Embed Size (px)
DESCRIPTION
OBO Foundry presentation delivered at Clinical Trial Ontology Meeting, Bethesda, 2007
Citation preview
The OBO Foundry
Chris MungallLawrence Berkeley Laboratory
NCBOGO 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
QuickTime™ and aTIFF (LZW) decompressor
are needed to see this picture.
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
ChEBICell
Anatomyquality
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
CONTINUANT OCCURRENT RELATION TO
TIME GRANULARITY INDEPENDENT DEPENDENT
ORGAN AND ORGANISM
Organism (NCBI
Taxonomy)
Anatomical Entity (FMA, CARO)
Organ Function (FMP, CPRO)
Organism-Level Process
(GO)
CELL AND CELLULAR
COMPONENT
Cell (CL)
Cellular Component (FMA,GO)
Cellular Function
(GO)
Phenotypic Quality (PaTO)
Cellular Process (GO)
MOLECULE Molecule
(ChEBI, SO, RnaO, PrO)
Molecular Function (GO)
Molecular Process (GO)
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 protected]
AcknowledgementsNCBO/BerkeleyNicole Washington
Mark Gibson
John Day-Richter
Suzanna Lewis
NCBO/StanfordNigam Shah
Daniel Rubin
Archana Verbakam
Lynn Murphy
Michael J Montague
Mark Musen
OntologiesAmelia Ireland
Jane Lomax
Jen Clark
Midori Harris
David Hill
Karen Eilbeck
Seth Carbon
Judith Blake
& GO
NCBO/BuffaloFabian Neuhaus
Werner Ceusters
Louis Goldberg
Barry Smith
NCBO/EugeneMelissa Haendel
Monte Westerfield
NCBO/CambridgeMichael Ashburner
George Gkoutos
NCBO/VictoriaChris Callender
Margaret-Anne Storey
NCBO/MayoJames Buntrock
Chris Chute
NIHPeter 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/UCSFSimona 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
CONTINUANT OCCURRENT RELATION TO
TIME GRANULARITY INDEPENDENT DEPENDENT
ORGAN AND ORGANISM
Organism (NCBI
Taxonomy)
Anatomical Entity (FMA, CARO)
Organ Function (FMP, CPRO)
Organism-Level Process
(GO)
CELL AND CELLULAR
COMPONENT
Cell (CL)
Cellular Component (FMA,GO)
Cellular Function
(GO)
Phenotypic Quality (PaTO)
Cellular Process (GO)
MOLECULE Molecule
(ChEBI, SO, RnaO, PrO)
Molecular Function (GO)
Molecular Process (GO)
