What is an ontology? Barry Smith 1

What is an ontology?

Barry Smithhttp://ontology.buffalo.edu/smith

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You’re interested in which genes control heart muscle development

17,536 results

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Selected Gene Tree: pearson lw n3d ...Branch color classification:Set_LW_n3d_5p_...

Colored by: Copy of Copy of C5_RMA (Defa...Gene List: all genes (14010)

attacked

time

control

Puparial adhesionMolting cyclehemocyanin

Defense responseImmune responseResponse to stimulusToll regulated genesJAK-STAT regulated genes

Immune responseToll regulated genes

Amino acid catabolismLipid metobolism

Peptidase activityProtein catabloismImmune response

Selected Gene Tree: pearson lw n3d ...Branch color classification:Set_LW_n3d_5p_...

Colored by: Copy of Copy of C5_RMA (Defa...Gene List: all genes (14010)

Microarray datashows changed expression ofthousands of genes.

How will you spot the patterns?

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Lab / pathology dataEHR dataClinical trial dataFamily history data Medical image dataMicroarray dataModel organism dataFlow cytometryMass specGenotype / SNP data

How will you find the data you need?

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− Human − Mouse− Rat − Fish− Yeast− E. coli

How will you find the compare the data? How will you integrate the data

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:.

The GO Idea

MouseEcotope GlyProt

DiabetInGene

GluChem

sphingolipid transporter

activity

:.

annotation using common ontologies yields integration of databases

MouseEcotope GlyProt

DiabetInGene

GluChem

Holliday junction helicase complex

ontologies are legends for data

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they provide a growing set of natural language labels

to make the data cognitively accessible to human beings and algorithmically accessible to reasoning systems

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compare: legends for mapscompare: legends for maps

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:.

legends for textbook diagrams

:.

ontologies as legends for images

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what lesion ?

what brain function ?

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legends for literature

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xi = vector of measurements of gene i k = the state of the gene ( as “on” or “off”)θi = set of parameters of the Gaussian model......

ontologies as legends for mathematical equations

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Pathway diagrams as ontologically annotated

dynamic cartoons

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two kinds of annotations

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names of instances

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names of types

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Ontologies are representations of types

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... types which are instantiated e.g. in the lab or clinic

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multiple kinds of relations between represented types provide a tool for algorithmic reasoning

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Gene Ontology: The Very Top

cellular component

molecular function

biological process

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Gene Ontology: The Very Top

continuant

cellular component

molecular function

occurrent

biological process

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BFO: The Very Top

continuant occurrent

biological processes

independentcontinuant

cellular component

dependentcontinuant

molecular function

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Basic Formal Ontology



dependentcontinuant

organism

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Basic Formal Ontology



dependentcontinuant

anatomical structure

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Continuants

• continue to exist through time, preserving their identity while undergoing different sorts of changes

• independent continuants – objects, things, ...

• dependent continuants – qualities, attributes, shapes, potentialities ...

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Qualitiestemperatureblood pressuremass...

are continuantsthey exist through time while undergoing changes

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Qualitiestemperature / blood pressure /

mass ...are dimensions of variation within the structure of the entity; a quality is something which can change while its bearer remains one and the same

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A Chart representing how John’s temperature

changes

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John’s temperaturethe temperature he has throughout his entire life, cycles through different determinate temperatures from one time to the next

John’s temperature is a physiology variable which, in thus changing, exerts an influence on other physiology variables through time

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BFO: The Very Top

continuant


dependentcontinuant

quality

occurrent

temperature 36

Blinding Flash of the Obvious


dependentcontinuant

quality

temperature types

instances

organism

John John’s

temperature 37



dependentcontinuant

quality

temperature types

instances

organism

John John’s

temperature 38


temperature types

instances

organism

John John’s

temperature

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inheres_in

temperature types

instances

John’s temperature

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37ºC37.1º

C37.5º

C37.2º

C37.3º

C37.4º

C

instantiates at t1

instantiates at t2

instantiates at t3

instantiates at t4

instantiates at t5

instantiates at t6

human types

instances

John

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embryo

fetus adultneonat

einfant child

instantiates at t1

instantiates at t2

instantiates at t3

instantiates at t4

instantiates at t5

instantiates at t6

• lower lever of types does not ‘carry identity’ in OntoClean terms

• are threshold divisions (hence we do not have sharp boundaries, and we have a certain degree of choice, e.g. in how many subtypes to distinguish, though not in their ordering)

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dependentcontinuant

quality

temperature types

instances

organism

John John’s

temperature

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dependentcontinuant

quality

temperature

organism

John John’s

temperature

occurrent

process

course of temperature

changes

John’s temperature history

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dependentcontinuant

quality

temperature

organism

John John’s

temperature

occurrent

process

life of an organism

John’s life

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BFO/GO: The Very Top


biological processes


cellular component

dependentcontinuant

molecular function

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BFO: The Very Top



dependentcontinuant

quality functionrole

disposition

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:.

Function - of liver: to store glycogen- of birth canal: to enable transport- of eye: to see- of mitochondrion: to produce ATP- of liver: to store glycogen

not optional; reflection of physical makeup of bearer; can malfunction

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:.

Role optional:exists because the bearer is in some special natural, social, or institutional set of circumstances in which the bearer does not have to be

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:.

Role - bearers can have more than one role

person as student / as staff member- roles often form systems of mutual dependence

husband / wife first in queue / last in queuedoctor / patient

host / pathogen 50

:.

Role of some chemical compound: to serve as analyte in an experiment

of a dose of penicillin in this human child: to treat a disease

of this bacteria in a primary host: to cause infection

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:.

Qualities are categorical features of reality – you just have them

Functions, roles and dispositions are potential featires of reality: they are realizable dependent continuants, realized in certain associated processes

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dependentcontinuant

role

drug role

portion of chemical compound

this portion of aspirin

role of this portion of aspirin

occurrent

process

process of drug

adminstration

John’s taking this portion of aspirin

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dependentcontinuant

role

drug role

portion of chemical compound

this portion of aspirin

role of this portion of aspirin

occurrent

process

process of drug

adminstration

John’s taking this portion of aspirin

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inheres_in

realized_in

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) Foundry55

• The Road to Convergence

All ontologies for each given domain (anatomy, chemistry…) should be part of a single suite of interoperable ontologies

should use a common top-level corefor subdomains with many variants, should

follow the strategy of canonical ontologies with extensions

should require acceptance of common, tested guidelines on all subscribing ontology developers

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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



Molecular Process

(GO)

initial OBO Foundry coverage, ontologies automatically semantically coupled

GRANULARITY

RELATION TO TIME

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Disposition (Internally-Grounded Realizable

Entity)disposition =def.

a realizable entity which if it ceases to exist, then its bearer is physically changed, and whose realization occurs when this bearer is in some special physical circumstances, in virtue of the bearer’s physical make-up

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Function

• A Disposition (Internally-Grounded Realizable Entity) that is designed or selected for

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OGMS• Ontology for General Medical

Science

http://code.google.com/p/ogms

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:.

Physical Disorder

– independent continuantfiat object part

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Big Picture

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A disease is a disposition rooted in a physical disorder in the organism and realized in pathological processes.

etiological process

produces

disorder

bears

disposition

realized_in

pathological process

produces

abnormal bodily features

recognized_as

signs & symptomsinterpretive process

produces

diagnosis

used_in63

Elucidation of Primitive Terms

• ‘bodily feature’ - an abbreviation for a physical component, a bodily quality, or a bodily process.

• disposition - an attribute describing the propensity to initiate certain specific sorts of processes when certain conditions are satisfied.

• clinically abnormal - some bodily feature that – (1) is not part of the life plan for an organism of the relevant

type (unlike aging or pregnancy), – (2) is causally linked to an elevated risk either of pain or other

feelings of illness, or of death or dysfunction, and – (3) is such that the elevated risk exceeds a certain threshold

level.*

*Compare: baldness64

Definitions - Foundational Terms

• Disorder =def. – A causally linked combination of physical components that is clinically abnormal.

• Pathological Process =def. – A bodily process that is a manifestation of a disorder and is clinically abnormal.

• Disease =def. – A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.

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Dispositions and Predispositions

• All diseases are dispositions; not all dispositions are diseases.• A predisposition is a disposition.• Predisposition to Disease of Type X =def. – A disposition in an

organism that constitutes an increased risk of the organism’s subsequently developing the disease X.

• HNPCC is caused by a – disorder (mutation) in a DNA mismatch repair gene that – disposes to the acquisition of additional mutations from

defective DNA repair processes, and thus is a– predisposition to the development of colon cancer.

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Cirrhosis - environmental exposure

• Etiological process - phenobarbitol-induced hepatic cell death

– produces

• Disorder - necrotic liver

– bears

• Disposition (disease) - cirrhosis

– realized_in

• Pathological process - abnormal tissue repair with cell proliferation and fibrosis that exceed a certain threshold; hypoxia-induced cell death

– produces

• Abnormal bodily features

– recognized_as

• Symptoms - fatigue, anorexia

• Signs - jaundice, splenomegaly

Symptoms & Signs used_in

Interpretive process produces

Hypothesis - rule out cirrhosis suggests

Laboratory tests produces

Test results - elevated liver enzymes in serum used_in


Result - diagnosis that patient X has a disorder that bears the disease cirrhosis

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Influenza - infectious

• Etiological process - infection of airway epithelial cells with influenza virus

– produces

• Disorder - viable cells with influenza virus

– bears

• Disposition (disease) - flu

– realized_in

• Pathological process - acute inflammation

– produces

• Abnormal bodily features

– recognized_as

• Symptoms - weakness, dizziness

• Signs - fever



Hypothesis - rule out influenza suggests


Test results - elevated serum antibody titers used_in


Result - diagnosis that patient X has a disorder that bears the disease flu

But the disorder also induces normal physiological processes (immune response) that can results in the elimination of the disorder (transient disease course).

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Huntington’s Disease - genetic

• Etiological process - inheritance of >39 CAG repeats in the HTT gene– produces

• Disorder - chromosome 4 with abnormal mHTT– bears

• Disposition (disease) - Huntington’s disease– realized_in

• Pathological process - accumulation of mHTT protein fragments, abnormal transcription regulation, neuronal cell death in striatum– produces

• Abnormal bodily features– recognized_as

• Symptoms - anxiety, depression• Signs - difficulties in speaking and

swallowing



Hypothesis - rule out Huntington’s suggests


Test results - molecular detection of the HTT gene with >39CAG repeats used_in


Result - diagnosis that patient X has a disorder that bears the disease Huntington’s disease

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HNPCC - genetic pre-disposition

• Etiological process - inheritance of a mutant mismatch repair gene– produces

• Disorder - chromosome 3 with abnormal hMLH1– bears

• Disposition (disease) - Lynch syndrome– realized_in

• Pathological process - abnormal repair of DNA mismatches– produces

• Disorder - mutations in proto-oncogenes and tumor suppressor genes with microsatellite repeats (e.g. TGF-beta R2)– bears

• Disposition (disease) - non-polyposis colon cancer– realized in

• Symptoms (including pain)

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The OBO Foundry Initiative

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A good solution to the data integration problem must be:

• modular• incremental• bottom-up• evidence-based • revisable• incorporate a strategy for motivating

potential developers and users

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GO is amazingly successful – but covers only three sorts of biological entities:–cellular components–molecular functions–biological processes

and does not provide representations of disease-related phenomena

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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



Molecular Process

(GO)

The Open Biomedical Ontologies (OBO) Foundry74

OBO Foundry provides

• tested guidelines enabling new groups to develop the ontologies they need in ways which counteract forking and dispersion of effort

• an incremental bottoms-up approach to evidence-based terminology practices in medicine that is rooted in basic biology

• automatic web-based linkage between medical terminologies and biological knowledge resources

• traffic laws and traffic police

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the strategy

establish common rules governing best practices for creating ontologies in coordinated fashion, with an evidence-based pathway to incremental improvement

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The methodology of cross-products

compound terms in ontologies to be defined as cross-products of simpler terms:E.g elevated blood glucose is a cross-product of PATO: increased concentration with FMA: blood and CheBI: glucose.

= factoring out of ontologies into discipline-specific modules (orthogonality)

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The methodology of cross-products

enforcing use of common relations in linking terms drawn from Foundry ontologies serves

• to ensure that the ontologies are maintained and revised in tandem

• logically defined relations serve to bind terms in different ontologies together to create a network

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CRITERIA

opennness

common formal language.

collaborative development

evidence-based maintenance

identifiers

versioning

textual and formal definitions

CRITERIA

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Orthogonality = modularity

• one ontology for each domain• no need for mappings (which are in

any case too expensive, too fragile, too difficult to keep up-to-date as mapped ontologies change)

• everyone knows where to look to find out how to annotate each kind of data

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Ontologies and research groups

using BFO and RO

– OBO Foundry (60 biomedical ontologies, including

GO, OBI, Protein Ontology, Cell Ontology, IDO …– National Cancer Institute (BiomedGT)– NIF (NIH Neuroscience Information Framework)– Cleveland Clinic Semantic Database– Siemens– AstraZeneca– EU (ACGT Cancer Ontology, RAPS, …)

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Because the ontologies in the Foundry

are built as orthogonal modules which form an incrementally evolving network

• scientists are motivated to commit to developing ontologies because they will need in their own work ontologies that fit into this network

• users are motivated by the assurance that the ontologies they turn to are maintained by experts

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More benefits of orthogonality

• helps those new to ontology to find what they need

• to find models of good practice• ensures mutual consistency of ontologies

(trivially)• and thereby ensures additivity of annotations

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More benefits of orthogonality

• it rules out the sorts of simplification and partiality which may be acceptable under more pluralistic regimes

• thereby brings an obligation on the part of ontology developers to commit to scientific accuracy and domain-completeness

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More criteria of a successful standard

1. intelligibility to users, consistent use of terms like ‘term’, ‘class’, ‘entity’, ‘object’ …)

2. track record of lessons learned (GO has 10 years of hard user testing)

3. lots of existing users (ontologies are like telephone networks)

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The ontology uses relations which are unambiguously defined following the pattern of definitions laid down in the Basic Formal Ontology (BFO) including the Relation Ontology (RO)

http://ifomis.org/bfo

http://www.obofoundry.org/ro/

COMMON ARCHITECTURE

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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*) OBO Foundry Modular Organization

top level

mid-level

domain level

Information Artifact Ontology

(IAO)

Ontology for Biomedical

Investigations(OBI)

Spatial Ontology(BSPO)

Basic Formal Ontology (BFO)

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BFO:continuant

BFO:occurrent

Example: The Cell Ontology

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*) OBO Foundry Modular Organization

top level

mid-level

domain level

Information Artifact Ontology

(IAO)

Ontology for Biomedical

Investigations(OBI)

Spatial Ontology(BSPO)

Basic Formal Ontology (BFO)

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Documents

What is an ontology? Barry Smith 1