Underlying Ontologies for Biomedical work - The Relation Ontology (RO) and Basic Formal Ontology...

Underlying Ontologies for Biomedical work - The Relation Ontology (RO) and Basic Formal Ontology (BFO)

Thomas BittnerSUNY Buffalo

[email protected]

Disclaimer: I recycle many slides originally made by Barry Smith

mailto:[email protected]

Overview

•Motivation

•BFO and RO

•Top-level categories and relations of BFO/RO

•Conclusions

Why do we need a top-level ontology

such as Basic Formal Ontology

(BFO) ?

Karen Eilbecksong.sf.netproperties and features of

nucleic sequencesSequence Ontology

(SO)

RNA Ontology Consortium(under development)three-dimensional RNA

structuresRNA Ontology

(RnaO)

Barry Smith, Chris Mungallobo.sf.net/relationshiprelationsRelation Ontology (RO)

Protein Ontology Consortium(under development)protein types and

modificationsProtein Ontology

(PrO)

Michael Ashburner, Suzanna Lewis, Georgios Gkoutos

obo.sourceforge.net/cgi-bin/ detail.cgi?

attribute_and_valuequalities of biomedical entities

Phenotypic Quality Ontology (PaTO)

Gene Ontology Consortiumwww.geneontology.orgcellular components, molecular functions, biological processes

Gene Ontology (GO)

FuGO Working Groupfugo.sf.netdesign, protocol, data

instrumentation, and analysis

Functional Genomics Investigation Ontology

(FuGO)

JLV Mejino Jr.,Cornelius Rosse

fma.biostr.washington.edu

structure of the human bodyFoundational Model of Anatomy (FMA)

Melissa Haendel, Terry Hayamizu, Cornelius Rosse,

David Sutherland, (under development)

anatomical structures in human and model organisms

Common Anatomy Refer-ence Ontology (CARO)

Paula Dematos,Rafael Alcantara

ebi.ac.uk/chebimolecular entitiesChemical Entities of Bio-logical Interest (ChEBI)

Jonathan Bard, Michael Ashburner, Oliver Hofman

obo.sourceforge.net/cgi-bin/detail.cgi?cell

cell types from prokaryotes to mammals

Cell Ontology (CL)

CustodiansURLScopeOntology



(SO)

RNA Ontology Consortium

(under development)three-dimensional RNA structures

RNA Ontology(RnaO)




(PrO)






Gene Ontology (GO)




(FuGO)













Cell Ontology (CL)


Many partly independent efforts

RELATION TO TIME

GRANULARITY

CONTINUANT

OCCURREN

T

INDEPENDENT

DEPENDENT

ORGAN

ANDORGANIS

M

Organism(NCBI

Taxonomy)

Anatomical Entity(FMA, CARO

)

Organ

Function(F

MP,

CPRO

)

Phenotypic

Quality

(PaTO

)

Biological

Process(GO)

CELL

AND CELLULAR

COMPONENT

Cell

(CL)

Cellular Component(FMA, GO)

Cellula

r Function

(GO)

MOLECULE

Molecule

(ChEBI, SO,RnaO, PrO)

Molecular

Function

(GO)

Molecular

Process(GO)

Domain ontologies organized according to formal ontological

principles


principles

RELATION TO TIME

GRANULARITY

CONTINUANT

OCCURREN

T

INDEPENDENT

DEPENDENT

ORGAN

ANDORGANIS

M

Organism(NCBI

Taxonomy)


)

Organ

Function(F

MP,

CPRO

)

Phenotypic

Quality

(PaTO

)

Biological

Process(GO)

CELL

AND CELLULAR

COMPONENT

Cell

(CL)


Cellula

r Function

(GO)

MOLECULE

Molecule


Molecular

Function

(GO)

Molecular

Process(GO)

FMA

Domain ontologies specify the semantics of the vocabulary of a particular domain:

RNAO ChEBI

Cell OntologyPaTO

FMA

RNAO ChEBI

Cell OntologyPaTO

Top-level ontology

TLO

All domain ontologies use the same top level notions

FMA

RNAO ChEBI

Cell OntologyPaTO

Top-level ontology

BFO


Ontologicalprinciples

FMA

RNAO ChEBI

Cell OntologyPaTO

BFO


Diversity in the specifics

Commonalityin the foundations

FMA

RNAO ChEBI

Cell OntologyPaTO

BFO


Facilitates interoperatibility

FMA

RNAO ChEBI

Cell OntologyPaTO


SharedOrganizational,Scientific, and Ontologicalprinciples

RO

More acronyms: BFO vs. BFO-FOL vs. BFO-DL vs. RO

Kinds of Ontologies

Terms

General Logic

Thesauri

formalTaxonomies

Frames(OKBC)

Data Models(UML, STEP)

Description Logics

(DAML+OIL)

Principled, informal hierarchies

ad hoc Hierarchies

(Yahoo!) structured Glossaries

XML DTDs

Data Dictionaries

(EDI)

‘ordinary’Glossaries

XML Schema

DB Schema

Glossaries & Data Dictionaries

MetaData,XML Schemas, & Data Models

Formal Ontologies & Inference

Thesauri, Taxonomies

Michael Gruninger, [email protected]

Ontologies:logical inferences

Non-ontologies:no logical inferences

Kinds of Ontologies

Terms

General Logic

Thesauri

formalTaxonomies

Frames(OKBC)

Data Models(UML, STEP)

Description Logics

(DAML+OIL)

Principled, informal hierarchies

ad hoc Hierarchies

(Yahoo!) structured Glossaries

XML DTDs

Data Dictionaries

(EDI)

‘ordinary’Glossaries

XML Schema

DB Schema

Kinds of Ontology Languages

General Logic

Description Logics

(DAML+OIL)

Tradeoff betweenexpressive power and computability

How well canwe specify intendedmeaning of terms

What can we compute automatically

We need BOTH kinds of languages

General Logic

Description Logics

(DAML+OIL)

Tradeoff betweenexpressive power and computability

How well canwe specify intendedmeaning

What can we compute automatically

Computational representations of BFO


• BFO-FOL• ‘implementation’ of

BFO in first order logic


• BFO-DL• ‘implementation’ of

BFO in the description logic OWL (Ontology WEB language)




• BFO-DL• ‘implementation’ of

BFO in OWL



Focus on logically sound formulation of ontological principles

high expressive power of FOL needed

Focus oncomputation based on logically verified principles

computational efficiency of a DLneeded

26

BFO vs. RO

• RO = Relation ontology

• RO is a sub-set of BFO-DL that has been included in the OBO framework of ontologies

27

What is ‘in’ the Relation Ontology (RO) ???

Logically verified terminology that is relevant to the OBO-framework

terminology for top-level categories

terminology for top-level relations

Two distinct kinds of entities

universals particulars

types tokens

classes instances

Mishainstances

Tom

Instance-of Instance-of

substance

siamese

Is-acat

Is-amammal

Is-aanimal

Is-aorganism

Is-a

Human being

Is-a

Universals,classes,types

Particulars:Continuants vs. occurrents

Persistent entities

Persistent entities

Continuant• Persists through time

in virtue of being wholly present at every time at which it exists at all.

• I exist in full at this moment in time

Persistent entities

Continuant• Persists through time

in virtue of being wholly present at every time at which it exists at all.

• I exist in full at this moment in time

Occurrent• Evolve over time• Do not exist in full at

any given moment

• This presentation does not exist in full right now

Continuants have

spatial parts

Occurrents (processes) have spatio-temporal parts

t i m e

process

Continuants do NOT have spatio-temporal parts

• I am a continuant

• The first 5-minute phase of my existence is not a spatio-temporal part of me

• It is a spatio-temporal part of my life

• My life is a process

RELATION TO TIME

GRANULARITY

CONTINUANT

OCCURREN

T

INDEPENDENT

DEPENDENT

ORGAN

ANDORGANIS

M

Organism(NCBI

Taxonomy)


)

Organ

Function(F

MP,

CPRO

)

Phenotypic

Quality

(PaTO

)

Biological

Process(GO)

CELL

AND CELLULAR

COMPONENT

Cell

(CL)


Cellula

r Function

(GO)

MOLECULE

Molecule


Molecular

Function

(GO)

Molecular

Process(GO)

Ontologies organized according to ontological

principles

38

Kinds of continuants

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

Independent

continuants

(substances)

Dependent

continuants

39


Independent

continuants

(substances)

Dependent

continuants

40


Independent

continuants

(substances)

Dependent

continuants

41


Independent

continuants

(substances)

Dependent

continuants

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture. •the yellow color of this car•the maximal speed of this car

42


Independent

continuants

(substances)

Dependent

continuants

•the mass of this planet•its disposition to sustain life

43


Independent

continuants

(substances)

Dependent

continuants

•the mass of this molecule•its disposition to engage in chemical reactions

RELATION TO TIME

GRANULARITY

CONTINUANT

OCCURREN

T

INDEPENDENT

DEPENDENT

ORGAN

ANDORGANIS

M

Organism(NCBI

Taxonomy)


)

Organ

Function(F

MP,

CPRO

)

Phenotypic

Quality

(PaTO

)

Biological

Process(GO)

CELL

AND CELLULAR

COMPONENT

Cell

(CL)


Cellula

r Function

(GO)

MOLECULE

Molecule


Molecular

Function

(GO)

Molecular

Process(GO)


principles

Universals and particulars(cont.)

Mishasubstanceinstances

Tom


substance

siamese

Is-acat

Is-amammal

Is-aanimal

Is-aorganism

Is-a

Human being

Is-a

substance-Universals

Accidents: Species and instances

quality

color

red

scarlet

R232, G54, B24

Barry Smith

Universals among dependent continuants

Is-a

Is-a

Is-a

Is-a

this individual token of redness (this token redness – here, now)

Inst-Of

Of dependent continuants

Universals and particulars

Accidents : Species and instances

substance

animal

mammal

human

Irishman

this individual token man

Of independent continuants

RELATION TO TIME

GRANULARITY

CONTINUANT

OCCURREN

T

INDEPENDENT

DEPENDENT

ORGAN

ANDORGANIS

M

Organism(NCBI

Taxonomy)


)

Organ

Function(F

MP,

CPRO

)

Phenotypic

Quality

(PaTO

)

Biological

Process(GO)

CELL

AND CELLULAR

COMPONENT

Cell

(CL)


Cellula

r Function

(GO)

MOLECULE

Molecule


Molecular

Function

(GO)

Molecular

Process(GO)

Substance universals


principles

RELATION TO TIME

GRANULARITY

CONTINUANT

OCCURREN

T

INDEPENDENT

DEPENDENT

ORGAN

ANDORGANIS

M

Organism(NCBI

Taxonomy)


)

Organ

Function(F

MP,

CPRO

)

Phenotypic

Quality

(PaTO

)

Biological

Process(GO)

CELL

AND CELLULAR

COMPONENT

Cell

(CL)


Cellula

r Function

(GO)

MOLECULE

Molecule


Molecular

Function

(GO)

Molecular

Process(GO)

Quality/function universals


principles

52





53





Mishainstances

Tom


substance

siamese

Is-acat

Is-amammal

Is-aanimal

Is-aorganism

Is-a

Human being

Is-a

is-a relation betweenUniversals

Mishainstances

Tom


substance

siamese

Is-acat

Is-amammal

Is-aanimal

Is-aorganism

Is-a

Human being

Is-a


Human Beingis-amammal

Every instanceof Human Beingis also an instanceof mammal

Mishainstances

Tom


hasPet

isPetOf

substance

siamese

Is-acat

Is-amammal

Is-aanimal

Is-aorganism

Is-a

Human being

Is-a


IsPetOf

Instance-level relations

universal-level relations

Mishainstances

Tom


hasPet

isPetOf

cat

Human being

Universals

HasPet

IsPetOf

Universal parthood:

Human anatomy

The universal human body

The universalhuman head Human heads

are parts of human bodies

Universal parthood

Human-headsHuman-bodies

Part-of

Part-of

Universal parthood

Human-headsHuman-bodies

HasPart

HasPart

The semantics of universal parthood

X PART-OF Y iffFor every instance x of X there exists an instance y of Y such thatx part-of y

ANDFor every instance y of Y there exists an instance x of X such thatx part-of y

General framework for defining universal-level relations in terms of relations between individuals

Rall-some(A, B) =: – ∀x (Inst(x, A) → ∃y( Inst(y, B) & Rxy))– For every instance x of A there is some instance y of B such

that R(x,y) holds

Rsome-all(A, B) =: – ∀y (Inst(y, B) → ∃x( Inst(x, A) & Rxy))– For every instance y of B there is some instance x of A such

that R(x,y) holds

Rall-all(A, B) =: Rall-some(A, B) & Rsome-all(A, B)

R can be ANY binary relation

63

Important Individual-level relations

IndependentContinuant

Occurrent

DependentContinuant

You, me,This molecule,My cat Misha

Individual-level relations


Occurrent

DependentContinuant

My temperature (now)My heightMy role as a presenter



Occurrent

DependentContinuant

Processes:My life,My presenting this talk



Occurrent

DependentContinuant

Part-of

• My heart part-of my body• Montana part-of United States



Occurrent

ParticipatesIn

Part-of

• the runner participates in the racing process• the molecule participates in the diffusion process

DependentContinuant


DependentContinuant


Occurrent

ParticipatesIn

Part-of

• the racing involves racers• the diffusion process involves molecules

Involves



Occurrent

DependentContinuant

ParticipatesIn

Part-of

Part-of • the first 10 minutes of the presentation are part of the presentation• my childhood is part of my life

Involves



Occurrent

DependentContinuant

ParticipatesIn RealizationOf

PartOf

PartOf

• The power of a catalytic RNA to catalyze a reaction is realized through a complex process of binding substrates in the correct orientation and stabilizing reaction intermediates

• The role of antibiotics in treating infections is realized via the killing of bacteria

Involves



Occurrent

DependentContinuant

ParticipatesIn RealizationOf

PartOf

PartOf

• A warming process yields a rise in temperature•The tenure process yields a rise in John’s status

Involves

Changesquality



Occurrent

DependentContinuant

ParticipatesIn

InheresIn

RealizationOf

Part-of

PartOf

• Your height inheres in you• The role the antibiotics inheres in the antibiotics

Involves

Changesquality



Occurrent

DependentContinuant

ParticipatesIn

InheresIn

RealizationOf

Part-of

PartOf

Involves

Changesquality


• Time-dependent relations• ternary relations• time as parameter• R xyt the relation R holds between x and y and t• My left hand is (individual) part of my left arm now

• Time-independent relations• binary relations• R xy the relation R holds between x and y • Left Human Hand is part of Left Human Body (Canonical anatomy)

Relations among independent persistent entities

76

Conclusions

FMA

RNAO ChEBI

Cell OntologyPaTO

Basedupon thetop-level ontologyBFO

RO




(SO)

RNA Ontology Consortium(under development)three-dimensional RNA

structuresRNA Ontology

(RnaO)




(PrO)






Gene Ontology (GO)




(FuGO)













Cell Ontology (CL)


RELATION TO TIME

GRANULARITY

CONTINUANT

OCCURREN

T

INDEPENDENT

DEPENDENT

ORGAN

ANDORGANIS

M

Organism(NCBI

Taxonomy)


)

Organ

Function(F

MP,

CPRO

)

Phenotypic

Quality

(PaTO

)

Biological

Process(GO)

CELL

AND CELLULAR

COMPONENT

Cell

(CL)


Cellula

r Function

(GO)

MOLECULE

Molecule


Molecular

Function

(GO)

Molecular

Process(GO)


principles

Underlying Ontologies for Biomedical work - The Relation Ontology (RO) and Basic Formal Ontology...

Documents

Transcript of Underlying Ontologies for Biomedical work - The Relation Ontology (RO) and Basic Formal Ontology...