1 The OBO Foundry . 2 A prospective standard designed to guarantee interoperability of ontologies from the very start (contrast

1

The OBO FoundryThe OBO Foundryhttp://obofoundry.org/http://obofoundry.org/

2

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

established March 2006

11 initial candidate OBO ontologies – focused primarily on

1. basic science domains of natural objects

2. investigation domains (of equipment and other artifacts)

3

Ontology Scope URL Custodians

Cell Ontology (CL)

cell types from prokaryotes to mammals

obo.sourceforge.net/cgi-

bin/detail.cgi?cell

Jonathan Bard, Michael Ashburner, Oliver Hofman

Chemical Entities of Bio-

logical Interest (ChEBI)

molecular entities ebi.ac.uk/chebiPaula Dematos,Rafael Alcantara

Common Anatomy Refer-

ence Ontology (CARO)

anatomical structures in human and model

organisms(under development)

Melissa Haendel, Terry Hayamizu, Cornelius

Rosse, David Sutherland,

Foundational Model of Anatomy (FMA)

structure of the human body

fma.biostr.washington.

edu

JLV Mejino Jr.,Cornelius Rosse

Functional Genomics Investigation

Ontology (FuGO)

design, protocol, data instrumentation, and

analysisfugo.sf.net FuGO Working Group

Gene Ontology (GO)

cellular components, molecular functions, biological processes

www.geneontology.org

Gene Ontology Consortium

Phenotypic Quality Ontology

(PaTO)

qualities of anatomical structures

obo.sourceforge.net/cgi

-bin/ detail.cgi?attribute_and_value

Michael Ashburner, Suzanna

Lewis, Georgios Gkoutos

Protein Ontology (PrO)

protein types and modifications

(under development)Protein Ontology

Consortium

Relation Ontology (RO)

relationsobo.sf.net/

relationshipBarry Smith, Chris

Mungall

RNA Ontology(RnaO)

three-dimensional RNA structures

(under development) RNA Ontology Consortium

Sequence Ontology(SO)

properties and features of nucleic sequences

song.sf.net Karen Eilbeck

http://www.geneontology.org/

http://www.geneontology.org/

4

RELATION TO TIME

GRANULARITY

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)

Annotations plus ontologies yield an ever-growing computer-interpretable map of biological reality.

5

RELATION TO TIME

GRANULARITY



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)

MOLECULE Molecule



Molecular Process

(GO)

Building out from the original GO

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Natural

Disease Ontology (DO)

Drug Ontology (DrO)

Environment Ontology (EnvO)

Systems Biology Ontology (SBO)

Upper Biomedical Ontology (OBO UBO)

Artifactual

Clinical Trial Ontology (CTO)

Biomedical Imaging Ontology (BIO)

(Upper-Level) Investigation Ontology (IO)

Unit Ontology (UO)

Under consideration:

7

RELATION TO TIME

GRANULARITY



ORGAN ANDORGANISM

Organism

NCBITaxonomy

?

Anatomical

Entity(FMA, CARO)

OrganFunction

(FMP, CPRO) Phenotypi

c Quality(PaTO)

Biological Process

(GO)CELL AND CELLULAR

COMPONENT

Cell(CL)

Cellular Compon

ent(FMA, GO)

Cellular Function

(GO)

MOLECULE Molecule



Molecular Process

(GO)

Pathological

Investigation

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InvestigationOntology

Functional Genomic

Investigation Ontology

Clinical Trial Ontology

Imaging Ontology

Unit Ontology

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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

The OBO FoundryThe OBO Foundry http://obofoundry.org/http://obofoundry.org/

10

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 working with other Foundry members to ensure that, for any particular domain, there is community convergence on a single controlled vocabulary.


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for science

if we annotate a database or body of literature or images with one high-quality biomedical ontology, we should be able to add annotations from a second such ontology without conflicts

orthogonality of ontologies implies additivity of annotations


12

CRITERIA

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

VERSIONING: The ontology provider has procedures for identifying distinct successive versions to ensure BACKWARDS COMPATIBITY with annotation resources already in common use

The ontology includes TEXTUAL DEFINITIONS and where possible equivalent formal definitions of its 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


15

Foundational is_apart_of

Spatial located_incontained_inadjacent_to

Temporal transformation_ofderives_frompreceded_by

Participation has_participanthas_agent

OBO Relation Ontology


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Further criteria will be added over time in light of lessons learned in order to bring about a gradual improvement in the quality of Foundry ontologies

ALL FOUNDRY ONTOLOGIES WILL BE SUBJECT TO CONSTANT UPDATE IN LIGHT OF SCIENTIFIC ADVANCE

IT WILL GET HARDER


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But not everyone needs to join

The Foundry is not seeking to serve as a check on flexibility or creativity

ALL FOUNDRY ONTOLOGIES WILL ENCOURAGE COMMUNITY CRITICISM, CORRECTION AND EXTENSION WITH NEW TERMS

IT WILL GET HARDER


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Single inheritance

All terms in ontology are singular nouns

Term-by-term versioning

Uniform naming conventions

Independence of ontology from computational idiom

PROPOSED NEW CRITERIA


19

to introduce some of the features of SCIENTIFIC PEER REVIEW into biomedical ontology development

CREDIT for high quality ontology development work

KUDOS for early adopters of high quality ontologies / terminologies e.g. in reporting clinical trial results

GOALS


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to providing a FRAMEWORK OF RULES to counteract the current policy of ad hoc creation of new annotation schemas by each clinical research group by

REUSABILITY: if data-schemas are formulated using a single well-integrated framework ontology system in widespread use, then this data will be to this degree itself become more widely accessible and usable

GOALS


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to serve as BENCHMARK FOR IMPROVEMENTS in discipline-focused terminology resources

once a system of interoperable reference ontologies is there, it will make sense to calibrate existing terminologies in its terms in order to achieve more robust alignment and greater domain coverage

exploit the avenue of EVIDENCE-BASED MEDICINE (NIH CLINICAL RESEARCH NETWORKS) to foster their use by clinicians

GOALS


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June 2006: establishment of MICheck:

reflects growing need for prescriptive checklists specifying the key information to include when reporting experimental results (concerning methods, data, analyses and results).

MICheck


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MICheck: ‘a common resource for minimum information checklists’ analogous to OBO / NCBO BioPortal

MICheck Foundry: will create ‘a suite of self-consistent, clearly bounded, orthogonal, integrable checklist modules’ *

* Taylor CF, et al. Nature Biotech, in press

MICheck Foundry


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From OBO to OBD: Open Biomedical Data

OBD is part of NCBO BioPortal:

houses data annotated using ontologies– open to all– with a flexible ontology-based schema

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OBD Foundry

The OBD Foundry– data annotated using OBO Foundry ontologies– emphasis on coordination especially with

NCBO Driving Biological Projects• linking genes to disease via model organism

mutant phenotypes• high-quality clinical trial data• additivity of annotations implies additivity of data

Documents

1 The OBO Foundry . 2 A prospective standard designed to guarantee interoperability of ontologies from the very start (contrast