The OBO Foundry Towards Gold Standard Terminology Resources in the Biomedical Domain

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The OBO Foundry

Towards Gold Standard Terminology Resources in

the Biomedical Domain

Thomas Bittner(based on a presentation by Barry Smith)

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UMLS, Semantic Web, Moby, wikis, etc.

let a million flowers bloom

integration relies on post hoc mappings

how create broad-coverage semantic annotation systems for biomedicine?

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O1

O2

O4

O3

On

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O1

O4

O2 O3

On

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for science

create an evolutionary path towards evidence-based terminology

a new approach

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O1

O2

O4

O3

On

FMA

RNAO ChEBI

Cell OntologyPaTO

SharedOrganizatorial,Scientific, and Ontologicalprinciples

TLO

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for science

create an evolutionary path towards evidence-based terminology

Terminologies/ontologies that

• have proven their usefulness through applications

• based on/ verified through scientific methodology

• structured/formalized according to ontological principles

a new approach

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a shared portal for (so far) 58 ontologies

originally called ‘GOBO’ (for Global Open Biological Ontologies)

First step (Oct. 11, 2001)

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GOBO PrinciplesAll ontologies will be welcome if, and only if, they conform to

the following principles of gobo:

1. They are ‘open’

2. They are in, or can be instantiated in, the GO syntax or extensions of this syntax.

3. They are orthogonal to other ontologies already lodged with gobo.

4. Shared ID space.

5. Terms are defined.

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Second step (March 2004)

Initiation by the Gene Ontology Consortium - logical reforms of the GO and related ontologies

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e.g. linking GO logically to other OBO ontologies via cross-products

id: CL:0000062name: osteoblastdef: "A bone-forming cell which secretes an extracellular matrix. Hydroxyapatite crystals are then deposited into the matrix to form bone." is_a: CL:0000055relationship: develops_from CL:0000008relationship: develops_from CL:0000375

GO

Cell type (CL)

New Definition

+

=Osteoblast differentiation: Processes whereby an osteoprogenitor cell or a cranial neural crest cell acquires the specialized features of an osteoblast, a bone-forming cell which secretes extracellular matrix.

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The OBO Foundryfurther principles added +

intense collaborative development

Third step (2005-6)

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a family of interoperable gold standard biomedical reference ontologies to serve the annotation of

scientific literature model organism databases clinical data à la Ida experimental results etc.

The OBO Foundry

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A prospective standarddesigned to guarantee interoperability of ontologies from the very start (contrast to: post hoc mapping à la UMLS)

several ontologies now being constructed ab initio

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Initial set of 10 principles

= 5 GOBO principles (with broadened family of allowable types of syntax, including OWL-DL syntaxes) plus:

6. Collaborative development

7. Intelligible documentation.

8. Plurality of independent users.

9. Clearly specified content.

10. Uses relations which are formally defined

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_value

qualities of biomedical entities

Phenotypic Quality Ontology

(PaTO)

Gene Ontology Consortium

www.geneontology.org

cellular 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 body

Foundational 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

CONTINUANT OCCURRENT

INDEPENDENT DEPENDENT

ORGAN ANDORGANISM

Organism(NCBI

Taxonomy)

Anatomical Entity

(FMA, CARO)

OrganFunction

(FMP, CPRO) Phenotypic

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 Function(GO)

Molecular Process

(GO)

OBO Foundry coverage

GRANULARITY

RELATION TO TIME

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)

Building out from the original GO

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Current state of OBO Foundry

1. Ontologies already mature but still undergoing continuous reform:

Cell Ontology (CL)

Foundational Model of Anatomy (FMA)

Gene Ontology (GO)

Zebrafish Anatomy Ontology (ZAO)

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2. Early versions existClinical Trial Ontology (CTO, part of OBI)Common Anatomy Reference Ontology

(CARO, DB1 & DB2)Mosquito Anatomy Ontology (MAO)Ontology for Biomedical Investigations (OBI)Phenotypic Quality Ontology (PATO, DB1 &

DB2)Protein Ontology (PRO)Relation Ontology (RO)RNA Ontology (RnaO)

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3. Still in need of thorough reviewChemical Entities of Biological Interest

(ChEBI)

Disease Ontology (DO)

Sequence Ontology (SO)

various other OBO ontologies (Mammalian Phenotype Ontology ...)

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4. Still in planning phaseBiobank/Biorepository Ontology (BrO, part of OBI)

Environment Ontology (EnvO) – inaugural meeting August, 2007 organized by NERC in OERC (Oxford E-Research Center)

Fish Multi-Species Anatomy Ontology (funding received; no acronym yet)

Infectious Disease Ontology (IDO)

Mouse Adult Neurogenesis Ontology (MANGO)

Xenopus Anatomy Ontology (XAO)

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OBO Foundry Listservs (Jan. 2007)

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Foundry developers have agreed in advance to accept a common set of principles designed to ensure

compatibility

interoperability

formal robustness

http://obofoundry.org/http://obofoundry.org/

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CRITERIA

The ontology is open and available to be used by all.

The ontology is in, or can be instantiated in, a common formal language.

The developers of the ontology agree in advance to collaborate with developers of other OBO Foundry ontology where domains overlap.

CRITERIA


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CRITERIA UPDATE: The developers of each ontology

commit to its maintenance in light of scientific advance, and to soliciting community feedback for its improvement.

ORTHOGONALITY: They commit to ensuring that there is community convergence on a single controlled vocabulary for each domain


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CRITERIA

IDENTIFIERS: The ontology possesses a unique identifier space within OBO.

VERSIONING: The ontology provider has procedures for identifying distinct successive versions.

The ontology includes textual definitions for all terms.

CRITERIA


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CLEARLY BOUNDED: The ontology has a clearly specified and clearly delineated content.

DOCUMENTATION: The ontology is well-documented.

USERS: The ontology has a plurality of independent users.

CRITERIA


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COMMON ARCHITECTURE: The ontology uses relations which are unambiguously defined following the pattern of definitions laid down in the OBO Relation Ontology.*

* Smith et al., Genome Biology 2005, 6:R46

CRITERIA


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The Foundational Model of Anatomy (FMA)

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The Foundational Model of Anatomy (FMA)

FMAUni-WashingtonProtégé – frame

systemhttp://

fme.biostr.washington.edu:8089/FME/index.html

Human anatomy

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High level scheme

Digital Anatomist Foundational Model of Anatomy (FMA)

Mejino & Rosse, KR-Med 04

FMA= (At, ASA, ATA, Mk)

where:

AtAt = Anatomy taxonomy

ASAASA = Anatomical Structural Abstraction

ATAATA = Anatomical Transformation Abstraction

MkMk = Metaknowledge

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Anatomical EntityAnatomical Entity

Physical Anatomical Entity

Physical Anatomical Entity -is a--is a- Non-physical

Anatomical Entity

Non-physicalAnatomical Entity

Anatomy Taxonomy (Mejino & Rosse, KR-Med 04)

Non-spatial entity(not located in space)

Spatial entity(located in space)

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Anatomical Entity


Non-material Physical Anatomical Entity


Material Physical Anatomical Entity


SpaceSpace SurfaceSurface LineLine


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QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.

Anatomical spaces (is-a hierarchy)

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Anatomical Entity






AnatomicalStructure

AnatomicalStructure

BodySubstance

BodySubstance SpaceSpace SurfaceSurface LineLine


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Anatomical Entity






AnatomicalStructure

AnatomicalStructure

BodySubstance

BodySubstance

BiologicalMacromolecule

BiologicalMacromolecule

AcellularAnatomicalStructure

AcellularAnatomicalStructure

CellPart

CellPart CellCell TissueTissue

BodyPart

BodyPart

HumanBody

HumanBody

SpaceSpace SurfaceSurface LineLine

OrganOrgan OrganSystem

OrganSystem

OrganPart

OrganPart


Universal parthood:

Human anatomy

The universal human body

The universalhuman head Human heads

are parts of human bodies

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

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The OBO Foundry Towards Gold Standard Terminology Resources in the Biomedical Domain