Ontology publishing pipeline 2009 (Archived): Difference between revisions
(New page: 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...) |
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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]] | 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. | 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) == | == Step 1 : publish editors version as GO-ext (extended GO) == | ||
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This step is a simple cp of [[gene_ontology_write.obo]] to ontology/obo_format_1_2/gene_ontology_ext.obo | 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 [http://www.geneontology.org/software/utilities/check-obo-for-standard-release.pl go/software/utilities/check-obo-for-standard-release.pl] | |||
== Step 2 : filter GO-ext and publish in usual place == | == Step 2 : filter GO-ext and publish in usual place == | ||
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This involves a new script that will filter out inter-ontology links and also intra-MF regulates links. | This involves a new script that will filter out inter-ontology links and also intra-MF regulates links. | ||
The script | The script is in go cvs: [http://www.geneontology.org/software/utilities/filter-obo-for-standard-release.pl ./software/utilities/filter-obo-for-standard-release.pl] | ||
we will need a cron that executes: | 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 | 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]] | 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]] | |||
[[Category:Ontology]] | |||
[[Category:Archived]] |
Latest revision as of 14:04, 24 January 2018
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