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The Gene Ontology : a real-life ontology, progress and future.

This article provides an overview of the Gene Ontology (GO), a controlled vocabulary used for annotation of proteins. It discusses the structure of GO, how it is maintained, and its future developments. The article also highlights the challenges and ongoing efforts to formalize and integrate GO with other biomedical vocabularies.

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The Gene Ontology : a real-life ontology, progress and future.

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  1. The Gene Ontology: a real-life ontology, progress and future. Jane Lomax EMBL-EBI

  2. What is the Gene Ontology? • Controlled vocabulary - GO • Terms and relationships • Bottom-up approach • Annotation of proteins to terms • Gene association files • Software/database development • Freely available

  3. The vocabulary • GO is divided into three sub-vocabularies: • biological process • broad series of events, can either be at the level of the cell or organism e.g. circulation, glycolysis • molecular function • direct activities e.g. catalysis, binding • cellular component • site of action e.g. nucleus, ribosome

  4. The vocabulary • Hierarchical • Directed Acyclic Graph • terms have one or more parents • is-a and part-of relations

  5. http://www.godatabase.org/cgi-bin/go.cgi

  6. How is GO maintained? • Several full-time editors • Requests from community • database curators, researchers, software developers • SourceForge tracker • GO Consortium meetings for large changes • Mailing lists

  7. OBO - Open Biological Ontologies • GO is a member vocabulary of OBO • A repository for biological structured vocabularies • Freely available without license • Common syntax • Orthogonal to existing ontologies http://obo.sourceforge.net/

  8. Future developments • File format • Current GO flat file format • partly redundant • difficult to parse • New format • Extensible e.g. new relationship types can be specified • minimal redundancy, but human readable • easier to parse • Moving to a database being the primary form of GO

  9. Formalizing GO • Informality is a common criticism of GO • developed by biologists, for biologists • Now beginning work ‘decomposing’ GO using ProLog • Terms broken down into constituent parts e.g. regulation of heartdevelopment • New terms could be created from orthogonal ontologies e.g. anotomical • Work translating GO in DL, reasoning across the ontologies

  10. GO into UMLS • GO now released as part of the NLM’s Unified Medical Language System Metathesaurus • Links biomedical vocabularies including MeSH and SNOMED. • The process of including GO in UMLS highlighted problems in both systems

  11. GO synonyms • Text strings associated with GO terms • Often do not have identical meaning to term • Reduces utility in e.g. semantic matching • Developed relationships between terms and synonyms • soon to be fully implemented in GO

  12. www.geneontology.org • FlyBase & Berkeley Drosophila Genome Project • Saccharomyces Genome Database • PomBase (Sanger Institute) • Rat Genome Database • Genome Knowledge Base (CSHL) • The Institute for Genomic Research • Compugen, Inc • The Arabidopsis Information Resource • WormBase • DictyBase • Mouse Genome Informatics • Swiss-Prot/TrEMBL/InterPro • Pathogen Sequencing Unit (Sanger Institute) The Gene Ontology Consortium is supported by an R01 grant from the National Human Genome Research Institute (NHGRI) [grant HG02273]. SGD is supported by a P41, National Resources, grant from the NHGRI [grant HG01315]; MGD by a P41 from the NHGRI [grant HG00330]; GXD by the National Institute of Child Health and Human Development [grant HD33745]; FlyBase by a P41 from the NHGRI [grant HG00739] and by the Medical Research Council, London. TAIR is supported by the National Science Foundation [grant DBI-9978564]. WormBase is supported by a P41, National Resources, grant from the NHGRI [grant HG02223]; RGD is supported by an R01 grant from the NHLBI [grant HL64541]; DictyBase is supported by an R01 grant from the NIGMS [grant GM064426].

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