Annotation Conf. Call November 26, 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: In yeast, CNB1 is the regulatory subunit and CNA1 and CMP2 are the catalytic subunits of the Calcineurin complex (http://www.yeastgenome.org/cgi-bin/GO/goTerm.pl?goid=5955, phosphatase complex).

• Would you add the substrate information in col-16 for phosphorylation BP annotation if we have already captured the substrate for the Kinase activity, MF annotation?

• Clarification on has_direct and has_indirect input