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.

Quality Checks and Internal Review

Before each release, ontology editors and curators should run some qc checks. In fact, these should be done on 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 (see below:).

The whole POC team should take a little time to do a internal review. Look for any inconsistencies, typos, broken links etc.

Check for any lines in the existing association files that reference obsolete or alternate IDs (see below:)

Updating the Filter Annotation Objects lists on the browser:

If annotations from new database groups or species are added, we should update the "Filter Annotation Objects" list on the browser

These lists should match what is in our database; as listed on the release notes page.

LC: new in V#16: Jaiswal Lab Fragaria vesca (strawberry) (note there is a typo on the V#16: release Notes Page).

Also, new annotations for Physcomitrella (currently coming from Gramene, but it would be good to be able to filter by species).

In the next release, we will have a large set from Physcomitrella and also Vitis vinifera.

JE: I know this is handled somewhere in NameMunger.pm, but my changes don't seem to take effect. Need to figure out how to add here.

Fixng Dbxrefs

The was an issue that was discussed and worked on a lot for the version #16 release.

For more details of the discussions see the minutes from [POC_Meetings_Minutes] on: 9-27-11 through 10-18-11.

Our current version of AmiGO has a built-in set of dbxrefs, in a Perl file, and it is not reading the current GO file.In order to update these, this file has to be edited manually.

We decided on the POC_Conf._Call_9-27-11 to use the PO_DBXref.txt file on the SVN to store the updated dbxrefs stanzas. Then the dbxrefs Perl file could be modified based on that.

An older version of this file is also available through the documentation page on the PO website:

We decided to change the link on the Documentation page to go to the current file on the SVN. This change should have been implemented in the current release.

Note from LC: Do we really need to have this file PO_DBXref.txt on our website, since it is just for our internal use?

Curators names in definitions, etc

- Curators names in definitions and synonyms should be spelled out in full example: GR:Pankaj_Jaiswal and these are not links

Po-Refs Page

- Links to references that do not have a PubMed ID, ISBN number, or stable URL should go to the new PO references page

For future releases:

The IT team should run a 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)

Summary of Changes Wiki Pages

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.

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.

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

plant_ontology.obo

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 moved over to a new beta branch (see below).

plant_ontology_assert.obo
plant_ontology_assert_basic.obo
po_anatomy.obo
po_temporal.obo

LC: Note: These files should not remain in the trunk folder with the dev version of the ontology once the release is out as they are no longer in sync with the editors version of the file and this will be confusing to have them in two places.

In hindsight, I think the additional files should only be generated once the review process is completed. If an Ontology problem is found, these will have to be recreated (see below:)

Beta version

Prior to the release, the ontology files will be copied/moved over to a new beta branch of the svn:

plant_ontology.obo (copied)

these should be moved to beta:

plant_ontology_assert.obo
plant_ontology_assert_basic.obo
po_anatomy.obo
po_temporal.obo

LC: Perhaps these should be named something like: plant_ontology_beta16.obo to differentiate them from the editor's version (plant_ontology.obo on dev).

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.

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

If a problem is found that needs to be fixed for the release:

In the event that a problem is found in the ontology file beta version prior to the release, the fix should be made in the DEV version and the process of generating the additional files and copying over to the new beta branch should be repeated anew. This ensures that the fixes are not lost from the editor's version in the process of the release. This is why it is important for the editors to do a thorough review and run QC checks prior to copying to beta.

Tbl version 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 in the SVN trunk folder 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>

LC: Should this correspond to the Ontology file version (ie: #16) or the version of the OWL software?

It currently says "<?xml version="1.0"?> We should have info here about which Ontology version it is as well.

OWL files available on trunk:

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

Only the plant_ontology.owl file is moved over to the live tag.

Preparing the Association files for the Release

~~Issues during version #16 with JE's script that splits the big files for loading- is this fixed for next time?~~ Fixed for release #16.

Check for any lines in the existing association files that reference obsolete or alternate IDs. Inform the collaborating group about what needs to be fixed and and fix those ourselves if necessary.

Any problems found in the association files should be fixed in the files in the trunk folder and the copied over to beta, replacing the existing file with the problems.

This accomplishes two things: it maintains the version history on trunk and makes sure the fixes are not lost.

Note: As number of annotations and the size of the association files increases, this process will take longer. The version #16 required 46 hours to load.

External Reviews

Once we have completed the editing, the Ontology should be open for review on the Beta browser. This may occur with or without the full set of annotations. Depending on what we want to test. (see below for more details on Beta)

Inviting Specific External Reviewers

For some releases, we may ask specific experts and or collaborators to take part in an External Review. This was done in Aug 2010 for the October 2010 release. The external experts will need at least a couple of weeks and up to one month.

To facilitate the review, the POC may need to make a presentation to them, such as the [Plant_Ontology_Webinar-_May_2011_release] PO-Physcomitrella presentation, to feature the new terms for non-vascular plants, in particular, Physcomitrella patens.

Add more details here of the external review process...

Beta Release Announcement

An announcement should be sent out on the mailing lists something like this:

"A beta version of the latest release of the PO is now available on our AmiGO Browser (http://beta.plantontology.org/amigo/go.cgi). Along with the Ontology itself the beta browser also is loaded with some test annotation files (not the full set of files at this point).

You can download the ontology files in OBO-Edit format from: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/branches/beta/ontology/OBO_format/

There is a readme.txt file on the same page explaining what the is different among the files available.

Further information on the upcoming release can be obtained from: Links to Release Pages: "Summary of Changes" and "New and Obsoleted Terms"

Please review the Plant Ontology and let us know asap about any important issues you observe."

Loading the Live Version

Once the review and internal checks and fixes are completed, the plant_ontology_assert.obofile and the whole database of annotations are loaded from the beta branch onto the beta browser.

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

Once the release is live on the Plant Ontology page, the ontology files should be copied from the beta branch to Live Tag.

This is a stable url that will not change, so it can be incorporated into users scripts etc.

In the October 2011 release, we introduced Japanese translations of the term names. Currently, JE is stripping out the Japanese synonyms before he loads the live version onto AmiGO. We had discussed whether or not to remove them from the live release and provide a separate file which included the translated terms, but that was rejected (meeting date: fill in date...). We have had complaints from some of our user groups (eg. Gramene) that their browsers cannot display the Japanese characters . We should reconsider this approach.

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??

Updating the Plant Ontology files on other sites:

The two main sites where people go to download the PO are:

Bioportal: Bioportal

OBO Foundry: OBO Foundry

Also featured at:

Gramene: Gramene

MaizeGDB: MaizeGDB

SGN: Solanaceae Genome network (SGN)

TAIR:

See this page for links to other sites that feature the PO: Links_to_sites_using_the_PO

PO Release SOP Page

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