Difference between revisions of "Manager 20November2013"

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(New Agenda Items)
(Annotations to non-UniProtKB identifiers)
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*Collecting use cases for non-UniProtKB identifiers for common annotation tool.
 
*Collecting use cases for non-UniProtKB identifiers for common annotation tool.
**email was sent to seven groups to ask for identifiers specifications.  So far, no response.
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**email was sent to seven groups to ask for identifiers specifications.  So far, responses from BHF-UCL and WB.
  
 
===Enhancing Taxon Constraints===
 
===Enhancing Taxon Constraints===

Revision as of 13:35, 19 November 2013

New Agenda Items

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?

Annotations to non-UniProtKB identifiers

  • Collecting use cases for non-UniProtKB identifiers for common annotation tool.
    • email was sent to seven groups to ask for identifiers specifications. So far, responses from BHF-UCL and WB.

Enhancing Taxon Constraints

The ontology group has created a new ticket and sub-tickets:

There are some technical issues to take care of, and making taxon constraints often leads to time-consuming refactors -these ultimately improve the ontology but take effort away from other priorities. Do we have some deadline and metric of success for the next meeting in Texas?

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 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.

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]


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