Difference between revisions of "WBConfCall 2014.04.03-Agenda and Minutes"
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== Gene Association Files (GAFs) == | == Gene Association Files (GAFs) == | ||
| − | * Anatomy, life stage, disease association files | + | * Anatomy, life stage, phenotype, disease association files |
* Kevin Howe will be generating these files, in general | * 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 | * Will be difficult or impossible to abide by GAF rules exactly, but can work it out | ||
| Line 17: | Line 17: | ||
* Disease terms can have multiple references and so each gets a separate line in the GAF | * 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 | * 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" approach, we could have a write up explaining where the data comes from | ||
Revision as of 15:57, 3 April 2014
Agenda
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
- 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" approach, we could have a write up explaining where the data comes from
