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The OBO Foundry
Chris Mungall
Lawrence Berkeley Laboratory
NCBO
GO Consortium
May 2007
The Open Biomedical
Ontologies (OBO) Foundry
 A collection of orthogonal reference
ontologies in the biological/biomedical
domain
 Each is committed to an agreed upon
set of principles governing best
practices in ontology development
Outline
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Motivation
History/Background
Organisation and dependencies
Foundry Principles
Results
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http://obofoundry.org
http://www.bioontologies.org
(NCBO)
Why is the OBO Foundry
necessary?
 For the sharing, integration and analysis
of biological and biomedical data
 Common standards are required
 Ontologies must be interoperable and
logically well-formed
 Ontologies should be developed
collaboratively
Origins of OBO: The Gene
Ontology (GO)
 3 ontologies intended primarily for the
annotation of genes and gene products
across a spectrum of organisms
 Molecular function
 Biological process
 Cellular component
 These ontologies are organised as a
collection of related terms, constituting nodes
in a graph
Annotation and GO
 187,000 genes and gene products have high
quality annotations to GO terms
 2.6m including automated predictions
 63,000 publications curated
 Variety of analysis tools
 http://www.geneontology.org/GO.tools.shtml#micro
 Annotation of primary and literature data is
one use of OBO Foundry ontologies
GO and the need for OBO
 GO terms implicitly reference kinds of entities
outwith the scope of GO
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Cysteine biosynthesis
Neural crest cell migration
Cardiac muscle morphogenesis
Regulation of vascular permeability
ChEBI
Cell
Anatomy
quality
 OBO was born from the need to create cross
products wth GO
 Also coincided with growth in model organism
anatomy ontologies
Organisation of the OBO
Foundry
 Ontologies should be orthogonal
 Minimise overlap
 Each distinct entity type (universal) should
only be represented once
 We can partition the OBO Foundry
rationally to help organise and
coordinate the ontologies
Partitions
 Type of entity
 Relationship to time
 Continuant
 Occurrent
 Dependent or
independent
 Granularity
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Molecular
Cellular
Organismal
Multi-organismal
 Generality
 Upper domain
ontology
 Core biology
 Species specific
 Occurrence
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Canonical
Variant
Pathological
Experimental
RELATI ON TO
TIME
GRANULARITY
ORGAN AND
ORGANISM
CELL AND
CELLUL AR
COMPONENT
MOL ECULE
CONTINUANT
INDEPENDENT
OCCURRENT
DEPENDENT
Organism
(NCBI
Taxonomy)
Anatomical
Entity
(FMA,
CARO)
Organ
Function
(FMP,
CPR O)
Cell
(CL)
Cellular
Compo nent
(FMA,GO)
Cellular
Function
(GO)
Molecule
(ChEBI, SO ,
RnaO, PrO)
Phenotypic
Quality
(PaTO)
Molecular Function
(GO)
OrganismLevel Process
(GO)
Cellular
Process
(GO)
Molecular
Process
(GO)
Connecting the Foundry: The
OBO Relation Ontology
 Standardized set of formally defined relations
between types and/or instances
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is_a
part_of
has_participant
…
 For use within and across OBO ontologies
 http://obofoundry.org/ro
 Molecules and cells participate in cellular
processes
 Cellular components are parts of cells which are
parts of larger anatomical entities
OBO Foundry Principles
 Open
 Well-defined exchange format
E.g. OBO or OWL
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Unique ID-Space
Ontology Life-cycle / versioning
Clearly specified and delineated content
Definitions
Use relations according to the standards of the OBO Relation
Ontology
 Well documented
 Plurality of users
 Collaborative development
http://obofoundry.org/crit.shtml
Results
 Phenotype Annotation
 Ontology for Biomedical Investigations
(OBI)
 GO cross-products
 Anatomy Ontologies
 Semantic Web Health Care and Life
Sciences (HCLS) interest group
Genotype-Phenotype
Annotation
 NCBO Driving Biological Project
 Deep genotype-phenotype association curation of
disease genes and genotypes
 Human, Fruitfly, Zebrafish
 Methodology: Flexible post-coordination of
phenotype descriptions using Foundry
ontologies
 Based on ‘PATO’ ontology of qualities
 E.g.
 Shortened length of dendrite of columnar neuron
OBI: Ontology for Biomedical
Investigations
 An integrated ontology for experiments
and investigations
 Reuses terms from OBO Foundry
ontologies in a modular way
 Classes representing experimental
artefacts, roles, hypotheses, variables
etc
 Adherence to upper ontology (BFO)
Results: GO cross-products
 Ongoing work:
 Processes and functions with chemical
entities as participants
 E.g. cysteine biosynthesis
 Processes defined in terms of types of cell
 E.g. neural crest cell migration
 Mutual feedback
Anatomy Ontologies
 Common Anatomy Reference Ontology
 Ontologies of gross anatomy have been
developed using divergent methodologies
 CARO was developed after an NCBO sponsored
meeting on anatomy ontologies
 Ontology based on structure of the FMA
 Common framework and upper-level terms for
taxon-specific anatomical ontologies
 Cell ontology
 Merge of EVOC and initial OBO Cell ontology
Finding out more and
participating
 http://obofoundry.org
 http://www.bioontology.org
 [email protected]
Acknowledgements
NCBO/Berkeley
NCBO/Cambridge Ontologies
Nicole Washington
Michael Ashburner
Amelia Ireland David Sutherland
Mark Gibson
George Gkoutos
Jane Lomax
Oliver Hofmann
Pascale Gaudet
Jen Clark
Sue Rhee
Paula de Matos
Midori Harris
Johnathan Bard
Rafael Alcantra
David Hill
Lindsay Cowell
Kirill Degtyarenko
John Day-Richter
Suzanna Lewis
NCBO/Stanford
Nigam Shah
Daniel Rubin
Archana Verbakam
NCBO/Eugene
Melissa Haendel
Monte Westerfield
NCBO/Victoria
Chris Callender
Margaret-Anne Storey
Lynn Murphy
Michael J Montague
NCBO/Buffalo
Mark Musen
Fabian Neuhaus
NCBO/Mayo
Werner Ceusters
James Buntrock
Chris Chute
Karen Eilbeck Erik Segerdell
Louis Goldberg
Barry Smith
Rex Chisholm
Pankaj Jaiswal
Seth Carbon
Alan Rector
Onard Mejino
Judith Blake
Cynthia Smith
Cornelius Rosse
& GO
Jannan Eppig
William Bug
Alan Ruttenberg
NCBO/UCSF NIH
Trish Whetzel
Simona Carini
Peter Good
Jennifer Fostel
Ida Sim
Carol Bean
& OBI Consortium
Nation Heart, Lung and
Blood Institute
 Ontology

 Scope

Cell Ontology
 (CL)


Chemical Entities
(ChEBI)
 Common Anatomy
Refer ence Ontology
(CARO)
 Foundational Model
of Anatomy (FMA)
 Functional Genomics
 Investigation
Ontology
 (FuGO)



anatomical structures in

human and model
organisms

structure of the human
body


design, protocol, data
instrumentation, and
analysis



cellular components,
molecular functions,
biological processes

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Protein Ontology
 (PrO)
 Relation Ontology
(RO)
 RNA Ontology
 (RnaO)

Sequence Ontology
 (SO)
qualities of biomedical
entities

protein types and

modifications

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

relations
three-dimensional RNA

structures
properties and features
of
obo.sourceforge.net
/cgibin/detail.cgi?cell


molecular entities

Gene Ontology
 (GO)
Phenotypic Quality
 Ontology
 (PaTO)
cell types from
prokaryotes
to mammals
 URL
ebi.ac.uk/chebi


(under
development)
fma.biostr.washingt
on.

edu

 Custodians

Jonathan Bard, Michael

Ashburner, Oliver
Hofman

Paula Dematos,

Rafael Alcantara

Melissa Haendel, Terry

Hayamizu, Cornelius
Rosse,

David Sutherland,



obi.sf.net
FuGO Working Group

www.geneontology
.org

obo.sourceforge.net
/cgi

-bin/ detail.cgi?

attribute_and_valu
e

(under
development)

obo.sf.net/relations
hip

(under
development)

song.sf.net



JLV Mejino Jr.,
Cornelius Rosse
Gene Ontology
Consortium
Michael Ashburner,
Suzanna
Lewis, Georgios Gkoutos

Protein Ontology
Consortium

Barry Smith, Chris
Mungall

RNA Ontology
Consortium

Karen Eilbeck
RELATI ON TO
TIME
GRANULARITY
ORGAN AND
ORGANISM
CELL AND
CELLUL AR
COMPONENT
MOL ECULE
CONTINUANT
INDEPENDENT
OCCURRENT
DEPENDENT
Organism
(NCBI
Taxonomy)
Anatomical
Entity
(FMA,
CARO)
Organ
Function
(FMP,
CPR O)
Cell
(CL)
Cellular
Compo nent
(FMA,GO)
Cellular
Function
(GO)
Molecule
(ChEBI, SO ,
RnaO, PrO)
Phenotypic
Quality
(PaTO)
Molecular Function
(GO)
OrganismLevel Process
(GO)
Cellular
Process
(GO)
Molecular
Process
(GO)