Gene Ontology

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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

Software Developement: Tools and Scripts

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

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