- 1 Manual Literature Curation
- 2 Semi-Automated, Textpresso-Based Curation
- 3 Phenotype2GO Mappings for Biological Process Annotation (Variation2GO and RNAiPhenotype2GO)
- 4 InterPro2GO Mappings for IEA Annotations
- 5 Reference Genome Inferential Annotations
- 6 Scripts
- 7 Term Requests
- 8 Annotation Practices
- 9 Plans/Projects in progress
Manual Literature Curation
- Reference Genome (see also Reference Genome Inferential Annotations)
Semi-Automated, Textpresso-Based Curation
- CCC - GO Cellular Component Curation using Textpresso
- MFC - GO Molecular Function Curation using Textpresso
Phenotype2GO Mappings for Biological Process Annotation (Variation2GO and RNAiPhenotype2GO)
- Phenotype2GO pipeline SOP
- Phenotype2GO Mappings File
- Phenotype2GO Mappings Sept. 09
- Phenotype2GO Paper Inclusion List
InterPro2GO Mappings for IEA Annotations
Reference Genome Inferential Annotations
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?
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:
- Cell Type Ontology:CL_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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