New Agenda Items
- 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.
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]
Gene Ontology annotation through association of Phenotype Ontology terms with GO Biological Process terms
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]
- 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?
- 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