Derived files in CVS
Every derived file checked into cvs should be registered here. Please note update frequency, manual vs automatic, program + version used etc
Files derived from the ontology
See also Ontology_CVS_Directory_Layout_Overhaul
*.ontology files
Directory: go/ontology
Files:
- *.ontology
Mechanism: obo2flat v1.1 via cron at Stanford
Frequency: nightly
Tests:
slims
Directory: go/GO_slims
Files:
- *.{obo,go}
Mechanism: Amelia runs oe / obo2obo? Periodicity?
obo2flat for obo->go, cron at SGD, M,W,Sa
Tests:
lists of terms, ids and obsoletes
Directory: go/doc
Files:
- GO.terms_alt_ids
- GO.terms_and_ids
Mechanism: Midori runs script to generate files; manual CVS commit; approx. daily.
Note: As far as I know, Amelia has a plan to generate these files from the database and commit them in some automated fashion. I'm just waiting to hear form someone that I can stop updating manually ... (midori)
- GO.terms_ids_obs
Note: I (midori) don't know anything about this one beyond observing that it exists.
- obsoletes-exact
- obsoletes-inexact
Mechanism: generated from the OBO flat file by a custom perl script.
xxx2go files
Directory: go/external2go
- ec2go
- metacyc2go
- reactome2go
- um-bbd_enzymeid2go
- um-bbd_pathwayid2go
Mechanism: generated from the OBO flat file by a custom perl script.