2 3 where in the body ? where in the cell ?
TRANSCRIPT
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where in the body ? where in the cell ?
what kind of organism ?
what kind of disease process ?
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to yield:
distributed accessibility of the data to humans
reasoning with the data
cumulation for purposes of research
incrementality and evolvability
integration with clinical data
Creating broad-coverage semantic annotation systems for biomedicine
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The OBO Foundry Idea
MouseEcotope GlyProt
DiabetInGene
GluChem
sphingolipid transporter
activity
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The OBO Foundry Idea
MouseEcotope GlyProt
DiabetInGene
GluChem
Holliday junction helicase complex
Sjöblöm et al.
analyzed 13,023 genes in 11 breast and 11 colorectal cancers
identified189 as being mutated at significant frequency and thus as providing targets for diagnostic and therapeutic intervention.
correlations between functional information captured by GO for given gene product types and the expression patterns detected experimentally in selected instances of these types can help to elucidate underlying pathologies
Sjöblöm T, et al. Science. 2006 Oct 13;314(5797):268-74.
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Five bangs for your GO buck
1. based in biological science
2. incremental approach (low hanging fruit)
3. cross-species data comparability (human, mouse, yeast, fly ...)
4. cross-granularity data integration (molecule, cell, organ, organism)
5. cumulation of scientific knowledge in algorithmically tractable form which links people to software
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a family of interoperable biomedical reference ontologies built around the Gene Ontology at its core and using the same principles
a modular annotation catalogue of English phrases
each module created by experts from the corresponding scientific community
http://obofoundry.org
The OBO Foundry
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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 Componen
t(FMA, GO)
Cellular Function
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)
The OBO Foundry building out from the original GO
http://ontologist.com 17Karen Eilbecksong.sf.netproperties and features of
nucleic sequencesSequence Ontology
(SO)
RNA Ontology Consortium(under development)three-dimensional RNA
structuresRNA Ontology
(RnaO)
Barry Smith, Chris Mungallobo.sf.net/relationshiprelationsRelation Ontology (RO)
Protein Ontology Consortium(under development)protein types and
modificationsProtein Ontology
(PrO)
Michael Ashburner, Suzanna Lewis, Georgios Gkoutos
obo.sourceforge.net/cgi-bin/ detail.cgi?
attribute_and_valuequalities of biomedical entities
Phenotypic Quality Ontology
(PaTO)
Gene Ontology Consortiumwww.geneontology.orgcellular components, molecular functions, biological processes
Gene Ontology (GO)
FuGO Working Groupfugo.sf.netdesign, protocol, data
instrumentation, and analysis
Functional Genomics Investigation Ontology
(FuGO)
JLV Mejino Jr.,Cornelius Rosse
fma.biostr.washington.edu
structure of the human bodyFoundational 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/chebimolecular entitiesChemical Entities of Bio-logical Interest (ChEBI)
Jonathan Bard, Michael Ashburner, Oliver Hofman
obo.sourceforge.net/cgi-bin/detail.cgi?cell
cell types from prokaryotes to mammals
Cell Ontology (CL)
CustodiansURLScopeOntology
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Ontologies being built to satisfy Foundry principles ab initio
Clinical Trial Ontology (CIO)Common Anatomy Reference Ontology (CARO, DB1
& DB2)Mosquito Anatomy Ontology (MAO)Ontology for Biomedical Investigations (OBI)Phenotypic Quality Ontology (PATO, DB1 & DB2)Protein Ontology (PRO)Relation Ontology (RO)RNA Ontology (RnaO)
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Entry point for creation of web-accessible biomedical data
GO initially low-tech to encourage users
Simple (web-service-based) tools created to support the work of biologists in creating annotations (data entry)
OBO OWL DL converters now making OBO Foundry annotated data immediately accessible to Semantic Web data integration projects
GO allows distributed web-based collaboration
the methodology gradually being evolved as service -based architecture by US National Center for Biomedical Ontology (http://ncbo.us)
companies vs. cross-border collaboration
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