OBO Foundry

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
Motivation
History/Background
Organisation and dependencies
Foundry Principles
Results

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
Cysteine biosynthesis
Neural crest cell migration
Cardiac muscle morphogenesis
Regulation of vascular permeability
OBO was born from the need to create cross products wth GO
Also coincided with growth in model organism anatomy ontologies
ChEBI Cell Anatomy quality

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
Molecular
Cellular
Organismal
Multi-organismal
Generality
Upper domain ontology
Core biology
Species specific
Occurrence
Canonical
Variant
Pathological
Experimental

Connecting the Foundry: The OBO Relation Ontology
Standardized set of formally defined relations between types and/or instances
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
Phenotypic qualities inhere in anatomical entities

OBO Foundry Principles
Open
Well-defined exchange format
E.g. OBO or OWL
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_address]

Acknowledgements NCBO/Berkeley Nicole Washington Mark Gibson John Day-Richter Suzanna Lewis NCBO/Stanford Nigam Shah Daniel Rubin Archana Verbakam Lynn Murphy Michael J Montague Mark Musen Ontologies Amelia Ireland Jane Lomax Jen Clark Midori Harris David Hill Karen Eilbeck Seth Carbon Judith Blake & GO NCBO/Buffalo Fabian Neuhaus Werner Ceusters Louis Goldberg Barry Smith NCBO/Eugene Melissa Haendel Monte Westerfield NCBO/Cambridge Michael Ashburner George Gkoutos NCBO/Victoria Chris Callender Margaret-Anne Storey NCBO/Mayo James Buntrock Chris Chute NIH Peter Good Carol Bean David Sutherland Oliver Hofmann Sue Rhee Johnathan Bard Lindsay Cowell Erik Segerdell Alan Rector Cynthia Smith Jannan Eppig Rex Chisholm Pascale Gaudet Paula de Matos Rafael Alcantra Kirill Degtyarenko Pankaj Jaiswal Onard Mejino Cornelius Rosse William Bug Alan Ruttenberg Trish Whetzel Jennifer Fostel & OBI Consortium NCBO/UCSF Simona Carini Ida Sim Nation Heart, Lung and Blood Institute

Karen Eilbeck
song.sf.net
properties and features of
nucleic sequences
Sequence Ontology
(SO)
RNA Ontology Consortium
(under development)
three-dimensional RNA
structures
RNA Ontology
(RnaO)
Barry Smith, Chris Mungall
obo.sf.net/relationship
relations
Relation Ontology (RO)
Protein Ontology Consortium
(under development)
protein types and
modifications
Protein 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 Group
obi.sf.net
design, 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/chebi
molecular entities
Chemical Entities (ChEBI)
Jonathan Bard, Michael
Ashburner, Oliver Hofman
obo.sourceforge.net/cgi-
bin/detail.cgi?cell
cell types from prokaryotes
to mammals
Cell Ontology
(CL)
Custodians
URL
Scope
Ontology

OBO Foundry

by Chris Mungall on Jun 25, 2007

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OBO Foundry — Presentation Transcript