Derived files in CVS: Difference between revisions
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[[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 === | ||
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Mechanism: obo2flat v1.1 via cron at Stanford | Mechanism: obo2flat v1.1 via cron at Stanford | ||
Frequency: | Frequency: monthly | ||
Tests: | Tests: | ||
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== 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.