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:

Dev version

Between releases, editing is done on the developers version of the plant_ontology.obo file located at: OBO Format.

This is the "dev" version and is loaded onto the Dev Browser nightly, along with the SVN version #. No annotations are loaded on this browser.

Once the editing and quality checks are completed for the release, the following additional versions of the Plant Ontology file are prepared prior to the release and copied over to a new beta branch:

At this time, editing may continue on the dev file, without disrupting the version on the beta browser (see below)

LC: Perhaps these should be named something like: plant_ontology_beta.obo to differentiate them from the editor's version (dev).

• 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

Tbl files:

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

• plant_ontology.tbl (currently named: po_all.tbl)
• po_anatomy.tbl
• po_temporal.tbl

These will contain the PO:id, term name, the definition, any synonyms and the aspect (in po_all.tbl)

Note: These files also include the obsoleted terms. This is indicated in the definition field of those terms.

These files are be located at TBL files on SVN trunk

The link from the PO download page goes to Live tag.

Note: Only the PO_all.tbl file is available at the Live tag.

LC: It would also be good to have a column listing the alt_ids. I also feel that it is confusing to have these located in two different locations- this is a problem if changes are made in the file on live which are not reflected in the trunk version.

OWL version

We also create OWL versions of the files for each release, which are located at: OWL_Format.

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

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

OWL files available:

• plant_ontology.owl (This corresponds to plant_ontology.obo from the live tag)
• po_anatomy.tbl
• po_temporal.tbl

These file were also moved over to

Beta version

Prior to the release, the ontology files will be copied over to the "beta" branch of the svn:

Link to beta branch

This is a temporary location for the curators and reviewers to look over the new version of the ontology for the planned release. This file is loaded onto the Beta Browser along with any annotation files that are being tested.

• We should also put the revised PO front page on the Beta Site for review, prior to publishing.

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.

"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??