These notes are for the EDITORS of pato
For more details on ontology management, please see the OBO tutorial:
Do you have an ID range in the idranges file (pato-idranges.owl), in this directory). If not, get one from the head curator.
The editors version is pato-edit.obo
** DO NOT EDIT pato.obo OR pato.owl **
pato.obo is the release version
The editors version can be edited using OBO-Edit. Protege can be used ONLY IF the version is 5beta-snapshot18 or higher. DO NOT EDIT WITH PREVIOUS VERSIONS.
TODO - these are not set up
These are stored in the file
** ONLY USE IDs WITHIN YOUR RANGE!! **
TODO add instructions here
First you should have docker installed. This release pipeline uses the obolibrary/osk container on dockerhub.
You should only attempt to make a release AFTER the edit version is committed and pushed, and the travis build passes.
to release:
cd src/ontology
./run make
If this looks good type:
./run make release
This generates derived files such as pato.owl and pato.obo and places them in the top level (../..). The versionIRI will be added.
Commit and push these files.
git commit -a -m 'new release'
And type a brief description of the release in the editor window
git push origin master
IMMEDIATELY AFTERWARDS (do not make further modifications) go here:
The value of the "Tag version" field MUST be
vYYYY-MM-DD
The initial lowercase "v" is REQUIRED. The YYYY-MM-DD must match
what is in the versionIRI of the derived pato.owl (data-version in
pato.obo - open with a text editor or type: more pato.obo in the command line). Note - docker is GMT, so the date may be the next day depending on which time zone you are in.
Release title should be YYYY-MM-DD, optionally followed by a title (e.g. "january release")
Then click "publish release"
IMPORTANT: NO MORE THAN ONE RELEASE PER DAY.
The PURLs are already configured to pull from github. This means that BOTH ontology purls and versioned ontology purls will resolve to the correct ontologies. Try it!
- http://purl.obolibrary.org/obo/pato.owl <-- current ontology PURL
Publish the release in GitHub. Then check the file using the link below.
- http://purl.obolibrary.org/obo/pato/releases/YYYY-MM-DD/pato.owl <-- change to the release you just made
For questions on this contact Chris Mungall or email Nicole Vasilevsky at vasilevs @ ohsu.edu
Check the build status here:
This replaces Jenkins for this ontology
See: http://wiki.geneontology.org/index.php/Curator_Guide:_General_Conventions