Ontology publishing pipeline 2009 (Archived)

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The current publishing pipeline essentially copies the gene_ontology_write.obo file to the public area, and then runs obo2obo in order to generate the legacy obof1.0 and go files. See Ontology CVS Directory Layout Overhaul 2007

With the addition of new inter-ontology relations in the core GO, we decided we needed to introduce a buffer to insulate ontology file consumers from these kinds of new changes. See GO_Timeline

Step 1 : publish editors version as GO-ext (extended GO)

This step is a simple cp of gene_ontology_write.obo to ontology/obo_format_1_2/gene_ontology_ext.obo

First of all some simple checks run; if these fail then the process is blocked at this stage go/software/utilities/check-obo-for-standard-release.pl

Step 2 : filter GO-ext and publish in usual place

This involves a new script that will filter out inter-ontology links and also intra-MF regulates links.

The script is in go cvs: ./software/utilities/filter-obo-for-standard-release.pl

we will need a cron that executes:

 filter-obo-for-standard-release.pl ontology/obo_format_1_2/gene_ontology_ext.obo > ontology/obo_format_1_2/gene_ontology.1_2.obo.tmp &&\
 mv ontology/obo_format_1_2/gene_ontology.1_2.obo.tmp ontology/obo_format_1_2/gene_ontology.1_2.obo

The following steps should be identical to the existing pipeline. See Ontology CVS Directory Layout Overhaul 2007

Step 3 : publish legacy GO files

1_0.obo and .ontology files

See Also

Ontology Release Files Proposal