1 Workshop 7.00 Welcoming Remarks 7.15 Barry Smith (Buffalo, NY) 7.40 Lindsay Cowell (Duke University, NC) 8.05 Nigam Shah (Stanford University, CA) 8.30.

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Workshop7.00 Welcoming Remarks

7.15 Barry Smith (Buffalo, NY)

7.40 Lindsay Cowell (Duke University, NC)

8.05 Nigam Shah (Stanford University, CA)

8.30 Break

8.40 Dave Parrish (Immune Tolerance Network, PA)

9.05 Yannick Legre (Healthgrid, France)

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The OBO Foundry: From Basic Biology to Genomic Medicine

Barry SmithUniversity at Buffalo

National Center for Biomedical Ontologyhttp://ontology.buffalo.edu/smith

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where in the body ? where in the cell ?

what kind of disease process ?

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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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for science

create an evolutionary path towards evidence-based terminology

a new approach

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a shared portal for 60+ ontologies (low regimentation)

http://obo.sourceforge.net

First step (2001)

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Second step (2004):logic-based reform efforts

GO linked to other OBO ontologies

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

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

Third step (2006)Third step (2006)

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

model organism databases scientific literature clinical data experimental results

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

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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/

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 fron the original GO

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

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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

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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

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

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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

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

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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

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

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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

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

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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

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

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Ontology of Biomedical Investigations

with thanks to Trish Whetzel (FuGO Working Group)

FuGO = Functional Genomics Investigation Ontology

OBI née FuGO

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

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controlled vocabulary for biomedical investigations including

protocols instrumentationmaterialdata types of analysis and statistical tools

applied to the data

OBI

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

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OBI Collaborating CommunitiesCrop sciences Generation Challenge Programme (GCP),Environmental genomics MGED RSBI Group, www.mged.org/Workgroups/rsbiGenomic Standards Consortium (GSC),

www.genomics.ceh.ac.uk/genomecatalogueHUPO Proteomics Standards Initiative (PSI), psidev.sourceforge.netImmunology Database and Analysis Portal, www.immport.orgImmune Epitope Database and Analysis Resource (IEDB),

http://www.immuneepitope.org/home.doInternational Society for Analytical Cytology, http://www.isac-net.org/Metabolomics Standards Initiative (MSI), Neurogenetics, Biomedical Informatics Research Network (BIRN),Nutrigenomics MGED RSBI Group, www.mged.org/Workgroups/rsbiPolymorphismToxicogenomics MGED RSBI Group, www.mged.org/Workgroups/rsbiTranscriptomics MGED Ontology Group

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Clinical Trial Ontology

To serve merger of data schemasTo serve flexibility of collaborative clinical

trial researchTo serve design and management of

clinical trialsTo serve data access and reuse – send

me all trials which ...

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Randomized controlled trials

http://rctbank.ucsf.edu/ontology/outline/index.htm

RCT Schema – a ‘frame-based ontology’

supporting TrialBank

RCT

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RCT Top-Level Class Hierarchy

Root – Secondary-study – Trial-details – Trial – Concept

• Generic-concept • Population-concept • Protocol-concept • Design-concept • Outcome-concept • Administrative-concept • Intervention-concept

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RCT: Trial Details

Trial-details • Erratum • Publication-details • Conclusion-details • Background-details • Stopping-details • Retraction-details • Correction-details • Fraud-details

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– Concept • Generic-concept

– Term-information – Time-entity – Rule-concept – Situation

• Population-concept – Subgroup – Population – Recruitment

• Protocol-concept – Follow-up-activity

RCT: Concept

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Ontology vs. Schema

Separate development of medical ontologies and terminologies such as SNOMED

and medical information models and database schemas

Rector, et al., Binding Ontologies and Coding Systems to Electronic Health Records and Messages

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Ontology vs. Schema

diabetes => disease

diabetes => string

temperature => quality

temperature => integer

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Valid Specifications for data structures“Valid diabetic data structures have: a topic of code for diabetes, a diagnosis code that is diabetes or one of its subcodes, and a brittleness code that is one of the subcodes for diabetic brittlenes and nothing else”

Ontology“All diabetes are metabolic diseases”“John has diabetes & it is brittle and long-standing”

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– Concept • Administrative-concept

– Publication-concept – Study-site – Person

• Intervention-concept – Blinding-concept – Intervention-step – Intervention

RCT: Concept

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Two kinds of entities

occurrents (processes, events, happenings)

continuants (objects, qualities, states...)

You are a continuant

Your life is an occurrent

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An instrument is a continuantA protocol is a continuant

A trial is an occurrentA selection process is an occurrent

Two kinds of entities

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OBI Top Level

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OBO Occurrent

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CTO

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CTO Continuant

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CTO Occurrent

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Clinical Trial Ontology Working Group

http://www.bioontology.org/wiki/

Workshop on May 16-17, 2007

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