Difference between revisions of "Gene Ontology"

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*chloride-activated potassium channel activity (2008)
*chloride-activated potassium channel activity (2008)
*transdifferentiation (2008)
*transdifferentiation (2008)
*regulation of ovulation terms (2008)
*Regulation of ovulation terms (2008)
*Process terms for gap junction proteins (2008)
*Process terms for gap junction proteins (2008)
*piRNA and 21U-RNA terms (2008)
*piRNA and 21U-RNA terms (2008)
Line 40: Line 40:
*palmitoyl-CoA 9-desaturase activity (2007)
*palmitoyl-CoA 9-desaturase activity (2007)
*response to hyperoxia (2007)
*response to hyperoxia (2007)
*cuticle component terms (2007)
*Cuticle component terms (2007)
*response to anoxia (2007)
*response to anoxia (2007)
*dynein light intermediate chain binding (2006)
*dynein light intermediate chain binding (2006)
*regulation terms for cell and nuclear division (2006)
*Regulation terms for cell and nuclear division (2006)
*Several child terms for apoptosis (2006)
*Several child terms for apoptosis (2006)
*cilium terms (2005)
*Cilium terms (2005)
*intraflagellar transport particle-component terms (2004)
*Intraflagellar transport particle-component terms (2004)
*oogenesis (non-species specific term)(2004)
*oogenesis (non-species specific term)(2004)

Revision as of 19:42, 7 September 2010

Manual Literature Curation

  1. Lung Development Targets (November 2009 - February 2010)

Semi-Automated Methods of Curation

Textpresso-Based Curation
  • CCC - GO Cellular Component Curation using Textpresso
  1. dictyBase
  2. FlyBase
  3. TAIR
  4. WormBase
  • MFC - GO Molecular Function Curation using Textpresso
Phenotype2GO Mappings for Biological Process Annotation (Variation2GO and RNAiPhenotype2GO)
InterPro2GO Mappings for IEA Annotations

Reference Genome Inferential Annotations


WormBase contributions to Gene Ontology content

New Terms
  • phosphatidylserine exposure on apoptotic cell surface (2009)
  • regulation of synaptic vesicle priming (2008)
  • chloride-activated potassium channel activity (2008)
  • transdifferentiation (2008)
  • Regulation of ovulation terms (2008)
  • Process terms for gap junction proteins (2008)
  • piRNA and 21U-RNA terms (2008)
  • dense body (sensu Nematoda) cellular component term (2007)
  • GO:0000775, GO:0000779, GO:0000780
  • D/V and A/P axon guidance terms (2007)
  • palmitoyl-CoA 9-desaturase activity (2007)
  • response to hyperoxia (2007)
  • Cuticle component terms (2007)
  • response to anoxia (2007)
  • dynein light intermediate chain binding (2006)
  • Regulation terms for cell and nuclear division (2006)
  • Several child terms for apoptosis (2006)
  • Cilium terms (2005)
  • Intraflagellar transport particle-component terms (2004)
  • oogenesis (non-species specific term)(2004)
Modifications to the Ontology
  • Add dense core vesicle synonym to dense core granule (2010)
  • Updated definition and moved parentage for intraflagellar transport (2009)
  • Added lethargus as synonym for sleep (2008)
  • Change to the definitions of the component terms: GO:0000775, GO:0000779, GO:0000780 which refer to the centromeres or chromosome, pericentric region (2007)
  • Change to parent of tail tip morphogenesis (sensu Nematoda) (2006)
  • GO:0046536, dosage compensation complex definition (2006)
Requests that are pending
  • response to drug withdrawel, 2010

Annotation Practices

1. When annotating to Cellular Component terms:

If a protein contains a transmembrane domain, but expression experiments are not at sufficient resolution to show membrane localization, what annotation should we make?

Example: WBPaper00036024

Plans/Projects in progress

Changes to the GO data model
  • Add tags for accommodating data in WormBase that are already in the gene association file:
    • Qualifying an annotation with the qualifiers 'NOT' 'contributes_to' or 'colocalizes with'
    • Using the generic GO_REF tags for generic references eg., for a NOT annotation, need to add the proper database and accession syntax (need to add a field in curation interface in OA).
    • 'With' or 'From', for the use of additional identifiers with the use of certain evidence codes like IPI, IGI, etc.
    • Annotation Extension, for containing cross references to other ontologies,one of:
      • DB:gene_id
      • DB:sequence_id
      • CHEBI:CHEBI_id
      • Cell Type Ontology:CL_id
      • GO:GO_id
    • Gene Product Form ID, a canonical entry for specific variants of gene products.
      • When the gene product form ID (column 17 of ga) is filled with a protein identifier, the value in DB object type (column 12 of ga) must be protein. Protein identifiers can include UniProtKB accession numbers, NCBI NP identifiers or Protein Ontology (PRO) identifiers.
      • When the gene product form ID (column 17 of ga) is filled with a functional RNA identifier, the DB object type (column 12 of ga) must be either ncRNA, rRNA, tRNA, snRNA, or snoRNA.
Changes to the GO_term model and updating the ontology in WormBase

Back to Caltech documentation