Difference between revisions of "Manager 20November2013"

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(Action points from last meeting)
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  Gene Ontology annotation through association of Phenotype Ontology terms with GO Biological Process terms
 
  Gene Ontology annotation through association of Phenotype Ontology terms with GO Biological Process terms
 
  WB
 
  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 using this reference may  contain one or more of the following in the With/From column (column 8) of the gene association file: 1) A variation or RNAi identifier that    indicates the perturbation that produced the phenotype, 2) The Phenotype Ontology term ID, 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 using this reference may  contain one or more of the following in the With/From column (column 8) of the gene association file: 1) A variation or RNAi identifier that    indicates the perturbation that produced the phenotype, 2) The Phenotype Ontology term ID, 3) A reference identifier for the publication    that reported the phenotype.  Mapping files ''will be made available'' here:  http://www.geneontology.org/external2go/wbphenotype2go.
  
 
'''Action Item:''' Update documentation about what can be included in the With/From column for IMP annotations to include paper identifiers. [Rachael, Rama]
 
'''Action Item:''' Update documentation about what can be included in the With/From column for IMP annotations to include paper identifiers. [Rachael, Rama]

Revision as of 10:19, 19 November 2013

Action points from last meeting

Action Item: Draft 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. [Kimberly]

Draft:

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 using this reference may   contain one or more of the following in the With/From column (column 8) of the gene association file: 1) A variation or RNAi identifier that    indicates the perturbation that produced the phenotype, 2) The Phenotype Ontology term ID, 3) A reference identifier for the publication     that reported the phenotype.  Mapping files will be made available here:  http://www.geneontology.org/external2go/wbphenotype2go.

Action Item: Update documentation about what can be included in the With/From column for IMP annotations to include paper identifiers. [Rachael, Rama]

Action Item: Survey existing annotations to find suspect (outlier) BP annotations. [Suzi, Chris]

Action Item: Assemble use cases where phenotype-based annotations would be either misleading or inconsistent with manual GO annotation practices. [GO Curators]

Reference Proteomes

  • Do we use the reference proteomes in GO as default?
  • Do we sync with QfO or with UniProt?
  • How do we deal with async issues, e.g. PAINT?


BioCurator Meeting

  • What are GO's plans for the meeting?
  • Would be good to have a coordinated set of talks - start a wiki page for ideas?
  • Submit a paper for the Database issue? Just abstracts?
  • Who is going to the meeting?

Action Item: Add abstract deadline to GO calendar - DONE [Suzi]

Papers - November 15th, 2013

Abstract for Posters - February 10, 2014

Action Item: Create wiki page for ideas.

Ideas: enrichment analysis strategies, MGI's phenotype to BP pipeline, apoptosis

Discussion points