Thaw Mail
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. 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 have a mail from SGD to 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