Derived files in CVS

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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 and Ontology_publishing_pipeline_2009

*.obo files

publishing ext file

As of Feb 09

  • ontology/editors/gene_ontology_write.obo -> ontology/obo_format_1_2/gene_ontology_ext.obo

This is currently a cp, but could in future include a verification step

publishing main public files

  • ontology/obo_format_1_2/gene_ontology_ext.obo -> ontology/obo_format_1_2/gene_ontology.1_2.obo (via ./software/utilities/filter-obo-for-standard-release.pl)
  • ontology/obo_format_1_2/gene_ontology.1_2.obo -> ontology/gene_ontology_edit.obo (via cp)
  • ontology/obo_format_1_2/gene_ontology.1_2.obo -> ontology/obo_format_1_0/gene_ontology.1_0.obo (via obo2obo)

*.ontology files

Directory: go/ontology

Files:

  • *.ontology

Mechanism: obo2flat v1.1 via cron at Stanford

Frequency: monthly

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.

Pipeline

Files derived from annotations