Revision as of 15:53, 3 April 2014

Agenda

Anatomy, life stage, 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

@@ Line 16: / Line 16: @@
 * 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