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. I

• 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

• Look for any lines in the association files that reference obsolete or alternate IDs.

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)

"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 Upcoming 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.

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/.

Announcements

• Prepare and post announcements for the PO front page, Jaiswal Lab Page
• Send out announcements to the mailing lists