POC Conf. Call 1-25-11

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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

  • Release #14 was up on the live browser on Jan 21, 2011. (Note new numbering scheme)

Final version was released as the merged file: 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 (see below).

-See Jan 2011_Release_Page and Summary_of_Changes_to_PO_Jan2011 for details of what was changed in this release.

For future releases, JE could perhaps 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.


  • Update on Annotations:

-see the New_terms_and_obsolete_terms_for_Jan2011_release for list of terms that had annotations we had to deal with.

TAIR: LC, JE and RW have been working with Tanya and Donghui on getting the changes made.

  • In order to update their annotation files, TAIR requested the 'final version', which we gave them: the release-ready plant_ontology.obo file version #1005 (1-12-11).

-Unfortunately, they had set up an automatic pipeline for updating the ontology files at TAIR which pulls data from the files on the SVN: po_anatomy.obo and po_temporal.obo files.

-So RW generated the separate files ( po_anatomy.obo and po_temporal.obo), through OBO Edit (#1012, 1-12-11). (Looks like we should maintain those, as least for the near future. TB said they will change their end, but it will take some time. Should not be too hard, as we will just have to do this after each release.)

- LC will follow up with TAIR as the annotation files on the svn appear to be missing the updated terms, and the PO on their website has not been updated either.


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 (stayed) on root hair cell (PO:0000256).


Gramene: No response from anyone at Gramene, LC fixed 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 fixed the annotations affected by: pollen tube (PO:0006345) and root hair (PO:0000256)

  • Discussion about 'has_part' relation: Justin Elser

New icon (orange square with black Hp) has been added, but we were not able to load those on the browser

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

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 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 dePamphilis is interested in working with the PO to add new terms to describe basal angiosperms.
  • Celia Arighi from the Protein Ontology would like to supply protein terms for describing PO cell types (similar to what CO does), if we need them.
  • Other items?

Bioportal- discussion with Trish Whetzel and she demonstrated the "notes" tool, which has many useful features. It might be worthwhile looking at it as an alternative to using Sourceforge.

  • We need to figure out a means to make it easy for other groups using the PO to keep up to date with our new versions: Need a stable URL to the most current version

Talked with Trish about this as their version is out of date- LC is working with them to get the admin rights to our metadata page on their site. Also and issue with Gramene, MaizeGDB, SSWAP, Virtual plant, TAIR

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.


In additions to the specific activities of the PO, we saw several talks where people said they were using or plan to use the PO for creating annotations.

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:

High priority items:

  • Plant Growth and development Stage Ontology restructuring

1. overall structure:

In the fall LC, RW and BS worked on restructuring PGDSO to meet BFO standards. Have a proposal to show group. For next meeting- 02/01/11??

2. Framework for non-angiosperm terms

As we work on a new overall structure, need to be sure it provides a framework for non-angiosperm terms

  • Compliance with OBO foundry guidelines

- All but 3 terms now have is_a parents. The last three will be dealt with when we restructure the PGDSO

- Restructuring of PGDSO should make PO compliant with BFO.

-need to double check that all terms have text definitions

  • User requests

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

  • New terms for non-angiosperm structures

- Ramona has a long list of new terms to add, but we need to choose an area for focus

- Begin with terms for mosses, requested by Physco group. If we can get their terms in by the next release, they will use PO instead of creating their own ontology.

-Also need to focus on: reproductive structures across plants, terms used by model systems (Physcomitrella, Selaginella, Loblolly pine, etc.), and terms are needed for the EST library from the Genomics of Seed Plants project.

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

  • Online outreach/exhibit at NYBG

- See separate item below for details

Medium Priority

  • Restructuring descendants of leaf (PO:0025034)

-many of the part_of children of vascular leaf can also be part of non-vascular leaf. Need to set up proper hierarchy so we can add terms for bryophytes.

  • 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.

-Images 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

  • Removing taxon names from terms

-Most of the terms with Zea or Poaceae in their name could probably be merged with other PO terms (e.g., Zea gynoecium merge with gynoecium)

-RW spoke to Mary Schaeffer (from MaizeGDB) at PAG, and she was happy to see the taxon specific terms go

Low Priority

  • Better organization of descendants of portion of plant tissue:

Needs to be organized better, add some new categories for tissue types

  • Adding annotations

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

  • Convert existing definitions to genus-differentia form

Ongoing.

NYBG outreach activities

Jan Stevenson from NYBG took part in discussion at NYBG on 11-6-2010. She is available to help with preparing text for a public audience, or producing AV materials.

An online audio-video exhibit will cost about $6000. A double display case with audio-video in the NYBG gallery will cost at least $12000.

-Possibly use flowering time examples from rice and brassicas

Look at mirroring NYBG AV material from the Plants and Fungi Exhibit on the POC web site. DWS will confirm the copyright issues etc.

Create modified version of the tree of life from NYBG exhibit for online exhibit. Can add different images to tips to tell different stories, such as different types of fruits or flowers in angiosperms.

-DWS will provide the tree diagrams and text and images of the sequenced genome plant examples.

Publications

-TIPS: An abstract/proposal was been submitted to Trends in Plant Science on Dec 31st, 2010. Unfortunately, it was declined. Need to think about another journal that would be appropriate for a short review/update type paper. Possibly add an example of an analysis using PO terms.

-Plant Physiology: Ramona and Lol are working on an outline for a manuscript to submit to Plant Physiology. This will be a more detailed description of the changes made to the PO in the past year, including restructuring of PSO and PGDSO. Will focus on how PO is now applicable to a wider range of plant species.

-Others? Maybe a short topics paper for American Journal of Botany?

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.

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