid-Level

Military

Geography

Elements

Terrorist Attack Types

Communications

People

TransnationalIssues Financial

Ontology

TerroristEconomy

NAICSTerroristAttacks

hellip

FranceAfghanistan

UnitedStates

DistributedComputing

BiologicalViruses

WMD

ECommerceServices

Government

Transportation

WorldAirports

Total Terms Total Axioms Rules

20399 67108 2500

14

entity physical object process dual object process intentional process intentional psychological process recreation or exercise organizational process guiding keeping maintaining repairing poking content development making constructing manufacture publication cooking searching social interaction maneuver motion internal change shape change abstract

14

entity physical object process dual object process intentional process intentional psychological process recreation or exercise organizational process guiding keeping maintaining repairing poking content development making constructing manufacture publication cooking searching social interaction maneuver motion internal change shape change abstract

15

corpuscular object =defA SelfConnectedObject whose parts have properties that are not shared by the whole

Subclass(es)organic object artifact

Coordinate term(s)content bearing object food substance

Axiom corpuscular object is disjoint from substance

substance =defAn Object in which every part is similar to every other in every relevant respect

16

advantages of SUMO

clear logical infrastructure FOL (too expressive for decidability more intuitive (human friendly) than eg OWL)

much more coherent than eg CYC upper level

much more coherent than the upper level hard wired into OWL-DL (and a fortiori into OWL-FULL)

FOL

17

problems with SUMO as Upper-Levelit contains its own tiny biology (protein

crustacean fruit-Or-vegetable )

it is overwhelmingly an ontology for abstract entities (sets functions in the mathematical sense )

no clear treatment of relations between instances vs relations between types

[all of these problems can be fixed]

18EXPO Experiment Ontology

19

representational style part_of experimental hypothesisexperimental actions part_of experimental design

20equipment part_of experimental design(confuses object with specification)

21

22

OBI

The Ontology of Biomedical Investigations

grew out of FuGE FuGO MGED PSI development activities

23

Overview of the Ontology of Biomedical Investigations

with thanks to Trish Whetzel (FuGO Working Group)

24

OBI neacutee FuGOPurpose

Provide a resource for the unambiguous description of the components of biomedical investigations such as the design protocols and instrumentation material data and types of analysis and statistical tools applied to the data NOT designed to model biology

Enables consistent annotation of data across different

technological and biological domains powerful queries semantically-driven data integration

25

Motivation for OBI

Standardization efforts in biological and technological domains Standard syntax - Data exchange formats

To provide a mechanism for software interoperability eg FuGE Object Model

Standard semantics - Controlled vocabularies or ontology Centralize commonalities for annotation term

needs across domains to describe an investigationstudyexperiment eg FuGO

26

Emerging FuGO Design Principles

OBO Foundry ontology utilize ontology best practices Inherit top level classes from an Upper Level ontology Use of the Relation Ontology Follow additional OBO Foundry principles Facilitates interoperability with other OBO Foundry

ontologiesOpen source approach

ProteacutegeacuteOWL Weekly conference calls Shared environment using Sourceforge (SF) and SF

mailing lists

27

OBI Collaborating CommunitiesCrop sciences Generation Challenge Programme (GCP)Environmental genomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiGenomic Standards Consortium (GSC)

wwwgenomicscehacukgenomecatalogueHUPO Proteomics Standards Initiative (PSI) psidevsourceforgenetImmunology Database and Analysis Portal wwwimmportorgImmune Epitope Database and Analysis Resource (IEDB)

httpwwwimmuneepitopeorghomedoInternational Society for Analytical Cytology httpwwwisac-netorgMetabolomics Standards Initiative (MSI) Neurogenetics Biomedical Informatics Research Network (BIRN)Nutrigenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiPolymorphismToxicogenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiTranscriptomics MGED Ontology Group

28

OBI also includes Clinical Trial Ontology

29

30

31

32

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

16

advantages of SUMO

clear logical infrastructure FOL (too expressive for decidability more intuitive (human friendly) than eg OWL)

much more coherent than eg CYC upper level

much more coherent than the upper level hard wired into OWL-DL (and a fortiori into OWL-FULL)

FOL

17

problems with SUMO as Upper-Levelit contains its own tiny biology (protein

crustacean fruit-Or-vegetable )

it is overwhelmingly an ontology for abstract entities (sets functions in the mathematical sense )

no clear treatment of relations between instances vs relations between types

[all of these problems can be fixed]

18EXPO Experiment Ontology

19

representational style part_of experimental hypothesisexperimental actions part_of experimental design

20equipment part_of experimental design(confuses object with specification)

21

22

OBI

The Ontology of Biomedical Investigations

grew out of FuGE FuGO MGED PSI development activities

23

Overview of the Ontology of Biomedical Investigations

with thanks to Trish Whetzel (FuGO Working Group)

24

OBI neacutee FuGOPurpose

Provide a resource for the unambiguous description of the components of biomedical investigations such as the design protocols and instrumentation material data and types of analysis and statistical tools applied to the data NOT designed to model biology

Enables consistent annotation of data across different

technological and biological domains powerful queries semantically-driven data integration

25

Motivation for OBI

Standardization efforts in biological and technological domains Standard syntax - Data exchange formats

To provide a mechanism for software interoperability eg FuGE Object Model

Standard semantics - Controlled vocabularies or ontology Centralize commonalities for annotation term

needs across domains to describe an investigationstudyexperiment eg FuGO

26

Emerging FuGO Design Principles

OBO Foundry ontology utilize ontology best practices Inherit top level classes from an Upper Level ontology Use of the Relation Ontology Follow additional OBO Foundry principles Facilitates interoperability with other OBO Foundry

ontologiesOpen source approach

ProteacutegeacuteOWL Weekly conference calls Shared environment using Sourceforge (SF) and SF

mailing lists

27

OBI Collaborating CommunitiesCrop sciences Generation Challenge Programme (GCP)Environmental genomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiGenomic Standards Consortium (GSC)

wwwgenomicscehacukgenomecatalogueHUPO Proteomics Standards Initiative (PSI) psidevsourceforgenetImmunology Database and Analysis Portal wwwimmportorgImmune Epitope Database and Analysis Resource (IEDB)

httpwwwimmuneepitopeorghomedoInternational Society for Analytical Cytology httpwwwisac-netorgMetabolomics Standards Initiative (MSI) Neurogenetics Biomedical Informatics Research Network (BIRN)Nutrigenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiPolymorphismToxicogenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiTranscriptomics MGED Ontology Group

28

OBI also includes Clinical Trial Ontology

29

30

31

32

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

17

problems with SUMO as Upper-Levelit contains its own tiny biology (protein

crustacean fruit-Or-vegetable )

it is overwhelmingly an ontology for abstract entities (sets functions in the mathematical sense )

no clear treatment of relations between instances vs relations between types

[all of these problems can be fixed]

18EXPO Experiment Ontology

19

representational style part_of experimental hypothesisexperimental actions part_of experimental design

20equipment part_of experimental design(confuses object with specification)

21

22

OBI

The Ontology of Biomedical Investigations

grew out of FuGE FuGO MGED PSI development activities

23

Overview of the Ontology of Biomedical Investigations

with thanks to Trish Whetzel (FuGO Working Group)

24

OBI neacutee FuGOPurpose

Provide a resource for the unambiguous description of the components of biomedical investigations such as the design protocols and instrumentation material data and types of analysis and statistical tools applied to the data NOT designed to model biology

Enables consistent annotation of data across different

technological and biological domains powerful queries semantically-driven data integration

25

Motivation for OBI

Standardization efforts in biological and technological domains Standard syntax - Data exchange formats

To provide a mechanism for software interoperability eg FuGE Object Model

Standard semantics - Controlled vocabularies or ontology Centralize commonalities for annotation term

needs across domains to describe an investigationstudyexperiment eg FuGO

26

Emerging FuGO Design Principles

OBO Foundry ontology utilize ontology best practices Inherit top level classes from an Upper Level ontology Use of the Relation Ontology Follow additional OBO Foundry principles Facilitates interoperability with other OBO Foundry

ontologiesOpen source approach

ProteacutegeacuteOWL Weekly conference calls Shared environment using Sourceforge (SF) and SF

mailing lists

27

OBI Collaborating CommunitiesCrop sciences Generation Challenge Programme (GCP)Environmental genomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiGenomic Standards Consortium (GSC)

wwwgenomicscehacukgenomecatalogueHUPO Proteomics Standards Initiative (PSI) psidevsourceforgenetImmunology Database and Analysis Portal wwwimmportorgImmune Epitope Database and Analysis Resource (IEDB)

httpwwwimmuneepitopeorghomedoInternational Society for Analytical Cytology httpwwwisac-netorgMetabolomics Standards Initiative (MSI) Neurogenetics Biomedical Informatics Research Network (BIRN)Nutrigenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiPolymorphismToxicogenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiTranscriptomics MGED Ontology Group

28

OBI also includes Clinical Trial Ontology

29

30

31

32

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

18EXPO Experiment Ontology

19

representational style part_of experimental hypothesisexperimental actions part_of experimental design

20equipment part_of experimental design(confuses object with specification)

21

22

OBI

The Ontology of Biomedical Investigations

grew out of FuGE FuGO MGED PSI development activities

23

Overview of the Ontology of Biomedical Investigations

with thanks to Trish Whetzel (FuGO Working Group)

24

OBI neacutee FuGOPurpose

Provide a resource for the unambiguous description of the components of biomedical investigations such as the design protocols and instrumentation material data and types of analysis and statistical tools applied to the data NOT designed to model biology

Enables consistent annotation of data across different

technological and biological domains powerful queries semantically-driven data integration

25

Motivation for OBI

Standardization efforts in biological and technological domains Standard syntax - Data exchange formats

To provide a mechanism for software interoperability eg FuGE Object Model

Standard semantics - Controlled vocabularies or ontology Centralize commonalities for annotation term

needs across domains to describe an investigationstudyexperiment eg FuGO

26

Emerging FuGO Design Principles

OBO Foundry ontology utilize ontology best practices Inherit top level classes from an Upper Level ontology Use of the Relation Ontology Follow additional OBO Foundry principles Facilitates interoperability with other OBO Foundry

ontologiesOpen source approach

ProteacutegeacuteOWL Weekly conference calls Shared environment using Sourceforge (SF) and SF

mailing lists

27

OBI Collaborating CommunitiesCrop sciences Generation Challenge Programme (GCP)Environmental genomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiGenomic Standards Consortium (GSC)

wwwgenomicscehacukgenomecatalogueHUPO Proteomics Standards Initiative (PSI) psidevsourceforgenetImmunology Database and Analysis Portal wwwimmportorgImmune Epitope Database and Analysis Resource (IEDB)

httpwwwimmuneepitopeorghomedoInternational Society for Analytical Cytology httpwwwisac-netorgMetabolomics Standards Initiative (MSI) Neurogenetics Biomedical Informatics Research Network (BIRN)Nutrigenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiPolymorphismToxicogenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiTranscriptomics MGED Ontology Group

28

OBI also includes Clinical Trial Ontology

29

30

31

32

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

19

representational style part_of experimental hypothesisexperimental actions part_of experimental design

20equipment part_of experimental design(confuses object with specification)

21

22

OBI

The Ontology of Biomedical Investigations

grew out of FuGE FuGO MGED PSI development activities

23

Overview of the Ontology of Biomedical Investigations

with thanks to Trish Whetzel (FuGO Working Group)

24

OBI neacutee FuGOPurpose

Provide a resource for the unambiguous description of the components of biomedical investigations such as the design protocols and instrumentation material data and types of analysis and statistical tools applied to the data NOT designed to model biology

Enables consistent annotation of data across different

technological and biological domains powerful queries semantically-driven data integration

25

Motivation for OBI

Standardization efforts in biological and technological domains Standard syntax - Data exchange formats

To provide a mechanism for software interoperability eg FuGE Object Model

Standard semantics - Controlled vocabularies or ontology Centralize commonalities for annotation term

needs across domains to describe an investigationstudyexperiment eg FuGO

26

Emerging FuGO Design Principles

OBO Foundry ontology utilize ontology best practices Inherit top level classes from an Upper Level ontology Use of the Relation Ontology Follow additional OBO Foundry principles Facilitates interoperability with other OBO Foundry

ontologiesOpen source approach

ProteacutegeacuteOWL Weekly conference calls Shared environment using Sourceforge (SF) and SF

mailing lists

27

OBI Collaborating CommunitiesCrop sciences Generation Challenge Programme (GCP)Environmental genomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiGenomic Standards Consortium (GSC)

wwwgenomicscehacukgenomecatalogueHUPO Proteomics Standards Initiative (PSI) psidevsourceforgenetImmunology Database and Analysis Portal wwwimmportorgImmune Epitope Database and Analysis Resource (IEDB)

httpwwwimmuneepitopeorghomedoInternational Society for Analytical Cytology httpwwwisac-netorgMetabolomics Standards Initiative (MSI) Neurogenetics Biomedical Informatics Research Network (BIRN)Nutrigenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiPolymorphismToxicogenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiTranscriptomics MGED Ontology Group

28

OBI also includes Clinical Trial Ontology

29

30

31

32

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

20equipment part_of experimental design(confuses object with specification)

21

22

OBI

The Ontology of Biomedical Investigations

grew out of FuGE FuGO MGED PSI development activities

23

Overview of the Ontology of Biomedical Investigations

with thanks to Trish Whetzel (FuGO Working Group)

24

OBI neacutee FuGOPurpose

Provide a resource for the unambiguous description of the components of biomedical investigations such as the design protocols and instrumentation material data and types of analysis and statistical tools applied to the data NOT designed to model biology

Enables consistent annotation of data across different

technological and biological domains powerful queries semantically-driven data integration

25

Motivation for OBI

Standardization efforts in biological and technological domains Standard syntax - Data exchange formats

To provide a mechanism for software interoperability eg FuGE Object Model

Standard semantics - Controlled vocabularies or ontology Centralize commonalities for annotation term

needs across domains to describe an investigationstudyexperiment eg FuGO

26

Emerging FuGO Design Principles

OBO Foundry ontology utilize ontology best practices Inherit top level classes from an Upper Level ontology Use of the Relation Ontology Follow additional OBO Foundry principles Facilitates interoperability with other OBO Foundry

ontologiesOpen source approach

ProteacutegeacuteOWL Weekly conference calls Shared environment using Sourceforge (SF) and SF

mailing lists

27

OBI Collaborating CommunitiesCrop sciences Generation Challenge Programme (GCP)Environmental genomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiGenomic Standards Consortium (GSC)

wwwgenomicscehacukgenomecatalogueHUPO Proteomics Standards Initiative (PSI) psidevsourceforgenetImmunology Database and Analysis Portal wwwimmportorgImmune Epitope Database and Analysis Resource (IEDB)

httpwwwimmuneepitopeorghomedoInternational Society for Analytical Cytology httpwwwisac-netorgMetabolomics Standards Initiative (MSI) Neurogenetics Biomedical Informatics Research Network (BIRN)Nutrigenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiPolymorphismToxicogenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiTranscriptomics MGED Ontology Group

28

OBI also includes Clinical Trial Ontology

29

30

31

32

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

21

22

OBI

The Ontology of Biomedical Investigations

grew out of FuGE FuGO MGED PSI development activities

23

Overview of the Ontology of Biomedical Investigations

with thanks to Trish Whetzel (FuGO Working Group)

24

OBI neacutee FuGOPurpose

Provide a resource for the unambiguous description of the components of biomedical investigations such as the design protocols and instrumentation material data and types of analysis and statistical tools applied to the data NOT designed to model biology

Enables consistent annotation of data across different

technological and biological domains powerful queries semantically-driven data integration

25

Motivation for OBI

Standardization efforts in biological and technological domains Standard syntax - Data exchange formats

To provide a mechanism for software interoperability eg FuGE Object Model

Standard semantics - Controlled vocabularies or ontology Centralize commonalities for annotation term

needs across domains to describe an investigationstudyexperiment eg FuGO

26

Emerging FuGO Design Principles

OBO Foundry ontology utilize ontology best practices Inherit top level classes from an Upper Level ontology Use of the Relation Ontology Follow additional OBO Foundry principles Facilitates interoperability with other OBO Foundry

ontologiesOpen source approach

ProteacutegeacuteOWL Weekly conference calls Shared environment using Sourceforge (SF) and SF

mailing lists

27

OBI Collaborating CommunitiesCrop sciences Generation Challenge Programme (GCP)Environmental genomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiGenomic Standards Consortium (GSC)

wwwgenomicscehacukgenomecatalogueHUPO Proteomics Standards Initiative (PSI) psidevsourceforgenetImmunology Database and Analysis Portal wwwimmportorgImmune Epitope Database and Analysis Resource (IEDB)

httpwwwimmuneepitopeorghomedoInternational Society for Analytical Cytology httpwwwisac-netorgMetabolomics Standards Initiative (MSI) Neurogenetics Biomedical Informatics Research Network (BIRN)Nutrigenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiPolymorphismToxicogenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiTranscriptomics MGED Ontology Group

28

OBI also includes Clinical Trial Ontology

29

30

31

32

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

22

OBI

The Ontology of Biomedical Investigations

grew out of FuGE FuGO MGED PSI development activities

23

Overview of the Ontology of Biomedical Investigations

with thanks to Trish Whetzel (FuGO Working Group)

24

OBI neacutee FuGOPurpose

Provide a resource for the unambiguous description of the components of biomedical investigations such as the design protocols and instrumentation material data and types of analysis and statistical tools applied to the data NOT designed to model biology

Enables consistent annotation of data across different

technological and biological domains powerful queries semantically-driven data integration

25

Motivation for OBI

Standardization efforts in biological and technological domains Standard syntax - Data exchange formats

To provide a mechanism for software interoperability eg FuGE Object Model

Standard semantics - Controlled vocabularies or ontology Centralize commonalities for annotation term

needs across domains to describe an investigationstudyexperiment eg FuGO

26

Emerging FuGO Design Principles

OBO Foundry ontology utilize ontology best practices Inherit top level classes from an Upper Level ontology Use of the Relation Ontology Follow additional OBO Foundry principles Facilitates interoperability with other OBO Foundry

ontologiesOpen source approach

ProteacutegeacuteOWL Weekly conference calls Shared environment using Sourceforge (SF) and SF

mailing lists

27

OBI Collaborating CommunitiesCrop sciences Generation Challenge Programme (GCP)Environmental genomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiGenomic Standards Consortium (GSC)

wwwgenomicscehacukgenomecatalogueHUPO Proteomics Standards Initiative (PSI) psidevsourceforgenetImmunology Database and Analysis Portal wwwimmportorgImmune Epitope Database and Analysis Resource (IEDB)

httpwwwimmuneepitopeorghomedoInternational Society for Analytical Cytology httpwwwisac-netorgMetabolomics Standards Initiative (MSI) Neurogenetics Biomedical Informatics Research Network (BIRN)Nutrigenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiPolymorphismToxicogenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiTranscriptomics MGED Ontology Group

28

OBI also includes Clinical Trial Ontology

29

30

31

32

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

23

Overview of the Ontology of Biomedical Investigations

with thanks to Trish Whetzel (FuGO Working Group)

24

OBI neacutee FuGOPurpose

Provide a resource for the unambiguous description of the components of biomedical investigations such as the design protocols and instrumentation material data and types of analysis and statistical tools applied to the data NOT designed to model biology

Enables consistent annotation of data across different

technological and biological domains powerful queries semantically-driven data integration

25

Motivation for OBI

Standardization efforts in biological and technological domains Standard syntax - Data exchange formats

To provide a mechanism for software interoperability eg FuGE Object Model

Standard semantics - Controlled vocabularies or ontology Centralize commonalities for annotation term

needs across domains to describe an investigationstudyexperiment eg FuGO

26

Emerging FuGO Design Principles

OBO Foundry ontology utilize ontology best practices Inherit top level classes from an Upper Level ontology Use of the Relation Ontology Follow additional OBO Foundry principles Facilitates interoperability with other OBO Foundry

ontologiesOpen source approach

ProteacutegeacuteOWL Weekly conference calls Shared environment using Sourceforge (SF) and SF

mailing lists

27

OBI Collaborating CommunitiesCrop sciences Generation Challenge Programme (GCP)Environmental genomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiGenomic Standards Consortium (GSC)

wwwgenomicscehacukgenomecatalogueHUPO Proteomics Standards Initiative (PSI) psidevsourceforgenetImmunology Database and Analysis Portal wwwimmportorgImmune Epitope Database and Analysis Resource (IEDB)

httpwwwimmuneepitopeorghomedoInternational Society for Analytical Cytology httpwwwisac-netorgMetabolomics Standards Initiative (MSI) Neurogenetics Biomedical Informatics Research Network (BIRN)Nutrigenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiPolymorphismToxicogenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiTranscriptomics MGED Ontology Group

28

OBI also includes Clinical Trial Ontology

29

30

31

32

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

24

OBI neacutee FuGOPurpose

Provide a resource for the unambiguous description of the components of biomedical investigations such as the design protocols and instrumentation material data and types of analysis and statistical tools applied to the data NOT designed to model biology

Enables consistent annotation of data across different

technological and biological domains powerful queries semantically-driven data integration

25

Motivation for OBI

Standardization efforts in biological and technological domains Standard syntax - Data exchange formats

To provide a mechanism for software interoperability eg FuGE Object Model

Standard semantics - Controlled vocabularies or ontology Centralize commonalities for annotation term

needs across domains to describe an investigationstudyexperiment eg FuGO

26

Emerging FuGO Design Principles

OBO Foundry ontology utilize ontology best practices Inherit top level classes from an Upper Level ontology Use of the Relation Ontology Follow additional OBO Foundry principles Facilitates interoperability with other OBO Foundry

ontologiesOpen source approach

ProteacutegeacuteOWL Weekly conference calls Shared environment using Sourceforge (SF) and SF

mailing lists

27

OBI Collaborating CommunitiesCrop sciences Generation Challenge Programme (GCP)Environmental genomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiGenomic Standards Consortium (GSC)

wwwgenomicscehacukgenomecatalogueHUPO Proteomics Standards Initiative (PSI) psidevsourceforgenetImmunology Database and Analysis Portal wwwimmportorgImmune Epitope Database and Analysis Resource (IEDB)

httpwwwimmuneepitopeorghomedoInternational Society for Analytical Cytology httpwwwisac-netorgMetabolomics Standards Initiative (MSI) Neurogenetics Biomedical Informatics Research Network (BIRN)Nutrigenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiPolymorphismToxicogenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiTranscriptomics MGED Ontology Group

28

OBI also includes Clinical Trial Ontology

29

30

31

32

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

25

Motivation for OBI

Standardization efforts in biological and technological domains Standard syntax - Data exchange formats

To provide a mechanism for software interoperability eg FuGE Object Model

Standard semantics - Controlled vocabularies or ontology Centralize commonalities for annotation term

needs across domains to describe an investigationstudyexperiment eg FuGO

26

Emerging FuGO Design Principles

OBO Foundry ontology utilize ontology best practices Inherit top level classes from an Upper Level ontology Use of the Relation Ontology Follow additional OBO Foundry principles Facilitates interoperability with other OBO Foundry

ontologiesOpen source approach

ProteacutegeacuteOWL Weekly conference calls Shared environment using Sourceforge (SF) and SF

mailing lists

27

OBI Collaborating CommunitiesCrop sciences Generation Challenge Programme (GCP)Environmental genomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiGenomic Standards Consortium (GSC)

wwwgenomicscehacukgenomecatalogueHUPO Proteomics Standards Initiative (PSI) psidevsourceforgenetImmunology Database and Analysis Portal wwwimmportorgImmune Epitope Database and Analysis Resource (IEDB)

httpwwwimmuneepitopeorghomedoInternational Society for Analytical Cytology httpwwwisac-netorgMetabolomics Standards Initiative (MSI) Neurogenetics Biomedical Informatics Research Network (BIRN)Nutrigenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiPolymorphismToxicogenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiTranscriptomics MGED Ontology Group

28

OBI also includes Clinical Trial Ontology

29

30

31

32

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

26

Emerging FuGO Design Principles

OBO Foundry ontology utilize ontology best practices Inherit top level classes from an Upper Level ontology Use of the Relation Ontology Follow additional OBO Foundry principles Facilitates interoperability with other OBO Foundry

ontologiesOpen source approach

ProteacutegeacuteOWL Weekly conference calls Shared environment using Sourceforge (SF) and SF

mailing lists

27

OBI Collaborating CommunitiesCrop sciences Generation Challenge Programme (GCP)Environmental genomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiGenomic Standards Consortium (GSC)

wwwgenomicscehacukgenomecatalogueHUPO Proteomics Standards Initiative (PSI) psidevsourceforgenetImmunology Database and Analysis Portal wwwimmportorgImmune Epitope Database and Analysis Resource (IEDB)

httpwwwimmuneepitopeorghomedoInternational Society for Analytical Cytology httpwwwisac-netorgMetabolomics Standards Initiative (MSI) Neurogenetics Biomedical Informatics Research Network (BIRN)Nutrigenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiPolymorphismToxicogenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiTranscriptomics MGED Ontology Group

28

OBI also includes Clinical Trial Ontology

29

30

31

32

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

27

OBI Collaborating CommunitiesCrop sciences Generation Challenge Programme (GCP)Environmental genomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiGenomic Standards Consortium (GSC)

wwwgenomicscehacukgenomecatalogueHUPO Proteomics Standards Initiative (PSI) psidevsourceforgenetImmunology Database and Analysis Portal wwwimmportorgImmune Epitope Database and Analysis Resource (IEDB)

httpwwwimmuneepitopeorghomedoInternational Society for Analytical Cytology httpwwwisac-netorgMetabolomics Standards Initiative (MSI) Neurogenetics Biomedical Informatics Research Network (BIRN)Nutrigenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiPolymorphismToxicogenomics MGED RSBI Group wwwmgedorgWorkgroupsrsbiTranscriptomics MGED Ontology Group

28

OBI also includes Clinical Trial Ontology

29

30

31

32

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

28

OBI also includes Clinical Trial Ontology

29

30

31

32

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

29

30

31

32

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

30

31

32

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

31

32

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

32

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

33

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

34

FuGO - Top Level Universals Continuant an entity that endureremains the same through time

bull Dependent Continuant depend on another entityEg Environment (depend on the set of ranges of conditions eg geographic location)

Eg Characteristics (entity that can be measured eg temperature unit)

- Realizable an entity that is realizable through a process (executedrun)Eg Software (a set of machine instructions)

Eg Design (the plan that can be realized in a process)

Eg Role (the part played by an entity within the context of a process)

bull Independent Continuant stands on its ownEg All physical entity (instrument technology platform document etc)

Eg Biological material (organism population etc)

Occurrent an entity that occursunfold in timebull Eg Temporal Regions Spatio-Temporal Regions (single actions or Event)

bull Process Eg Investigation (the entire lsquoexperimentalrsquo process)Eg Study (process of acquiring and treating the biological material)Eg Assay (process of performing some tests and recording the results)

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

35

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

36

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

37

Basic Formal Ontologya true upper level ontologyno interference with domain ontologiesno interference with physics cognitionno abstractano negative entitiesexplicit treatment of instances types and relations

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

38

Three dichotomies

instance vs type

continuant vs occurrent

dependent vs independent

everything in the ontology is a type

types exist in reality through their instances

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

39

instance vs type

experiments as instances

experiments as types

ontologies relate to types (kinds universals)

we need to keep track of instances in databases

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

40

BFO

ContinuantOccurrent(Process)

IndependentContinuant

DependentContinuant

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

41

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

42

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

43

Measurements and the Unit Ontology

with thanks to Chris Mungall

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

44

Reality has various measurable dimensions

length

weight

temperature

specific gravity

etc

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

45

Fiat boundaries

The product of (our) gridding activity

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

46Artistrsquos Grid

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

47

Measurement belongs to the realm of partitions

0 10 10 20 20 30 30 40

massivelyincreased normal increased chronic

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

48

An Act of Measurement

portion of reality

dependent magnitude (here distance)

+ independent bearer

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

49

The Act of Measurement

tape measure (grid) projected onto reality with endpoints mapped to endpoints

l l l l

l l l l

l l l l

l l l l

l l l l

l l l

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

50

Scalar qualities

A scalar quality can be partitioned on a linear scalendash fiat boundaries

Scalar qualities can be measuredMeasurements involve units

ndash A unit is a fiat subtype of a scalar qualities

Measurements are the simplest sorts of experiments (depend on equipment )

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

51

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short long heavy lighthellip

quality

hot

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

52

fiat subtypes of scalar qualities

spatial quality

length weighttemperature

is_a

short [length] light [weight]hellip

quality

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

53

Units are fiat subtypes of qualities

spatial quality

length weighttemperature

is_a

1mm 1cm 1g 1kghellip

quality

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

54

Representation of measurements

spatial quality

length weighttemperature

is_a

mm

cm

kg

g

qualityunit

measurement_of

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

55

Ontology of measurement types (units)

units are artifacts created through specific measurement practices

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

56

International System of Units(with thanks to Ingvar Johansson)

The International System of Units (abbreviated SI from the French language name Systegraveme international duniteacutes) is the modern form of the metric system It is the worlds most widely used system of units both in everyday commerce and in science

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

57

7 Base Quantity Dimensions

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

58

Base and Derived Units

Units based on undefined SI dimensions meter second kilogram ampere candela kelvin mole

Units based on defined SI dimensions volume area velocity acceleration newton joule pascal coulomb farad henry hertz lumen lux ohm etc

Dimensions can be multiplied and divided (v = ms)

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

59

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

60

The Units are Conventional (a matter of fiat)

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

61

The Dimensions are Not Conventional

All specific lengths can be compared with another but no specific length can be compared with a quantity from any other dimension

And this is not so because we have constructed the dimensions this way

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

62

Laws for Dimensions

It makes no sense to say that 5kg is more than or longer than 4m

The addition 5kg + 4m makes no sense

A thing can be both 5kg and 4m but it cannot possibly at one and the same time be both 5kg and 4kgnor both 5m and 4m

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

63

Quantities Contain a Duality

It is impossible to understand scales and additions if one does not accept that each determinate quantity (eg5kg 4m) contains a duality

a physical dimension (mass length) that it shares with other determinate quantities and

a unique determinateness that is referred to by means of the numeral (5 4)

A physical dimension might also be called a determinable

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

64

Quantities are Universals

Many different things can simultaneously have a mass of 5kg (length of 4m etc)

Determinate quantities are lsquorepeatablesrsquo or universals

When a determinate quantity is repeated its dimension is repeated too

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

66

Scales and Similarity Relations

0 1 2 3 4 5 6 7 8 9 10 cm

7 cm is more like 4 cm in length than 1 cm

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

67

Amount of Substance

What is a mole

It is simply a number such as dozen (12) or gross (144) It is 6022 x 10-23

ldquoWhen the mole is used the elementary entities must be specified and may be atoms molecules ions electrons other particles or specified groups of such particlesrdquo (Resolution 3 of the 14th CGPM 1971)

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

69

Some True Base Dimensionsconnected to

Amount of Substance

number of molecules of kind X

number of ions of kind X

number of atoms of kind X

number of fermions of kind X

number of bosons of kind X

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

71

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

72

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

73

Unifying goal integration

Integrating datandash within and across these domainsndash across levels of granularityndash across different perspectives

Requiresndash Rigorous formal definitions in both ontologies

and annotation schemas

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

74

Some thoughts on the ontology itself

Outlinendash Definitions

bull how do we define PATO termsbull what exactly is it wersquore defining

ndash is_a hierarchybull what are the top-level distinctionsbull what are the finer grained distinctions

ndash shapes and colors

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

75

Itrsquos all about the definitions

Everything is doomed to failure without rigorous definitionsndash even more so with PATO than other

ontologies

OBO Foundry Principlendash Definitions should describe things in reality

not how terms are usedbull definitions should not use the word lsquodescribingrsquo

Scope of PATO = Phenotypic qualities

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

76

Old PATOEntity ndash Attribute ndash Value

Eye ndash Red ndash Dark

New PATOEntity ndash Quality

Eye ndash Red Eye ndash Dark Red

Dark Red is_a Red

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

77

What a quality is NOT

Qualities are not measurementsndash Instances of qualities exist independently of their

measurementsndash Qualities can have zero or more measurements

These are not the names of qualitiesndash percentagendash processndash abnormalndash high

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

78

Some examples of qualities

The particular redness of the left eye of a single individual flyndash An instance of a quality type

The color lsquoredrsquondash A quality type

Note the eye does not instantiate lsquoredrsquo

PATO represents quality types (universals)ndash PATO definitions can be used to classify quality

instances by the types they instantiate

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

79

the particular case ofredness (of a particularfly eye)

the type ldquoredrdquo

instantiates

an instance of an eye(in a particular fly)

the type ldquoeyerdquo

instantiates

inheresin (is aquality ofhas_bearer)

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

80

Qualities are dependent entities

Qualities require bearersndash Bearers can be physical objects or processes

Examplendash A shape requires a physical object to bear itndash If the physical object ceases to exist (eg it

decomposes) then the shape ceases to exist

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

81

BFO

ContinuantOccurrent(Process)

IndependentContinuant

(molecule cell organorganism)

DependentContinuant

(quality functiondisease)

Functioning Side-Effect Stochastic Process

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

83

Scale Bearer Quality Definition (proposed)

Physical Continuant Mass Equivalent to the sum of the mass of the parts of the bearer (mass at the particle level is primitiveoutwith PATO)

Physical Continuant Opacity An optical quality manifest by the capacity of the bearer to block light

PhysChem Liquid Concentration A compositional relational quality manifest by the relative quantity of some chemical type contained by the bearer

Molecular Gene splicing quality manifest by the splicing processes undergone by the bearer

Cellular Cell ploidy A cellular quality manifest by the number of genomes that are part of the bearer

Cellular Cell transformative potency

A cellular quality manifest by the capacity of the bearer cell to differentiate to different cell types

Organismal Tissue tone

Organismal Organism reproductive quality

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

85

How many types of shape are there

notched T-shaped Y-shaped branched unbranched antrose retrose curled curved wiggly squiggly round flat square oblong elliptical ovoid cuboid spherical egg-shaped rod-shaped heart-shaped hellip

How do we define them

How do we compare them

Shapes cannot be organized in a linear scale

Compare problem of classifying RNA structures

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

87

Standard case monadic qualitiesExamples

ndash E=kidney Q=hypertrophiedndash autodef a kidney which is hypertrophied

We assume that there is more contextual data (not shown)ndash eg genotype environment number of organisms

in study that showed phenotype

Interpretation (with the rest of the database record)ndash all fish in this experiment with a particular

genotype had a hypertrophied kidney at some point in time

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

88

Who should use PATO

Originallyndash model organism mutant phenotypes

But alsondash ontology-based evolutionary systematicsndash neuroscience BIRNndash clinical uses

bull OMIMbull clinical records (clinical manifestations)bull drug effects chemical effects

ndash to define terms in other ontologiesbull eg diploid cell invasive tumor engineered gene

condensed chromosome

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

89

Biomedical Investigation

Ontology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

MeasurementOntology

Phenotype (Quality)Ontology

UnitOntology

DocumentOntology

ImageOntology

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

90

DocumentOntology

ImageOntology

information objects

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

91

Towards a Theory of Document Acts

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

93

We are interested in time-sensitive transactional documents

identification documents

commercial documents

legal documents

medical documents

Thus not in novels recipes diaries

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

95

OED

1 2 Teaching lesson learned (cf doctor docile docent)

3 That which serves to show point out or prove something evidence proof

4 Something written inscribed etc which furnishes evidence or information upon any subject as a manuscript title-deed tombstone coin picture etc

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

96

Scope of document act theorythe social and institutional (deontic quasi-legal)

powers of documents

the sorts of things we can do with documents

the social interactions in which documents play an essential role

the enduring institutional systems to which documents belong

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

97

Basic distinctions

ndash document as stand-alone entity vs document with all its different types of proximate and remote attachments

ndash document template vs filled-in documentndash document vs the piece of paper upon which it is

writtenprinted ndash authentic documents vs copies forgeriesndash allographic vs autographic entities

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

100

What happens when you sign your passport

bull you initiate the validity of the passportbull you attest to the truth of the assertions it contains (autographic)

bull you provide a sample pattern for comparison (allographic)

Three document acts for the price of one

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

101

Passport acts

I use my passport to prove my identity

You use my passport to check my identity

He renews my passport

They confiscate my passport

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

102

The creative power of documents

title deeds create property

stock and share certificates create capital

examination documents create PhDs

marriage licenses create bonds of matrimony

bankruptcy certificates create bankrupts

statutes of incorporation create business organizations

charters create universities cities guilds

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

104

Identity documents

create identity (and thereby create the possibility of identity theft)

what is the ontology of identity

what is the epistemology of identity (of the technologies of identification)

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

110

What can we do with a document [DOCUMENT ACTS]

Sign it

Stamp it

Copy it

Witness it

Fill it in

Revise it

Register it

Archive it

Realize (interrupt abort ) the actions mandated by it

Deliver it (de facto de jure)

Declare it activeinactive

Display it (price list)

Attest to its validity

Nullify it

Destroy it

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

111

Who can engage in document acts

creator of document of document-template (legislator drafter )

signer attestor

filler-in of template

checker (solicitor notary administrative official)

recipient

addressee (executor of an estate)

beneficiary (will )

registrar archivist

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

112

The ontology of signatures

signednot signedsigned

incorrectlyfraudulentlyand stampedand countersignedby proxywith a singlewith a plurality of signatories

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

113

Document Systems

the system of identity documents (of birth and death certificates and public records offices of visas passports consulates and border posts)

the system of legal documents (of codes of law summonses police reports court proceedings)

the system of credentialing documents (of degree certificates examinations class lists charters of credentialing organizations)

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

114

as document systems evolve

human beings acquire associated documentary skills in widening circles

they thereby acquire the capacity to concretize the relevant kinds of lsquowersquo intentionality to occupy the relevant kinds of positional roles within larger corporate wholes

through documents the actions of countless individuals become coordinated over space and time

documents thereby form the unifying threads of civilization

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END

115

END

• The Ontology of Experiments
• Plan
• EXPO
• Slide 4
• EXPO Formalisation of Science
• Slide 6
• Slide 7
• Slide 8
• Suggested Upper Merged Ontology
• SUMO top level
• Suggested Upper Merged Ontology
• SUMO Structure
• SUMO+Domain Ontology
• Slide 14
• Slide 15
• advantages of SUMO
• problems with SUMO as Upper-Level
• Slide 18
• Slide 19
• Slide 20
• Slide 21
• OBI
• Overview of the Ontology of Biomedical Investigations
• OBI neacutee FuGO
• Motivation for OBI
• Emerging FuGO Design Principles
• OBI Collaborating Communities
• OBI also includes Clinical Trial Ontology
• Slide 29
• Slide 30
• Slide 31
• Slide 32
• Slide 33
• FuGO - Top Level Universals
• Slide 35
• Slide 36
• Basic Formal Ontology
• Three dichotomies
• instance vs type
• BFO
• Slide 41
• Slide 42
• Measurements and the Unit Ontology
• Reality has various measurable dimensions
• Fiat boundaries
• Artistrsquos Grid
• Measurement belongs to the realm of partitions
• An Act of Measurement
• The Act of Measurement
• Scalar qualities
• fiat subtypes of scalar qualities
• Slide 52
• Units are fiat subtypes of qualities
• Representation of measurements
• Ontology of measurement types (units)
• International System of Units (with thanks to Ingvar Johansson)
• 7 Base Quantity Dimensions
• Base and Derived Units
• Slide 59
• The Units are Conventional (a matter of fiat)
• The Dimensions are Not Conventional
• Laws for Dimensions
• Quantities Contain a Duality
• Quantities are Universals
• Scales and Similarity Relations
• Amount of Substance
• Some True Base Dimensions connected to Amount of Substance
• Slide 71
• Slide 72
• Unifying goal integration
• Some thoughts on the ontology itself
• Itrsquos all about the definitions
• Old PATO Entity ndash Attribute ndash Value Eye ndash Red ndash Dark
• What a quality is NOT
• Some examples of qualities
• Slide 79
• Qualities are dependent entities
• Slide 81
• Slide 83
• How many types of shape are there
• Standard case monadic qualities
• Who should use PATO
• Slide 89
• Slide 90
• Towards a Theory of Document Acts
• We are interested in time-sensitive transactional documents
• OED
• Scope of document act theory
• Basic distinctions
• What happens when you sign your passport
• Passport acts
• The creative power of documents
• Identity documents
• What can we do with a document [DOCUMENT ACTS]
• Who can engage in document acts
• The ontology of signatures
• Document Systems
• as document systems evolve
• END