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

bittner3@buffalo.edu

Disclaimer: I recycle many slides originally made by Barry Smith

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

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

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

RNA Ontology Consortium

(under development)three-dimensional RNA structures

RNA Ontology(RnaO)

Gene Ontology (GO)

(FuGO)

Cell Ontology (CL)

Many partly independent efforts

RELATION TO TIME

GRANULARITY

CONTINUANT

OCCURREN

INDEPENDENT

DEPENDENT

ANDORGANIS

Organism(NCBI

Taxonomy)

Anatomical Entity(FMA, CARO

Function(F

Phenotypic

Quality

Biological

Process(GO)

AND CELLULAR

COMPONENT

Cellular Component(FMA, GO)

Cellula

r Function

MOLECULE

Molecule

(ChEBI, SO,RnaO, PrO)

Molecular

Function

Molecular

Process(GO)

Domain ontologies organized according to formal ontological

principles

RELATION TO TIME

GRANULARITY

CONTINUANT

OCCURREN

INDEPENDENT

DEPENDENT

ANDORGANIS

Organism(NCBI

Taxonomy)

Function(F

Phenotypic

Quality

Biological

Process(GO)

AND CELLULAR

COMPONENT

Cellula

r Function

MOLECULE

Molecule

Molecular

Function

Molecular

Process(GO)

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

RNAO ChEBI

Cell OntologyPaTO

RNAO ChEBI

Cell OntologyPaTO

Top-level ontology

All domain ontologies use the same top level notions

RNAO ChEBI

Cell OntologyPaTO

Top-level ontology

Ontologicalprinciples

RNAO ChEBI

Cell OntologyPaTO

Diversity in the specifics

Commonalityin the foundations

RNAO ChEBI

Cell OntologyPaTO

Facilitates interoperatibility

RNAO ChEBI

Cell OntologyPaTO

Facilitates interoperatibility

RNAO ChEBI

Cell OntologyPaTO

SharedOrganizational,Scientific, and Ontologicalprinciples

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

Kinds of Ontologies

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

‘ordinary’Glossaries

XML Schema

DB Schema

Glossaries & Data Dictionaries

MetaData,XML Schemas, & Data Models

Formal Ontologies & Inference

Thesauri, Taxonomies

Michael Gruninger, gruning@nist.gov

Ontologies:logical inferences

Non-ontologies:no logical inferences

Kinds of Ontologies

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

‘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

General Logic

Description Logics

(DAML+OIL)

General Logic

Description Logics

(DAML+OIL)

We need BOTH kinds of languages

General Logic

Description Logics

(DAML+OIL)

How well canwe specify intendedmeaning

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

BFO vs. RO

• RO = Relation ontology

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

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

Instance-of Instance-of

substance

siamese

Is-acat

Is-amammal

Is-aanimal

Is-aorganism

Human being

Universals,classes,types

Particulars:Continuants vs. occurrents

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

INDEPENDENT

DEPENDENT

ANDORGANIS

Organism(NCBI

Taxonomy)

Function(F

Phenotypic

Quality

Biological

Process(GO)

AND CELLULAR

COMPONENT

Cellula

r Function

MOLECULE

Molecule

Molecular

Function

Molecular

Process(GO)

Ontologies organized according to ontological

principles

Kinds of continuants

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

Independent

continuants

(substances)

Dependent

continuants

Independent

continuants

(substances)

Dependent

continuants

Independent

continuants

(substances)

Dependent

continuants

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

Independent

continuants

(substances)

Dependent

continuants

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

Independent

continuants

(substances)

Dependent

continuants

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

RELATION TO TIME

GRANULARITY

CONTINUANT

OCCURREN

INDEPENDENT

DEPENDENT

ANDORGANIS

Organism(NCBI

Taxonomy)

Function(F

Phenotypic

Quality

Biological

Process(GO)

AND CELLULAR

COMPONENT

Cellula

r Function

MOLECULE

Molecule

Molecular

Function

Molecular

Process(GO)

principles

RELATION TO TIME

GRANULARITY

CONTINUANT

OCCURREN

INDEPENDENT

DEPENDENT

ANDORGANIS

Organism(NCBI

Taxonomy)

Function(F

Phenotypic

Quality

Biological

Process(GO)

AND CELLULAR

COMPONENT

Cellula

r Function

MOLECULE

Molecule

Molecular

Function

Molecular

Process(GO)

principles

Universals and particulars(cont.)

Mishasubstanceinstances

substance

siamese

Is-acat

Is-amammal

Is-aanimal

Is-aorganism

Human being

substance-Universals

Accidents: Species and instances

quality

scarlet

R232, G54, B24

Barry Smith

Universals among dependent continuants

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

Irishman

this individual token man

Of independent continuants

RELATION TO TIME

GRANULARITY

CONTINUANT

OCCURREN

INDEPENDENT

DEPENDENT

ANDORGANIS

Organism(NCBI

Taxonomy)

Function(F

Phenotypic

Quality

Biological

Process(GO)

AND CELLULAR

COMPONENT

Cellula

r Function

MOLECULE

Molecule

Molecular

Function

Molecular

Process(GO)

Substance universals

principles

RELATION TO TIME

GRANULARITY

CONTINUANT

OCCURREN

INDEPENDENT

DEPENDENT

ANDORGANIS

Organism(NCBI

Taxonomy)

Function(F

Phenotypic

Quality

Biological

Process(GO)

AND CELLULAR

COMPONENT

Cellula

r Function

MOLECULE

Molecule

Molecular

Function

Molecular

Process(GO)

Quality/function universals

principles

Mishainstances

substance

siamese

Is-acat

Is-amammal

Is-aanimal

Is-aorganism

Human being

is-a relation betweenUniversals

Mishainstances

substance

siamese

Is-acat

Is-amammal

Is-aanimal

Is-aorganism

Human being

Human Beingis-amammal

Every instanceof Human Beingis also an instanceof mammal

Mishainstances

hasPet

isPetOf

substance

siamese

Is-acat

Is-amammal

Is-aanimal

Is-aorganism

Human being

IsPetOf

Instance-level relations

universal-level relations

Mishainstances

hasPet

isPetOf

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

Universal parthood

Human-headsHuman-bodies

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

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

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

• 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

• 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

Conclusions

RNAO ChEBI

Cell OntologyPaTO

Basedupon thetop-level ontologyBFO

RNA Ontology Consortium(under development)three-dimensional RNA

structuresRNA Ontology

(RnaO)

Gene Ontology (GO)

(FuGO)

Cell Ontology (CL)

RELATION TO TIME

GRANULARITY

CONTINUANT

OCCURREN

INDEPENDENT

DEPENDENT

ANDORGANIS

Organism(NCBI

Taxonomy)

Function(F

Phenotypic

Quality

Biological

Process(GO)

AND CELLULAR

COMPONENT

Cellula

r Function

MOLECULE

Molecule

Molecular

Function

Molecular

Process(GO)

principles

underlying ontologies for biomedical work - the relation ontology (ro) and basic formal ontology...

toplevel ontology

mammals cell ontology

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cell cell types

cornelius rosse fma

barry smith slide

model organisms common

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bfo 1976 1977

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chapter 8: basic formal ontology at work (draft: this ......

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