WBConfCall 2014.04.03-Agenda and Minutes
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Minutes
Gene Association Files (GAFs)
- Anatomy, life stage, phenotype, disease association files
- Kevin Howe will be generating these files, in general
- Will be difficult or impossible to abide by GAF rules exactly, but can work it out
- Column 6 needs to be resolved: Reference or WormBase object (WBPaper or other) [primary source of the association]
- Generally, each reference (paper) gets its own line in the GAF
- Some anatomy terms are linked to multiple references, causes a problem
- Phenotypes don't always have a reference, causes a problem
- When we can't follow a publication, we reference a WB object
- Sometimes GO annotations do not have a paper, and so use a different reference object, method
- Proposal: Use a WormBase object as a reference (in column 6) for all GAFs aside from the GeneOntology GAFs
- Kevin Howe: this can be problematic, not preferred
- Disease terms can have multiple references and so each gets a separate line in the GAF
- OMIM IDs can go in column 8; multiple OMIM IDs can be pipe separated
- Anatomy, life stage, phenotype, disease GAFs: what is the referencing procedure? Currently using bogus WBPaper object (WBPaper00000000)
- If we use a "Method"/"Analysis" approach, we could have a write up explaining where the data comes from
- Anatomy GAFs can use ?Expr_pattern objects
- Life stage GAFs can use RNA-Seq experiments