Difference between revisions of "Gene Ontology"
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==Semi-Automated Methods of Curation== | ==Semi-Automated Methods of Curation== | ||
− | ===Textpresso-Based Curation=== | + | ====Textpresso-Based Curation==== |
*CCC - GO Cellular Component Curation using Textpresso | *CCC - GO Cellular Component Curation using Textpresso | ||
#[[dictyBase]] | #[[dictyBase]] | ||
Line 13: | Line 13: | ||
*MFC - GO Molecular Function Curation using Textpresso | *MFC - GO Molecular Function Curation using Textpresso | ||
− | ===Phenotype2GO Mappings for Biological Process Annotation (Variation2GO and RNAiPhenotype2GO)=== | + | ====Phenotype2GO Mappings for Biological Process Annotation (Variation2GO and RNAiPhenotype2GO)==== |
*[[Phenotype2GO pipeline SOP]] | *[[Phenotype2GO pipeline SOP]] | ||
*[[Phenotype2GO Mappings File]] | *[[Phenotype2GO Mappings File]] | ||
Line 19: | Line 19: | ||
*[[Phenotype2GO Paper Inclusion List]] | *[[Phenotype2GO Paper Inclusion List]] | ||
− | ===InterPro2GO Mappings for IEA Annotations=== | + | ====InterPro2GO Mappings for IEA Annotations==== |
− | ==Reference Genome Inferential Annotations== | + | ===Reference Genome Inferential Annotations=== |
==Scripts== | ==Scripts== | ||
Line 27: | Line 27: | ||
==WormBase contributions to Gene Ontology content== | ==WormBase contributions to Gene Ontology content== | ||
− | ===New Terms=== | + | ====New Terms==== |
*phosphatidylserine exposure on apoptotic cell surface (2009) | *phosphatidylserine exposure on apoptotic cell surface (2009) | ||
*regulation of synaptic vesicle priming (2008) | *regulation of synaptic vesicle priming (2008) | ||
Line 49: | Line 49: | ||
*oogenesis (non-species specific term)(2004) | *oogenesis (non-species specific term)(2004) | ||
− | ===Modifications to the Ontology=== | + | ====Modifications to the Ontology==== |
*Add dense core vesicle synonym to dense core granule (2010) | *Add dense core vesicle synonym to dense core granule (2010) | ||
*Updated definition and moved parentage for intraflagellar transport (2009) | *Updated definition and moved parentage for intraflagellar transport (2009) | ||
Line 69: | Line 69: | ||
==Plans/Projects in progress== | ==Plans/Projects in progress== | ||
− | ===Changes to the GO data model=== | + | ====Changes to the GO data model==== |
*Add tags for accommodating data in WormBase that are already in the gene association file: | *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' | **Qualifying an annotation with the qualifiers 'NOT' 'contributes_to' or 'colocalizes with' |
Revision as of 19:36, 7 September 2010
Contents
Manual Literature Curation
- Reference Genome (see also Reference Genome Inferential Annotations)
Semi-Automated Methods of Curation
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)
- 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
Back to Caltech documentation