Gene Ontology

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Manual Literature Curation

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

Semi-Automated, 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

Scripts

WormBase contributions to Gene Ontology content

New Terms

  • regulation of synaptic vesicle priming, 2008-11-07
  • chloride-activated potassium channel activity, 2008-10-28
  • transdifferentiation 2008-08-05
  • regulation of ovulation terms 2008-07-24
  • process terms for gap junction proteins 2008-07-18
  • dense body (sensu Nematoda) cellular component term, 2007-07-31
  • GO:0000775, GO:0000779, GO:0000780
  • D/V and A/P axon guidance terms, 2007-07-24
  • Child terms for apoptosis, 2006-03-15
  • palmitoyl-CoA 9-desaturase activity, 2007-01-29
  • response to hyperoxia, 2007-11-12
  • Dynein light intermediate chain binding, 2006-03-17
  • change to parent of tail tip morphogenesis (sensu Nematoda), 2006-01-24
  • regulation terms for cell and nuclear division, 2006-01-03
  • positive and negative regulation of ion transport definitions, 2005-10-13
  • cuticle component terms, 2007-04-09
  • cilium terms, 2005-06-14
  • piRNA and 21U-RNA terms, 2008-06-27
  • intraflagellar transport particle-component terms, 2004-08-23
  • Added lethargus as synonym for sleep, 2008-11-07


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