Derived files in CVS: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
mNo edit summary
(16 intermediate revisions by 5 users not shown)
Line 1: Line 1:
[[Category:Archived]]
Every derived file checked into cvs should be registered here. Please note update frequency, manual vs automatic, program + version used etc
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 ==
== 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 [http://www.geneontology.org/software/utilities/filter-obo-for-standard-release.pl ./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 [http://oboedit.org/docs/html/obo2obo.htm obo2obo])


=== *.ontology files ===
=== *.ontology files ===


Location: go/ontology/*.ontology
Directory: go/ontology
 
Files:
* *.ontology


Mechanism: obo2flat v1.1 via cron at Stanford
Mechanism: obo2flat v1.1 via cron at Stanford
Frequency: monthly
Tests:


=== slims ===
=== slims ===


Location: go/GO_slims/*.{obo,go}
Directory: go/GO_slims
 
Files:
* *.{obo,go}


Mechanism: Amelia runs oe / obo2obo? Periodicity?
Mechanism: Amelia runs oe / obo2obo? Periodicity?
obo2flat for obo->go
 
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 ==
== Files derived from annotations ==

Revision as of 13:03, 13 April 2019

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