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


Term Requests

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 the proper database and accession syntax
    • '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) 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) is filled with a functional RNA identifier, the DB object type (column 12 of ga) must be either ncRNA, rRNA, tRNA, snRNA, or snoRNA.

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