PO Release SOP Page

This page is a place to list all the steps we need to take for the database releases.

This page is under development:

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:

Once the editing and quality checks are completed, the following versions of the Plant Ontology file are prepared prior to the release:

These files are kept at: OBO Format

• plant_ontology.obo
• plant_ontology_assert.obo
• plant_ontology_assert_basic.obo
• po_anatomy.obo
• po_temporal.obo

see: Readme file for description of each

We will also prepare simple tab-delimited files corresponding to the ontology files:

• plant_ontology.tbl
• po_anatomy.tbl
• po_temporal.tbl

These should contain the PO:id, term name, the definition,any synonyms and the aspect. These files should be located at TBL files on SVN and linked from the PO download page

Note: These files also include the obsoletes. This is indicated in the definition line.

Can we also have this file include definitions? (RW)

Note: currently this links to live tag

Beta version

Prior to the release, these files will be copied (moved?) over to the "beta" branch of the svn:

Add a link here once this has been done:

http://palea.cgrb.oregonstate.edu/viewsvn/Poc/branches/beta/

Live Version

When the files are ready for live release, they are transferred to Live Tag. This is a stable url that will not change, so it can be incorporated into users scripts etc.

Note that it is the "plant_ontology_assert.obo " file that should be loaded onto AmiGO browser on the live site.

OWL version

We also create an OWL version (plant_ontology.owl) for each release, located at: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OWL_format/. This will correspond to plant_ontology.obo.

The owl file should have a version stamp added to the header, updated with each release:

<owl:versionInfo> xml:lang="en" version ##</owl:versionInfo>

"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.

Changes to the HTML Files for the PO web page:

• Update PO front page and post release announcements
• Prepare "Release notes" page
• Update the "Filter Annotation Objects Counts" for new species, data types in release

This good time to incorporate any changes or fixes to the web pages:

List needed fixes here:

• update any "Upcoming Events", move older event to the archive page

• Documentation page: replace link to old dbxrefs file with a link to the current one on the svn.

Announcements

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

other places??