Thaw Mail

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Thaw Mail

Hi,

The 'regulates' relationships, the electron transport changes, and the new cvs layout have been implemented, and the ontology editing freeze is now over.  
For those who edit the ontologies, please now *only* edit the ontology file go/ontology/editors/gene_ontology_write.obo 
as your changes will otherwise be automatically over-written. If you are having trouble seeing the 'regulates' links in OBO-Edit, make sure
that your Global Filters are updated to remove this one: "Select links where Type that have a 'Is Transitive'" (and you could also try restarting).

The layout of the go/ontology directory has been overhauled for a couple of reasons:
 
1) To simplify file identification for users.
2) To provide a private version of the ontology file, in 
which we can test for file problems before we release a 
separate public copy for users. We are hoping that this  will 
help reduce the incidence of small file errors causing big
problems for daily database loads at the mods. The new file 
will also enable us to add features to the private file for 
testing, but to have them stripped out in the public version.
This helps us get new features fully tested within the file, 
rather than having a rushed merge and release.

The old cvs structure will continue to be supported:

go/
  ontology/
    gene_ontology.obo			(OBO 1.0 format)
    gene_ontology_edit.obo	     (OBO 1.2 format)


The new structure looks like this:

go/
   ontology/
	obo_format_1_0/
	        gene_ontology.1_0.obo		(OBO 1.0 format)
	obo_format_1_2/
		gene_ontology.1_2.obo		(OBO 1.2 format)
	editors/
		gene_ontology_write.obo		(OBO 1.2 format)


Ontology editors should only edit gene_ontology_write.obo.
Users who wish to download a copy of the file in OBO 1.0 format should use gene_ontology.1_0.obo.
Users who wish to download a copy of the file in OBO 1.2 format should use gene_ontology.1_2.obo.
 
Please note that the script is not yet in place to handle the file conversions between 
the write file and the 1.0 and 1.2 files, but we will receive a mail from SGD via the GO list when it is. 

Thanks for reading. :-)

Jen


Further details here:
http://wiki.geneontology.org/index.php/Ontology_CVS_Directory_Layout_Overhaul#Proposed_new_layout