Annotation Conf. Call November 26, 2013: Difference between revisions
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==Agenda== | ==Agenda== | ||
===GO_Ref for phenotype2GO mapping annotations (Kimberley)=== | |||
Here is a draft of a GO_REF for BP annotations inferred from Phenotype Ontology annotations that documents curation pipeline and entities included in the With/From column, e.g. Variation IDs, RNAi experiment IDs, Phenotype Ontology terms, Paper IDs. These annotations will have IEA with this Reference. Please note that IEAs require ID in the With column and IEA annotations >1 year will be removed. | Here is a draft of a GO_REF for BP annotations inferred from Phenotype Ontology annotations that documents curation pipeline and entities included in the With/From column, e.g. Variation IDs, RNAi experiment IDs, Phenotype Ontology terms, Paper IDs. These annotations will have IEA with this Reference. Please note that IEAs require ID in the With column and IEA annotations >1 year will be removed. | ||
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Transitive assignment of GO terms based on mappings between Phenotype Ontology terms and GO Biological Process terms. GO terms are obtained from a file, generated manually by WormBase curators, containing mappings to Worm Phenotype Ontology (WPO) terms. Annotations made using this reference may contain one or more of the following in the With/Fro column (Column 8): 1) A variation or RNAi identifier used by WB to indicate the perturbation; 2) The WPO term; 3) A reference identifier for the publication that reported the phenotype. Mapping files will be made available here: http://www.geneontology.org/external2go/wbphenotype2go. | Transitive assignment of GO terms based on mappings between Phenotype Ontology terms and GO Biological Process terms. GO terms are obtained from a file, generated manually by WormBase curators, containing mappings to Worm Phenotype Ontology (WPO) terms. Annotations made using this reference may contain one or more of the following in the With/Fro column (Column 8): 1) A variation or RNAi identifier used by WB to indicate the perturbation; 2) The WPO term; 3) A reference identifier for the publication that reported the phenotype. Mapping files will be made available here: http://www.geneontology.org/external2go/wbphenotype2go. | ||
===Column-16 curation questions=== | |||
* Forward annotation example: Yeast CNB1 is the regulatory subunit of the Calcineurin complex (http://www.yeastgenome.org/cgi-bin/GO/goTerm.pl?goid=5955, phosphatase complex). CNA1 and CMP2 are the catalytic subunits. | |||
* Would you add the substrate information in col-16 for phosphorylation BP annotation if we have already captured the Kinase, MF annotation? | |||
* Clarification on had_direct and has_indirect input | |||
Revision as of 15:29, 22 November 2013
Agenda
GO_Ref for phenotype2GO mapping annotations (Kimberley)
Here is a draft of a GO_REF for BP annotations inferred from Phenotype Ontology annotations that documents curation pipeline and entities included in the With/From column, e.g. Variation IDs, RNAi experiment IDs, Phenotype Ontology terms, Paper IDs. These annotations will have IEA with this Reference. Please note that IEAs require ID in the With column and IEA annotations >1 year will be removed.
GO_REF:0000058
Gene Ontology annotation through association of Phenotype Ontology terms with GO Biological Process terms
WB
Transitive assignment of GO terms based on mappings between Phenotype Ontology terms and GO Biological Process terms. GO terms are obtained from a file, generated manually by WormBase curators, containing mappings to Worm Phenotype Ontology (WPO) terms. Annotations made using this reference may contain one or more of the following in the With/Fro column (Column 8): 1) A variation or RNAi identifier used by WB to indicate the perturbation; 2) The WPO term; 3) A reference identifier for the publication that reported the phenotype. Mapping files will be made available here: http://www.geneontology.org/external2go/wbphenotype2go.
Column-16 curation questions
- Forward annotation example: Yeast CNB1 is the regulatory subunit of the Calcineurin complex (http://www.yeastgenome.org/cgi-bin/GO/goTerm.pl?goid=5955, phosphatase complex). CNA1 and CMP2 are the catalytic subunits.
- Would you add the substrate information in col-16 for phosphorylation BP annotation if we have already captured the Kinase, MF annotation?
- Clarification on had_direct and has_indirect input