POC Conf. Call 1-25-11

POC meeting, Webex Conference Call; Date: Tuesday Jan 25th, 2011 10am (PST)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC Conf. Call 1-11-11?

Report on new release of the PO

Final version was released as plant_ontology.obo, but we also prepared updated versions of po_anatomy.obo and po_temporal.obo, for users that still need the separate files.

For future releases, JE could create a script to parse out the two parts and post them on the svn automatically, but we should encourage users to use merged file.

The "Download Ontologies" page needs to be updated- take off the links to the really old files?

• See Jan 2011_Release_Page and Summary_of_Changes_to_PO_Jan2011

• Update on annotations:

TAIR: We have been working with Tanya and Donghui on getting the changes made. Tanya has created the GO terms we requested. We gave them the release ready plant_ontology.obo file and they can updated their annotation files.

MaizeGDB: LC has been working with Mary Schaeffer, they are not submitting any new file at this time. Annotations on root hair (PO:0000256) can move (stay) on root hair cell (PO:0000256).

Gramene: No response from anyone at Gramene, LC will look after fixing the annotation files- Affected by: pollen tube (PO:0006345), primary root elongation zone (PO:0003003), root hair (PO:0000256) and elongation zone (PO:0020125).

SGN: No response, LC will contact Naama again; affected by: pollen tube (PO:0006345) and root hair (PO:0000256)

• Discussion about 'has_part' relation:

New icon (orange square with black Hp) has been added.

Report on PAG 2011

Laurel, Ramona, and Justin Preece attended the PAG 2011 Plant and Animal Genome XIX Conference. DWS and PJ attended for the weekend.

Presentations

• Ramona gave a computer demonstration "Recent advances at the Plant Ontology: Tools for linking plant anatomy and development to genomics across plant taxa (see Outline for PAG2011 Computer Demo and Computer Demonstrations Schedule) on Saturday early Afternoon, January 15, 2011

• Laurel presented "The Plant Ontology: Linking phenotypes and genomics across plant taxa" at the Plant Phenotypes workshop panel discussion on Sunday Morning, 16 January 2011

• Laurel and Ramona presented a poster (PO Poster) on Monday from 3:00 pm - 4:30 pm, and throughout the meeting.

Collaborators workshop

The PAG_2011_Collaborators_Workshop and meeting with collaborators on Sunday was a great success!

The workshop's wiki page has links to all of the presentations. The diversity of projects presented gives some indication of the widespread applications of the PO, and the non-presenting participants represent an even wider user base. We had one-on-one discussions with many of the attendees.

• Mary Schaeffer and Maize GDB will be using PO terms to annotate a new, large expression data set.

• Stephan Rensing said that the Physco group would like to use PO terms for annotations, rather than continuing to develop their own ontology, as long as we can get the new terms added quickly.

• Claude DePamphalis is interested in working with the PO to add new terms to describe basal angiosperms.

• Other items?

Outreach Booth

• The PO participated in an Outreach booth organized by MaizeGBD (Booth number 427). The space was shared with: MaizeGDB, GrainGenes, Gramene, SGN, Oryzabase, NIAS Rice Databases, SCRI, PMN/TAIR, SoyBase, PLEXdb, SoyKB, CottonDB, LIS, PlantGDB

This was a great opportunity to network with other plant database people.

Adding foreign language synonyms to the PO

At the collaborators workshop, Stephan Rensing said he could supply German synonyms for PO terms. At the outreach booth, Y. Y. (need name) of Oryzabase said she could supply Japanese synonyms. She was very excited about this and felt it would be very helpful for getting other people in Japan to use the PO. We would need to work out the technical details of how to get include Japanese characters in the obo file, or create a bridge file.

Priorities for the Next Round of Revisions

Target date for the next release

Next release should come out in mid-March. (Before spring break!)

Will coincide with manuscript for Plant Physiology.

Defining Goals and Priorities for the next round of revisions:

• Deal with and complete the list of user requests on SourceForge (see [1]). High priority

• Plant Growth and development Stage Ontology restructuring should be a focus -- to add terms from non-angiosperms

-In the fall LC, RW and BS worked on restructuring PGDSO to meet BFO standards. Have a proposal to show group. For next meeting- 1/25/11?? High priority

-Once overall structure is decided upon, need to create a better framework for non-angiosperm terms

• Better organization of descendants of portion of plant tissue: Needs to be organized better, add some new categories for tissue types

• add terms for non-angiosperm structures- need to select areas of focus and create list

-From 10-6-10 minutes: Ramona will work on list. Should focus on reproductive structures, terms used by model systems such as Phsyco, Selaginella, Loblolly pine, etc., plus whatever terms are needed for the EST library from the Genomics of Seed Plants project.

Establish 'working groups' to add lower level terms? For example: RW and DWS (and MAG?) could add the Phsyco terms using the NYBG numberspace.

-Work with Physco group to add terms for mosses

• Adding links to images through PlantSystematics.org-

Ramona visited with Ale in October 20th, 2010 to work on this and we discussed it at the November, 2010 POC meeting at NYBG.

Note: tepal is only term linked right now (no longer working?). Should be linked to the PO ids - have PO ids embedded in the Plantsystematics.org database.

MAG has a lot of the images ready and so these can be part of the next release. Need to get our 'prototype page' up

• Laurel and Ramona will focus more on adding annotations-

LC set up a call with RW and PJ to discuss. 1-2 days per week. EST libraries, RNA seq datasets.

• Complete compliance with OBO foundry principles-

Once the release is out, Laurel will ask BS what stage we are in the acceptance process. is_a completeness is a priority for this.

• Convert existing definitions to genus-differentia form? Ongoing...

Upcoming meetings 2011:

• Phenotype Ontology RCN Summit

The Phenotype Ontology RCN

February 25-27, 2010 at the National Evolutionary Synthesis Center in Durham, NC,

Laurel and Pankaj will be attending.

From RW: -What is official PO strategy for dealing with phenotypes?

-Should it differ between description of mutant phenotypes and descriptions needed for systematic studies?

-Should PO develop a list of terms to be submitted to PATO (rather than our current piecemeal suggestions)?

-Possible case study: description of inflorescence types.

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Dennis and Alejandra are planning to attend IBC2011 and speak in other symposia.

Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the genetics, genomics and bioinformatics theme.

Pankaj will give the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona will present the talk on the Plant Ontology. Abstracts have been submitted.

No additional abstracts were submitted for our proposal, and Angelica does not think she will be able to attend because of lack of funds.

Dennis will speak in place of Angelica. PJ invited two other speakers. Gavin Kennedy will talk about the ontology application in large scale phenomics projects. Rudi Appels will speak on crop genomics and phenomics. Ramona has contacted these speakers to get their information and abstract; waiting for responses from them.

We received permission to use the 6th time slot for a discussion session. PJ will lead the discussion.