Lecture 3 BFO: A Standard Upper Level Ontology. 2 BFO als standard upper-level Ontologie Introduces...

Lecture 3BFO: A Standard Upper

Level Ontology

2

BFO als standard upper-level Ontologie

• Introduces Basic Formal Ontology (BFO)• Shows how BFO is extended by the

Information Artifact Ontology (controlled vocabulary for describing diagrams, images, documents, data, …)

3

The idea of ontological realism

• Before we build a data model we need to look at the reality we are trying to represent (= let’s look at the best scientific theory we have of this reality)

• Let’s constrain our data models so that our databases are veridical representations of the world outside

4

Scientific ontologies have special features

Every term in a scientific ontology must be such that the developers of the ontology believe it to refer to some entity* in reality on the basis of the best current evidence

*in first approximation: instances of a type

located near

LatrineWell

‘VT 334 569’

Distance Measurement

Result

Village Name

‘Khanabad Village’

Village

is_a

instance_of

Geopolitical Entity

Spatial Region

GeographicCoordinates

Setdesignates

instance_of

located in

instance_of

has location designates

has location

instance_of

instance_of

’16 meters’

instance_of

measurement_of

5

Universals and Instances (from Bill Mandrick)

6

For science, and thus for scientific ontologies,

it is generalizations that are of prime important = universals,

types, kinds, species

7

For scientific ontologies

• reusability, openness is crucial• intelligibility to humans is crucial• revisability is crucial • there is always an open world assumption• testability is crucial• compatibility with neighboring scientific

ontologies is crucial it should not be too easy to add new terms to an ontology

8

For scientific ontologiesthe issue of how the ontology will be used is not a factor relevant for determining how entities are treated by the ontology

If this decision is made to reflect specific, local practical needs, this will thwart reusability of the data the ontology is used to annotate

BFO

A simple top-level ontology to support information integration in scientific research

Defining a framework that will help to ensure consistency and non-redundancy of the ontologies created in its terms

9

Three Fundamental Dichotomies

• Continuant vs. occurrent

• Dependent vs. independent

• Type vs. instance

http://ontology.buffalo.edu/bfo/ 10

Continuant

thing, quality …

Occurrent

process, event

11

depends_on

Continuant Occurrent

process, eventIndependentContinuant

thing

DependentContinuant

quality

quality dependson bearer

12

depends_on



thing

DependentContinuant

quality, … event dependson participant

13

instance_of



thing

DependentContinuant

quality

.... ..... .......

types

instances 14

depends_on


process

IndependentContinuant

thing

DependentContinuant

quality

.... ..... .......temperature dependson bearer

15

3 kinds of (binary) relations• Between types

• human is_a mammal• human heart part_of human

• Between an instance and a type• this human instance_of the type human• this human allergic_to the type tamiflu

• Between instances• Mary’s heart part_of Mary• Mary’s aorta connected_to Mary’s heart

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Clark et al., 2005

part_of

is_a

Definitions of relations

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Barry Smith, et al., “Relations in Biomedical Ontologies”, Genome Biology 2005, 6 (5), R46.

Type-level relations presuppose the underlying instance-level relations

A part_of B =def. All instances of A are instance-level-parts-of some instance of B

e.g. human heart part_of human

A has_participant B =def. All instances of A have an instance of B as instance-level participant

e.g. cell binding has_participant cell

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Blinding Flash of the Obvious

Continuant Occurrent(Process, Event)


DependentContinuant

How to create an ontology from the top down

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Example: The Cell Ontology

Benefits of coordination

No need to reinvent the wheel

Can profit from lessons learned through mistakes made by others

Can more easily reuse what is made by others

Can more easily inspect and criticize results of others’ work (PATO)

Leads to innovations (e.g. Mireot) in strategies for combining ontologies

21

Users of BFO

PharmaOntology (W3C HCLS SIG)

MediCognos / Microsoft Healthvault

Cleveland Clinic Semantic Database in Cardiothoracic Surgery

Major Histocompatibility Complex (MHC) Ontology (NIAID)

Neuroscience Information Framework Standard (NIFSTD) and Constituent Ontologies

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Users of BFO

Interdisciplinary Prostate Ontology (IPO)

Nanoparticle Ontology (NPO): Ontology for Cancer Nanotechnology Research

Neural Electromagnetic Ontologies (NEMO)

ChemAxiom – Ontology for Chemistry

Ontology for Risks Against Patient Safety (RAPS/REMINE) (EU FP7)

IDO Infectious Disease Ontology (NIAID)

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Users of BFO

National Cancer Institute Biomedical Grid Terminology (BiomedGT)

US Army Universal Core Semantic Layer (UCore SL)

US Army Biometrics Ontology

United Nations Environment Programme

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Infectious Disease Ontology Consortium

• MITRE, Mount Sinai, UTSouthwestern – Influenza• IMBB/VectorBase – Vector borne diseases (A.

gambiae, A. aegypti, I. scapularis, C. pipiens, P. humanus)

• Colorado State University – Dengue Fever• Duke University – Tuberculosis, Staph. aureus, HIV• Case Western Reserve – Infective Endocarditis• University of Michigan – Brucilosis

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– GO Gene Ontology– CL Cell Ontology– SO Sequence Ontology– ChEBI Chemical Ontology – PATO Phenotype (Quality) Ontology– FMA Foundational Model of Anatomy– ChEBI Chemical Entities of Biological Interest – PRO Protein Ontology– Plant Ontology– Environment Ontology– Ontology for Biomedical Investigations– RNA Ontology

OBO Open Biomedical Ontologies

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RELATION TO TIME

GRANULARITY

CONTINUANT OCCURRENT

INDEPENDENT DEPENDENT

ORGAN ANDORGANISM

Organism(NCBI

Taxonomy)

Anatomical Entity(FMA, CARO)

OrganFunction

(FMP, CPRO) Phenotypic

Quality(PaTO)

Biological Process

(GO)CELL AND CELLULAR

COMPONENT

Cell(CL)

Cellular Compone

nt(FMA, GO)

Cellular Function

(GO)

MOLECULEMolecule

(ChEBI, SO,RnaO, PrO)

Molecular Function(GO)

Molecular Process

(GO)

The Open Biomedical Ontologies (OBO) Foundry27

Blinding Flash of the Obvious

Continuant Occurrent(Process, Event)


DependentContinuant

How to create an ontology from the top down

28

Specifically Dependent Continuant

Red color of my skin

You Me

Accidens non migrat de subjecto in subjectum.

Accidents do not migrate from one substance to another

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Red color of your skin

depends_on depends_on

Continuant


DependentContinuant

..... .....

Non-realizableDependentContinuant(quality)

Realizable DependentContinuant(function, role, disposition)

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Realizable dependent continuants

planfunctionroledispositioncapabilitytendency

continuants

31

Their realizations

execution expression exercise realization applicationcourse

occurrents

32

Continuant


DependentContinuant

..... .....

Non-realizableDependentContinuant(quality)


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realization depends_on realizable



bearer

DependentContinuant

disposition

.... ..... .......Process of realization

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Specific Dependenceon the instance level

a depends_on b =def. a is necessarily such that if b ceases to exist than a ceases to exist

on the type level

A specifically_depends_on B =def. for every instance a of A, there is some instance b of B such that a depends_on b.

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depends_on



thing

DependentContinuant

quality


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The (Aristotelian) Ontological Sextet

Substances Quality entities Processes

UniversalsSubstance-universals

Quality-universals

Process-universals

ParticularsIndividual

Substances

Quality-instances (Tropes…)

Process-instances

Specifically dependent continuants

• the quality of whiteness of this cheese

• your role as lecturer

• the disposition of this patient to experience diarrhea

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the particular case of redness (of a particular fly eye)

the universal red

instantiates

an instance of an eye (in a particular fly)

the universal eye

instantiates

depends on

40

the particular case of redness (of a particular fly eye)

red

instantiates

an instance of an eye (in a particular fly)

eye

instantiates

depends on

color anatomical structure

is_a is_a

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depends_on


process


thing

DependentContinuant

quality


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Specifically Dependent Continuants

SpecificallyDependentContinuant

Quality, Pattern

Realizable Dependent Continuant

if the bearer ceases to exist, then its quality, function, role ceases to exist

the color of my skin

the function of my heart to pump blood

my weight43

RELATION TO TIME

GRANULARITY



ORGAN ANDORGANISM

Organism(NCBI

Taxonomy)

Anatomical Entity(FMA, CARO)

OrganFunction


Quality(PaTO)

Biological Process

(GO)CELL AND CELLULAR

COMPONENT

Cell(CL)

Cellular Compone

nt(FMA, GO)

Cellular Function

(GO)

MOLECULEMolecule

(ChEBI, SO,RnaO, PrO)


Molecular Process

(GO)

The Open Biomedical Ontologies (OBO) Foundry44



ORGAN ANDORGANISM

Organism(NCBI

Taxonomy)

Anatomical Entity

(FMA, CARO)

OrganFunction


Quality(PaTO)

Organism-Level Process

(GO)

CELL AND CELLULAR

COMPONENT

Cell(CL)

Cellular Compone

nt(FMA, GO)

Cellular Function

(GO)

Cellular Process

(GO)

MOLECULEMolecule

(ChEBI, SO,RNAO, PRO)


Molecular Process

(GO)

rationale of OBO Foundry coverage

GRANULARITY

RELATION TO TIME

45

Continuant


Specifically DependentContinuant

..... .....Quality


46

Specific Dependenceon the instance level

a depends_on b =def. a is necessarily such that if b ceases to exist than a ceases to exist

on the type level

A specifically_depends_on B =def. for every instance a of A, there is some instance b of B such that a depends_on b.

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Generically Dependent Continuants

GenericallyDependentContinuant

Information Object

Gene Sequence

if one bearer ceases to exist, then the entity can survive, because there are other bearers

(copyability)

the pdf file on my laptop

the DNA (sequence) in this chromosome 48

Continuant



..... .....Quality


49

Realizable dependent continuants

plan

function

role

disposition

capability

tendency

continuants

50

Their realizations

execution

expression

exercise

realization

application

course

occurrents

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SpecificallyDependentContinuant

Quality

Disposition

Functioning

Function


Realizable

Role

Information Artifact

Sequence…

IAO• IAO: The Information Artifact Ontology, developed

by scientific researchers as a vehicle for annotating data about measurement results, publications, protocols, databases, consent forms, licenses

in a way that will allow discovery, integration and analysis

Two kinds of data about data:– 1. what are the data about Domain Ontologies– 2. how the data are packaged (collected, presented,

formatted, stored) IAO Ontologies

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http://bioportal.bioontology.org/ontologies/IAO

http://bioportal.bioontology.org/ontologies/IAO

IAO-Intel

• IAO-Intel – an extension of IAO and incorporating features of the AIRS Information Ontology – to provide common resources for the consistent description of information artifacts of relevance to the intelligence community

IAO: Report / IAO-Intel: Intelligence Report

IAO-Intel terms are defined by using terms from the ontologies in the yellow box via relations such as:•is-about•created-by•derives-from and so forth

Anatomy Ontology(FMA*, CARO)

Environment

Ontology(EnvO)

Infectious Disease

Ontology(IDO*)

Biological Process

Ontology (GO*)

Cell Ontology

(CL)

CellularComponentOntology

(FMA*, GO*) Phenotypic Quality

Ontology(PaTO)

Subcellular Anatomy Ontology (SAO)Sequence Ontology

(SO*) Molecular Function

(GO*)Protein Ontology(PRO*) Extension Strategy + Modular Organization

top level

mid-level

domain level

Information Artifact Ontology

(IAO)

Ontology for Biomedical

Investigations(OBI)

Spatial Ontology

(BSPO)

Basic Formal Ontology (BFO)

57

Information Artifactsartifact =def. an entity created through some deliberate act or acts by one or more human beings and which endures through time

information artifact: an artifact that can be the bearer of information

(a) information artifact (IA) – a hard drive, a passport, a piece of paper with a drawing of a map(b) information content entity (ICE) – an entity which is about something and which can potentially exist in multiple (for example digital or printed) copies – a jpg file, a pdf file

Types and tokens

Copyable information artifacts can exist both as tokensPeirce and as typesPeirce

Token = the particular information artifact of interest, tied to some particular physical information bearer: the photographic image on this piece of paper retrieved from this enemy combatantType = The copyable information content that is carried by the artifact in question. The same photographic image type may be printed out in multiple paper tokensWarning: this is not the same as the instance-class distinction

IAO is designed to address the need for metadata standards, not by

replacing existing standards,• but rather by providing a single, consistent

framework for tagging (‘semantic enhancement’) of existing data stores

• Its purpose is to provide a uniform, non-redundant, algorithmically processable and easily extendible consensus system of tags

Core of IAOType Definition IAO

Information Content Entity (ICE)

a generically dependent continuant that stands in the relation of aboutness to some entity

ICE

Information Structure Entity (ISE)

a generically dependent continuant that is not an ICE but which is complemented or complementable by one or more ICEs to create another ICE (example: cell in a spreadsheet, hard line break, space between words, semi-colon)

(new)

Information Quality Entity (IQE)

a quality that concretizes some ICE or ISE. (Comment: Typically an IQE will be a complex pattern made up of multiple qualities joined together spatially)

Information Carrier

Artifact a Material Entity that was created or modified or selected by some Agent to realize a certain function or to fulfill a certain role (Example: a screwdriver, a hard drive, a traffic sign)

(new)

Information Artifact (IA)

an artifact whose function is to bear an IQE.(Examples: a hard drive, a blank sheet of paper, a passport, a currency note)

(new)

Plan added as primitive (new)61

Attributes of IAs

• Information artifacts have attributes along a number of distinct dimensions, treated in low-level ontology modules

• Terms in these modules will be applied to explicate information relating to IAs of different sorts, and to annotate data pertaining to IA instances

• Attributes of IAs vs. Attributes of subject-matters, targets, topics, …

Attributes of IAs (cont.)

• Some dimensions of IA attributes are common to all areas, both military and non-military – Purpose– Life cycle Stage (draft, finished version, revision)– Language,– Format– Provenance– Source (person, organization)

Generic Attributes of IAs (for IAO)• Purpose

– Descriptive purpose: scientific paper, newspaper article, after-action report

– Prescriptive purpose: legal code, license, statement of rules of engagement

– Directive purpose (of specifying a plan or method for achieving something): instruction, manual, protocol

– Designative purpose: a registry of members of an organization, a phone book, a database linking proper names of persons with their social security numbers

• Purposes specific to IAO-Intel– Inform ing the commander,– Providing targeting support– Intelligence preparation of the battlefield.

Descriptive purpose=def. the purpose of describing some portion of

realityExamples: scientific paper, newspaper article,

diary, experimenter log notebookPrescriptive purpose=def. the purpose of prescribing or permitting or

allowing some activityExamples: a legal code, a license

Purpose of an Information Artifact

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Directive purpose=def. the purpose of specifying a plan or method for

achieving somethingExamples: instruction, manual, recipe, protocolDesignative purpose=def. the purpose of uniquely designating some

entity or the members of some class of entitiesExamples: a registry of members of an organization,

a phone book, a database linking proper names of persons with their social security numbers.

Purpose of an Information Artifact

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Examples of Generic Attributes of IAs

• Purpose• Lifecycle Stage (draft, finished version, revision)• Language• Format• Provenance• Source (person, organization)

These terms will be included in IAOEach corresponds to a specific low level ontology

Other IAO-Intel Attribute Dimensions• Classification

– Unclassified, open source– Secret– Top Secret

• Level– Strategic– Operational– Tactical

• Encryption Status• Encryption Strength

Strategy for Building IAO-Intel• Incremental expansion; the ontology is planned to

include artifacts spanning the entire range of IAs, from authoritative data sources to unprocessed reports

• Identify orthogonal dimensions of IA attributes and create Low-Level Ontology modules (LLOs)– Small, shallow, and structured following the principle

of single inheritance– Used to

• Construct more complex terms and define IAO terms• Explicate the meanings of terms standardly used by

different agencies• Annotate instance data

IAO and BFO

BFO: Generically Dependent Continuant

BFO: Independent Continuant

BFO: Specifically Dependent Continuant

Information Content

Entity (ICE)

Information Quality Entity

(Pattern) (IQE)

Information Structure

Entity (ISE)


Generically Dependent Continuant


pdf filejpg file

Gene Sequence

if one bearer ceases to exist, then the entity can survive, because there are other bearers

(copyability)

the pdf file on my laptop

the DNA (sequence) in this chromosome

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Information artifacts

pdf file

email

poem

symphony

algorithm

symbol

– can migrate from one information artifact to another

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Continuant



Quality

Disposition

Information Artifact

Role

Realizable DependentContinuant

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Gene Sequence

Continuant



Quality Information Artifact

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Gene Sequence

Material Entity

Information Bearing

Entity

Continuant



QualityInformation

Artifact

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Material Entity

Information Bearing

Entity (yourhard drive

Information Quality Entity (pattern on

your hard drive)depends_on

Continuant



Quality Information Artifact

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Material Entity

Information Bearing

Entity

Information QualityEntity

depends_on concretized_by

IAO: information content entity=def. an entity that is generically dependent on some artifact and stands in the relation of aboutness to some entity

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IA IBE ISE ICE

MS Word file (.doc, .docx)

Hard drive (magnetized sector)

MS Word format Varies

KML file Hard drive (magnetized sector)

KML Map overlay

JPEG file (.jpg)Hard drive (magnetized sector)

JPEG format Image

Email fileHard drive (magnetized sector)

Internet Message Format (e.g., RFC 5322 compliant) Message

USMTF Message file

A specific government network

USMTF Format Message

PassportPaper document; (may include photographs, RFID tags)

ID formats, security marking formats …

Name, Personal data, Passport number, Visas

Title Deed Official paper document Varies Varies

Report Varies Varies Varies

Overlay Sheet( e.g. Map Overlay Sheet)

Acetate sheetMIL-STD-2525 Symbols; FM 101-1-5 Operational Terms and Graphics

Map overlay

IAO and BFO

BFO: Generically Dependent Continuant

BFO: Independent Continuant

BFO: Specifically Dependent Continuant

Information Content

Entity (ICE)

Information Quality Entity

(Pattern) (IQE)

Information Structure

Entity (ISE)


IAO and BFO (cont.)

• BFO relations between ICEs, ISEs, IQEs and IBEs can be set forth as follows:– ICE generically-depends-on IBE– ISE generically-depends-on IBE– IQE specifically-depends-on IBE– ICE concretized-by IQE– ISE concretized-by IQE

• IAO contains in addition relations which allow to formulate metadata concerning attributes of IAs such as author, creation date, classification status, and so forth

Lecture 3 BFO: A Standard Upper Level Ontology. 2 BFO als standard upper-level Ontologie Introduces...

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