PO Release SOP Page
This page is a place to list all the steps we need to take for the database releases.
Let's not reinvent the wheel every 4 months.
Ontology quality control
Checks done by ontology editors
Before each release, ontology editors should run some qc checks. In fact, these should be done one a regular basis in between releases, but it is crucial to do them immediately before a release.
- Run the reasoner to remove any redundant links.
- Do a search for extra space and odd characters in terms, definitions, and dbxrefs.
Checks done by the IT team
- Get any broken dbxrefs working and fixed
- Check for any lines in the existing association files that reference obsolete or alternate IDs.
- Run script to check for needed column 16 annotations; see list at PO Suggestions for Col 16 and more info at: PO Annotation Extensions (column 16)
Internal and external reviews
Once we have completed the editing, the Ontology should be open for review- could use Dev browser (no annotations) or Beta (with annotations)
Preparing ontology files for release
Four versions of the Plant Ontology file are prepared for each live release:
- plant_ontology.obo,
- plant_ontology.owl, plant_ontology_assert.obo, and plant_ontology_assert_basic.obo (see readme file for description of each).
These files should b prepared immediately before each release, after all edits and quality checks are finished. Different working versions of these files are kept at http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/ and http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OWL_format/.
When the files are ready for live release, they are transferred to http://palea.cgrb.oregonstate.edu/viewsvn/Poc/tags/live/.
"Summary of Changes" page
- During the time between the releases, while we are editing the ontology, we will create a page (or pages) to keep track of the changes being made
For example: see October_2011_Release_Page this has links to the "Summary of Changes" page, e.g.: Summary of Changes to PO October 2011
- On this page there should be a list (or a link to a page) of any new terms and terms that have been obsoleted see: New_terms_and_obsolete_terms_for_October 2011_release
- Also should list terms that have been merged, changed definitions, or renamed.
- If possible, it is also good to list new synonyms for existing terms, especially if those synonyms are quite different from the original name. For example, we would want to highlight the cone is a synonym of strobilus, but it is not that important to note that portion of epidermal tissue is a synonym for epidermis.
Announcements
- Prepare and post announcements for the PO front page, Jaiswal Lab Page
- Send out announcements to the mailing lists
