The OBO Foundry

1
The OBO Foundry

• Chris Mungall
• Lawrence Berkeley Laboratory
• NCBO
• GO Consortium
• May 2007

2
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

3
Outline

• Motivation
• History/Background
• Organisation and dependencies
• Foundry Principles
• Results

4
http//obofoundry.org
http//www.bioontologies.org (NCBO)
5
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

6
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

7
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.shtmlmicro
• Annotation of primary and literature data is one
  use of OBO Foundry ontologies

8
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
9
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

10
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

11
(No Transcript)
12
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

13
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
14
Results

• Phenotype Annotation
• Ontology for Biomedical Investigations (OBI)
• GO cross-products
• Anatomy Ontologies
• Semantic Web Health Care and Life Sciences (HCLS)
  interest group

15
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

16
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)

17
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

18
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

19
Finding out more and participating

• http//obofoundry.org
• http//www.bioontology.org
• obo-discuss_at_lists.sourceforge.net

20
Acknowledgements
NCBO/Berkeley Nicole Washington Mark Gibson John
Day-Richter Suzanna Lewis
Ontologies Amelia Ireland Jane Lomax Jen
Clark Midori Harris David Hill Karen Eilbeck Seth
Carbon Judith Blake GO
NCBO/Cambridge Michael Ashburner George Gkoutos
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/Eugene Melissa Haendel Monte Westerfield
NCBO/Stanford Nigam Shah Daniel Rubin Archana
Verbakam Lynn Murphy Michael J Montague Mark Musen
NCBO/Victoria Chris Callender Margaret-Anne Storey
NCBO/Buffalo Fabian Neuhaus Werner Ceusters Louis
Goldberg Barry Smith
NIH Peter Good Carol Bean
NCBO/UCSF Simona Carini Ida Sim
NCBO/Mayo James Buntrock Chris Chute
Nation Heart, Lung and Blood Institute
21

• Custodians

• URL

• Scope

• Ontology

• Jonathan Bard, Michael
• Ashburner, Oliver Hofman

• obo.sourceforge.net/cgi-
• bin/detail.cgi?cell

• cell types from prokaryotes
• to mammals

• Cell Ontology
• (CL)

• Paula Dematos,
• Rafael Alcantara

• ebi.ac.uk/chebi

• molecular entities

• Chemical Entities (ChEBI)

• Melissa Haendel, Terry
• Hayamizu, Cornelius Rosse,
• David Sutherland,

• (under development)

• anatomical structures in
• human and model organisms

• Common Anatomy Refer-
• ence Ontology (CARO)

• JLV Mejino Jr.,
• Cornelius Rosse

• fma.biostr.washington.
• edu

• structure of the human body

• Foundational Model of Anatomy (FMA)

• FuGO Working Group

• obi.sf.net

• design, protocol, data
• instrumentation, and analysis

• Functional Genomics
• Investigation Ontology
• (FuGO)

• Gene Ontology Consortium

• www.geneontology.org

• cellular components,
• molecular functions,
• biological processes

• Gene Ontology
• (GO)

• Michael Ashburner, Suzanna
• Lewis, Georgios Gkoutos

• obo.sourceforge.net/cgi
• -bin/ detail.cgi?
• attribute_and_value

• qualities of biomedical entities

• Phenotypic Quality
• Ontology
• (PaTO)

• Protein Ontology Consortium

• (under development)

• protein types and
• modifications

• Protein Ontology
• (PrO)

• Barry Smith, Chris Mungall

• obo.sf.net/relationship

• relations

• Relation Ontology (RO)

• RNA Ontology Consortium

• (under development)

• three-dimensional RNA
• structures

• RNA Ontology
• (RnaO)

• Karen Eilbeck

• song.sf.net

• properties and features of
• nucleic sequences

• Sequence Ontology
• (SO)

22
(No Transcript)