Difference between revisions of "WBConfCall 2014.04.03-Agenda and Minutes"
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* If we use a "Method"/"Analysis" approach, we could have a write up explaining where the data comes from | * 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 in column 6 | * Anatomy GAFs can use ?Expr_pattern objects in column 6 | ||
+ | * Life stage GAFs can use RNA-Seq experiments in column 6 | ||
+ | * Disease GAFs will use ?Paper in column 6 | ||
* Phenotype GAFs: use ?RNAi or ?Variation objects in column 6? | * Phenotype GAFs: use ?RNAi or ?Variation objects in column 6? | ||
− | * | + | * RNAi experiments all have WBPaper (or WBPerson at least), so that can be used; only ?Variation-to-?Gene connections are an issue |
− | * | + | * Many ?Variation-to-?Gene connections can be attributed to a WBPerson (e.g. from Allele curation form) in a Phenotype GAF |
+ | * If a paper does not exist for ?Variation-to-?Gene or ?RNAi-to-?Gene connection, use the ?Variation or ?RNAi object in column 6 of the Phenotype GAF | ||
+ | * Typically, a paper reference will go in column 6; WormBase data object (e.g. ?Variation or ?RNAi) will go in column 8 | ||
+ | * In the event that a paper reference does not exist, the WormBase object will go in BOTH column 8 and column 6 |
Latest revision as of 16:30, 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, 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 in column 6
- Life stage GAFs can use RNA-Seq experiments in column 6
- Disease GAFs will use ?Paper in column 6
- Phenotype GAFs: use ?RNAi or ?Variation objects in column 6?
- RNAi experiments all have WBPaper (or WBPerson at least), so that can be used; only ?Variation-to-?Gene connections are an issue
- Many ?Variation-to-?Gene connections can be attributed to a WBPerson (e.g. from Allele curation form) in a Phenotype GAF
- If a paper does not exist for ?Variation-to-?Gene or ?RNAi-to-?Gene connection, use the ?Variation or ?RNAi object in column 6 of the Phenotype GAF
- Typically, a paper reference will go in column 6; WormBase data object (e.g. ?Variation or ?RNAi) will go in column 8
- In the event that a paper reference does not exist, the WormBase object will go in BOTH column 8 and column 6