Gene Ontology
From WormBaseWiki
Contents
- 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 WormBase contributions to Gene Ontology content
- 8 Modifications to the Ontology
- 9 Requests that are pending
- 10 Annotation Practices
- 11 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
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 2008-08-05
- regulation of ovulation terms 2008-07-24
- process terms for gap junction proteins 2008-07-18
- piRNA and 21U-RNA terms, 2008-06-27
- 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
- cuticle component terms, 2007-04-09
- response to anoxia, 2007-12-17
- dynein light intermediate chain binding, 2006-03-17
- regulation terms for cell and nuclear division, 2006-01-03
- positive and negative regulation of ion transport definitions, 2005-10-13
- cilium terms, 2005-06-14
- intraflagellar transport particle-component terms, 2004-08-23
- oogenesis (non-species specific term)
Modifications to the Ontology
- Add dense core vesicle synonym to dense core granule, 2010-01-25
- Updated definition and moved parentage for intraflagellar transport, 2009-03-11
- Added lethargus as synonym for sleep, 2008-11-07
- Change to parent of tail tip morphogenesis (sensu Nematoda), 2006-01-24
- GO:0046536, dosage compensation complex definition, 2006-10-02
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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