| layout | rule | |||||
|---|---|---|---|---|---|---|
| id | GORULE:0000001 | |||||
| title | Basic GAF checks | |||||
| contact | cherry@genome.stanford.edu | |||||
| status | Implemented | |||||
| implementations |
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The following basic checks ensure that submitted gene association files conform to the GAF spec, and come from the original GAF check script.
- Each line of the GAF file is checked for the correct number of columns, the cardinality of the columns, leading or trailing whitespace
- Col 1 and all DB abbreviations must be in GO.xrf_abbs (case may be incorrect)
- All GO IDs must be extant in current ontology
- Qualifier, evidence, aspect and DB object columns must be within the list of allowed values
- DB:Reference, Taxon and GO ID columns are checked for minimal form
- Date must be in YYYYMMDD format
- All IEAs over a year old are removed
- Taxa with a 'representative' group (e.g. MGI for Mus musculus, FlyBase for Drosophila) must be submitted by that group only