POC Conf. Call 3-27-12

POC meeting, Webex Conference Call; Date: Tuesday Mar 27th, 2012 10am PST/1pm EST

In attendance:

POC members:Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Preece (OSU), Marie Alejandra Gandolfo (Cornell), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG), Justin Elser (OSU), Barry Smith (University at Buffalo, NY), Justin Elser (OSU).

Absent: Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: none

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=63521917&rKey=a80d503d0f16bf27

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=63521917&rKey=6ad2a5e167b16679

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_3-20-12?

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Upcoming PO Release:

Apache update:

JE has transferred all the html content on the web pages to the new Apache version and all seem to go smoothly.

There may be a few remaining link to :8080 addresses will have to be fixed. There were only about 30, and most of them seem to be links to wiki.plantontology.org.

Please let JE know if you find anything that is not working correctly so that he can fix it.

e.g., link to relations page from icons box on browser

People will need to update their bookmarks as well, if you have not already done so

Timeline:

• Target date for finishing edits: end of the day Thursday March 22st

Most of the needed edits were completed on schedule.

We will review any additional loose ends and get them completed by the end of the day today.

• Target date for release: Before March 30th

• Beta is currently being loaded with the full annotation database and the plant_ontology.obo dev file.

• The new Physcomitrella and Cotton datasets were moved out of the test folders yesterday and are part of the load today.

• LC went through the annotation files and made one change- there was only 1 annotation on xylem element (PO:0000273) and I changed it to tracheary element (PO:0000290). Will ask TAIR to hold auto submission till we know if there are any further errors.

Goals and Priorities:

For more details see: New terms and obsolete terms-March 2012 Release

PO_Release_SOP_Page

After the release in October 2011, LC put together this page to help facilitate the releases

Everyone should review this list and let me know if there are things that need to be added, modified etc.

JE will make a corresponding document to outline the steps that is needed to be done from his end.

Revisions of PSDS (formerly PGDSO):

Status to 3-19-12

• ~34 new terms added
• many existing terms have been modified, eg changed all the 'phase' names to 'stage'
• all PSDS term names are now singular. Some still need to have "stage" appended
• focus has been on the whole plant development stage (PO:0007033) and its children
• Addition of Wood development stages: (See: SF tracker), started at the NYBG Workshop

New and Revised Terms for the PAE

• ~125 new terms for this release
• Addition of new terms and revisions to existing terms to encompass wood- see Goal_1._Anatomical_Entities
• Please see New terms and obsolete terms-March 2012 Release for a complete list
• Complete old user requests/SF tracker items: This is an ongoing process

New association files:

• Physcomitrella (released Jan 2012) -move out of "test folder"

• Small set of cotton annotations- -move out of "test folder"

• Updated annotations from SGN received

• RW will create an association file for the spruce tree genes that are referenced in the papers. This could be in a non-model plant association file.

RW: In order to make this file, we will need to create a database (DB, column 1) and database number (DB_Object_ID, column 2). For DB, we could use something like PO_gene, PO_qtl, etc., and create numbers for DB_Object_ID.

Will create short annotation file with only the 2 or 3 genes mentioned in the IAWA paper. Can add other annotations later.

Use Jaiswal_lab for DB for now. May be able to use genbank or uniprot id for DB object ID.

Glossary of PO Anatomy terms

See PO Glossary on dev

• Currently links to the dev version of the ontology database, but on the live site it should read from the live version.

Translations

Status report:

• Ale has completed the new Spanish translations. RW is updating the table file so JE can use it to insert the translations into the obo file.

• Yukiko will try to do the Japanese translations this week, but may not be able to in time. If necessary, we can add them in the next release. She will be at the BioCuration meeting next week.

icons for new relations

• New icon has been added for the has_participant relation so it can be included in the upcoming release.
• icons need to be stored in the folder on the SVN:

Need to add link "Defintions" to relations page from icons table on live browser.

On the wikipage: Relations in the Plant Ontology, add link to SVN folder for icons.

Add Link to SVN folder at the top of the page, and embed images, linked to external files, next to each relation.

Should share the icons with OBO Foundry, so they can be used consistently across ontologies. How will this be done?

Remaining Ontology Things to be fixed

test image links to Plantsystematics.org

Image_at_PlantSystematics:1597 to septum (PO:0000030) and fruit septum (PO:0025268)

See http://www.plantsystematics.org/imagebyid_1597.html

Image_at_PlantSystematics:14891 and Image_at_PlantSystematics:8662 to pappus (PO:0025393) and pappus element (PO:0025394)

See http://www.plantsystematics.org/imagebyid_14891.html and http://www.plantsystematics.org/imagebyid_8662.html

Change link to say "PlantSystematics_image_archive".

DS has good images for staminodes on PlantSystematics.org.

BS pointed out that this could be a little misleading, because people might not assume that a plant systematic database will have images of plant parts. We will test it out and see how this works, because it is easy to change the name of the link. The database was set up for organismic botanists.

We still need an automated way to link between their database and ours.

reaction wood

The following terms have been added to the ontology:

reaction wood (PO:0025472): A portion of secondary xylem (PO:0005848) found on either the upper or lower side of a shoot axis (PO:0025029) that is leaning or crooked, with anatomical characteristics that depend on whether it is compression wood (PO:0025473) or tension wood (PO:0025474).

Comment: Functions in restoring a leaning stem (PO:0009047) or branch (PO:0025073) to its original position. May be either compression wood, found on the lower side of a gymnosperm shoot axis or tension wood, found on the upper side of an angiosperm shoot axis.

compression wood (PO:0025473): A portion of reaction wood (PO:0025472) found on the lower side of a shoot axis (PO:0025029) that is leaning or crooked and has as parts heavily lignified tracheids (PO:0000301) that are rounded in transverse section and bear spiral cell wall checks.

Comment: Functions in restoring a leaning stem (PO:0009047) or branch (PO:0025073) to its original position. Found in gymnosperms.

tension wood (PO:0025474): A portion of reaction wood (PO:0025472) found on the upper side of a shoot axis (PO:0025029) that is leaning or crooked and has as parts gelatinous fiber cells (PO:0025422).

Comment: Secondary xylem tracheary elements (PO:0025445) in tension wood are often longer than the tracheary elements in non-tension wood of the same plant. Functions in restoring a leaning stem (PO:0009047) or branch (PO:0025073) to its original position. Found in angiosperms.

References: IAWA Mulitlingual Glossary (PO_REF:00012), Carlquist 2010 (ISBN:3540411739)

Need to add comment to all of these that these tissue develop as a response to gravity (tension or compression). Will post new comment on SF.

Upcoming meetings and Presentations 2012:

5th International Biocuration Conference

April 2-4, 2012, Washington DC

• Abstract was submitted and has been selected for a poster presentation.

See link: File:Abs Biocuration 2012 (LC 12-9-11).pdf

• LC is attending and is taking part in the BioCreative workshop

Semantics of Biodiversity Workshop

From Barry:

May (16 optional) 17 - 18, 2012

University of Kansas Biodiversity Institute

Lawrence, Kansas

link

PJ suggested that someone from USDA germplasm management group should attend. BS will send PJ the email of the organizer. PJ can work with organizers to extend invitations to the appropriate people.

SPNHC 2012

Annual meeting of the Society for the Preservation of Natural History Collections

Yale University, New Haven Connecticut June 11-16, 2012

Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).

The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).

From PJ: If we can show progress in the FNA work or Morphobank yes we should

Crop Ontology Workshop

For more information see the wiki page: Crop_Ontology_Workshop_at_OSU,_2012

We are looking at the tentative dates of either: June 11-13th or Aug 6th to 8th

The focus of the workshop will be on mostly development stages and traits for the crop plants

Ruth Bastow is contacting some of the interested people to see which of these dates work best.

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

• PO workshop for Sunday, July 8th, 9:00AM - 12:00PM

link to Wiki page: Plant Ontology Workshop, Botany 2012

see: Botany 2012 workshops

The meeting web site has been fixed so this is now listed as a half-day (morning) workshop. The schedule now links to the correct abstract.

RW will prepare an announcement for the PO home page and FB page.

Workshop goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.

PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrices.

exhibitor's booth

We should also consider hosting an outreach booth.

Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)

• 2 months of Rotating Banner Ads in the online American Journal of Botany

• A Rotating Banner Ad in one edition of the online Plant Science Bulletin

• A Rotating Banner Ad on the Botany 2012 abstract submission site

• A Rotating Banner Ad on the 2012 Conference Registration site.

PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.

• Annotation wiki: JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.

Bio-Ontologies SIG 2012

Where: July 13 - 14, 2012, Long Beach, CA. Co-located with ISMB 2012

When: Submissions Due: April 13th, 2012 (Fri)

See: Bio-Ontologies SIG 2012

Three types of submissions.

- Short papers, up to 4 pages. - Poster abstracts, up to 1 page. - Flash updates, up to 1 page

Successful papers will be presented at the Bio-Ontologies SIG.

Poster abstracts: time will be allocated during the 2 days for at least one poster session.

Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.

ASPB Plant Biology 2012

July 20 - 24, 2012 - Plant Biology 2012, Austin, TX

Link to meeting page: ASPB2012

Abstract was submitted for submission for minisymposia consideration.

Joint workshop is planned with PO, Gramene and TAIR

Registration is open, early Bird Registration: by May 11

Advance Discounted: May 12-June 15

ICBO 2012

International Conference on Biomedical Ontologies (ICBO 2012), July 22nd-25th, Graz, Austria

co-located with the 7th International Conference on Formal Ontologies in Information Systems (FOIS 2012)

RW and BS (with JE, AG, DWS and PJ) submitted a short paper describing a plant disease extension of the Infectious Disease Ontology. This paper was accepted and is being revised. Wiki page for notes on Plant Disease Ontology.

Relevant dates

• Feb. 28th, 2012: Notification of paper acceptance
• April 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
• May 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance
• June 30th 2012: Deadline for all camera-ready copies for the proceedings

RW is working on an abstract summarizing the PO-FNA collaboration, with the folks from FNA. Will circulate soon. This will be either for a poster or a short talk in the Early Career Researcher session.

BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts