POC Conf. Call 1-29-13

POC meeting, Webex Conference Call; Date: Tuesday Jan 29th, 2013 10am PST/1pm EST

In attendance: Laurel Cooper (OSU), Barry Smith (University at Buffalo, NY), Justin Preece (OSU), Pankaj Jaiswal (OSU)

Absent: Justin Elser (OSU), Dennis W Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell)

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=71812867&rKey=899b35bc355f9bcb

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=71812867&rKey=8974dc4bb6e2c35d

Updates

- Release #19 is out Dec 31st, 2012- Release_19

Highlights: Addition of 35 new terms, for both the Plant Anatomical Entity (20) and Plant Structure Development Stage (15) branches. It also includes new and updated annotation data for Oryza sativa, Vitis vinifera, Gossypium hirsutum and Arabidopsis thaliana.

This release also includes a new feature: Japanese translations displayed on the browser as synonyms for the Plant Anatomical Entity terms.

- Status of new hire at NYBG? DWS has posted an ad on the BSA site and the NYBG site and has not had very many responses from interested candidates. He will send it to LC and we will send it out on PO-announce and circulate it. It could also be posted on the ASPB site.

-Update from NYBG: Images analysis project: DWS has a bunch of images with different leaf venation patterns, the example would go from GO terms to images. Across monocots, margin characters, could do an in situ

- DWS will send some sample images to JP, will test them to see if they can be recognized. Can they label with terms from other ontologies, such as GO.

- Need high contrast images, leaf margin images, serrated vs regular

- Active learning component is more complex, but could be a good use case

- Images on PlantSytematics.org- PJ is working on a format for what info needs to be filled in- making a template and will send it to DWS

- Put PO:IDs in as well as the term name in the labels on the images

- Priorities for PO terms to be labeled in images:

PJ: Anything related to model plant species (ie: ones we host data for already?). Also, brassicaceae, grape, eucalyptus (have terms for calyptra etc), grass flower structures- spikes, panicles, different inflorescences; Physcomitrella (DWS will ask Stefan Rensing for access to pictures).

- Need to have a sample database in place when we prepare the new proposal- mid march

PJ: we can spend about a week and get a few reference images annotated

- Publications - met with RW in PAG about PSDS paper, pj said she is having difficulties doing the homology searches

cROP proposal and ERA-CAPS

• LC has been talking with EA and RB: Meeting planned for Thurs Jan 31, 2013- webex call has been sent out

• ERA-CAPS planning meeting Jan 24th in Paris- see notes on cROP Vision and ERA-CAPS proposal

"We need to get a half page description from you/Pankaj on what the US project will do as we need this to submit our grant. We also need to write a section on how the grants will interact and I can’t do that with out knowing what you guys will do.

So if at all possible do you think you/Pankaj might be able to get us something by the end of the week as you know the deadline is the 15th and I am starting to worry. Ruth"

See notes on cROP-OSU Proposal Plan

New terms added during last release: PSDS Terms

Tabled for next meeting... Check the Items_for_future_meetings

Meeting Report

PAG 2013, San Diego, CA; January 12th - 16th, 2013

We hosted a workshop focusing on:

Applications of Ontologies for Plant and Animal Genomics

• Date and Time: Saturday, January 12, 2013: 08:00 AM - 10:10 AM, Royal Palm Salon 5-6

Speakers: Eva Huala, Reinhard Simon, Elizabeth Arnaud, Chris Mungall, and Pankal presented the cROP Vision

posters: LC presented a poster #P0936 "Development of the Reference Plant Trait Ontology: A Unified Resource for Plant Phenomics".

JP presented an AISO Computer Demo: Date and Time: Sunday, January 13, 2013; 5:20 PM, California room

Update on planning for cROP proposal

EU consortium is moving ahead with the ERA-CAPs proposal- they will had a meeting last week in Paris to proceed with writing

See notes on gdocs

Schema: see 1-28-13 ppt

From EA: "As our project (ie:GCP) cannot be a BREAD idea and EAGER project, Diana suggested that The GCP/Bioversity entry point in the proposal can be through SAVI, Science Across Virtual Institutes, showing that the product we are all aiming at will be the glue between the centers. Particularly if our product is web based. We can also be partners in the PGRP proposal."

Components of cROP

Plant Ontology

Central reference for all the others

Reference Trait Ontology

• Ref-TO should be hosted and coordinated at OSU, but should solicit input on it from the EU partners- responsibility for various aspects

Plant Disease Ontology-PDO

- involvement of pathologist at OSU?

Environment Ontology

Group at Jurlich is interested in taking responsibility for it-

Upcoming meetings and Presentations 2013:

Phenotype Ontology RCN Annual Summit Meeting, Feb. 25th - 27th, 2013, Durham, NC

Phenotype Ontology RCN

The workshop and meeting will be held at the National Evolutionary Synthesis Center in Durham, NC, from Monday morning, February 25 through Wednesday noon, February 27th (you would arrive Sunday evening).

Overall goals: To introduce and establish communication and collaboration among scientists from different research backgrounds. The two primary themes: The use of text mining phenotypes and representing behavior in ontologies.

For more information: please contact Paula Mabee (pmabee@usd.edu)

Biocuration 2013 conference, Cambridge, 7-10th April 2013

submission deadline for abstracts for posters is Jan 31st.

website and registration are now open: Biocuration 2013

PRO-PO-GO meeting, May 15-16th 2013

Please see this page for more information: PRO-PO-GO_Meeting

Location: Buffalo, NY

Dates: May 15-16th, 2013.

Goals:

1. To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination
2. To identify potentially fruitful applications which such enhanced coordination might bring
3. To enhance the Protein Ontology treatment of plant-related proteins
4. To address coordination issues between the GO and PO, for example as concerns treatment of development stages
5. To further those aspects of CROP which relate to PRO and GO [this is assuming that PRO is included as one of the external ontologies in CROP]

Tentative participant list:

PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others?

GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?

PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)

BS would like a list of who we would like to include in the meeting and whose costs can be covered by PO

10th Extended Semantic Web Conference (ESWC) Montpellier, 26-30 May 2013

Extended Semantic Web Conference Montpellier

Location: Montpellier, 26-30 May 2013.

Agropolis Montpellier, the University of Montpellier and Bioversity are collaborating to organize a one-day workshop entitled 'Agrobiodiversity semantics' as part of the larger conference.

Paraphrased from email exchange with EA (Bioversity):

workshop proposal

"We are finalizing a workshop proposal to be submitted in the 23rd to the conference organizing committee. In parallel, we are developing a proposal for raising some support funds.

Ontologies will be part of the workshop discussion. The latest development sent by Justin on AISO also raised interest of the organizing committee. So, we would you like that the Plant Ontology team be represented in the scientific committee of our workshop.

This is a very first draft of course but will provide you with the context, scientific objectives, and expected outputs. Would you accept in principle (if the workshop is accepted and funds raised) to join our committee and submit a a paper for a presentation and/or poster? Deadline will be March and April.

MONOCOTS V Meeting at NYBG, July 5th - 14th, 2013

MONOCOTS V:

5th International Conference on Comparative Biology of Monocotyledons Friday, July 05, 2013 7:00 AM - Sunday, July 14, 2013 12:00 PM (Eastern Time)

The New York Botanical Garden & Fordham University