POC Conf. Call 1-25-11

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

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Elser (OSU), Maire Alejandra Gandolfo; (Cornell University), Barry Smith (University at Buffalo, NY).

Absent: Pankaj Jaiswal (OSU), Justin Preece (OSU), Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: none

Acceptance of the minutes from the POC Conf. Call 1-11-11? There were no additions, deletions or changes to the minutes of the last meeting.

Report on new release of the PO

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

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

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).

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.

RW said it is not that hard to create the separate files in OboEdit using a filtered save. JE said that if we are only going to create them whenever we have a new release, it may not be worth the effort of writing a perl script. We will probably continue to use a filtered save to create the separate ontology files. Will still work toward getting users to use merged file.

Note from LC: It would be handy if in the header of the separate files we could indicate the namespace, as both of them say default namespace: plant_ontology.

• 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 (stay) on root hair cell (PO:0000256).

Gramene: No response from anyone at Gramene, so 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, so 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?

JE said that whenever he tries to load the ontologies with the has_part relations in, the loading script hangs up or crashes, so he wrote a script to remove the has_part relations from the version that is visible on the Amigo browser. Needs to talk to Chris Mungal to find out if installing the new version of Amigo will solve this problem. Users can still see has_part relations if they download the ontology and view in OboEdit or other software.

We should a note in the icon legend box (or a link to a note) explaining that the has_part relations are not visible in the online version of the ontology.

• 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 (more on this below)

-suggestions were a separate folder on the SVN called "live" or calling our 'dev' version plant_ontology_test.obo (but we have been discouraged from doing this)

-JE suggested having a 'tagged version' (details?). We should discuss this further in a separate "technical issues" meeting. JE created the following link : http://palea.cgrb.oregonstate.edu/viewsvn/Poc/tags/live/plant_ontology.obo?view=co This file will always be the current one used on the live site.

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 dePamphilis is interested in working with the PO to add new terms to describe basal angiosperms.

• Nick Provart and his group are interested in using the PO terms to make comparisons of gene expression between homologous structures across plant taxa.

• Celcia Arighi (Protein Ontology) would like to supply protein terms for describing PO cell types (similar to what CO does), if we need them.

• Ken McNally and the group at IRRI are sequencing a large number of rice lines and developing a developing a centralized database (“eRice”, Chiangzhi Liang, IRRI) for data capture of Pedigrees, germplasm stocks, phenotype studies, SNP data with plans to link to external genome annotation DBs and make full use of PO, EO, MO, TO, GO, Crop Ontology (GCP).

• 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.

LC has contacted the Bioportal support folks to be given admin rights on the PO metadata, as it needs to be updated as well. In progress...

• 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 (see above)

- Talked with Trish Whetzel (Bioportal) 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 an issue with Gramene, MaizeGDB, SSWAP, Virtual plant, TAIR, PLEXDB etc

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, GCP.

• This was a great opportunity to network with other plant database people and talk with users.

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, Stefan Rensing said he could supply German synonyms for PO terms. At the outreach booth,Yukiko Yamazaki 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.

We will see if we can get the Japanese translations in romaji (Roman characters). Alejandra can also translate terms in to Spanish. Ramona will prepare a spread sheet with all the term names to be translated, and send it to Alejandra, Stefan and Yukiko. Need to get Yukiko's contact info- (yyamazak@lab.nig.ac.jp), National Institute of Genetics, OryzaBase

BS said that as far as he knows, no other ontologies are dealing with foreign languages, except some Latin terms in the FMA. Ramona will look in to whether or not OboEdit has a way of specifying that synonyms are a foreign language.

Note from LC after the meeting: Maybe we could add a Translator widget to the browser? Google translator is one I have seen. As Google chrome is supposed to translate web pages automatically.

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:

1. The top priority for right now is to get a publication out:

-TIPS: An abstract/proposal was 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. Possible target journal: 'Current Opinions in Plant Biology'

-Plant Physiology: RW and LC 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?

While we were at PAG, DWS mentioned the editor of AJBOT wants him to put together a short paper for them- maybe can focus on PO?

This is also a requirement for OBO Foundry acceptance (see discussion below).

2. 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

3. User requests need to be cleaned up and used to fill-in PSO that we have created.

- Deal with and complete the list of user requests on SourceForge see: POC_Conf._Call_2-01-11.

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

TAIR requests on SF: stomatal meristemoid cell ovary septum vs carpel septum dispersed meristematic cell

4. Restructuring descendants of leaf (PO:0025034)

-many of the part_of children of vascular leaf can also be part of non-vascular leaf. This needs to be done before we can add terms for bryophytes.

5. Reproductive structures across plants: RW and DWS (and MAG?) could work together to add the terms using the NYBG numberspace.

- terms used by model systems (Physcomitrella, Selaginella, Loblolly pine, poplar etc.), and terms are needed for the EST library from the Genomics of Seed Plants project.

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

6. Plant Growth and Development Stage Ontology restructuring

A. 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??

B. 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

7. 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

Should start with the terms needed by the Physco group, plus terms for reproductive structures (see #4 above)

Medium Priority

• 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 $12,000.

-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.

Post-poned for a future meeting, since DWS and PJ were not present. Ramona will follow up with Dennis at NYBG.

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.

* ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York

URL: icbo.buffalo.edu

CALL FOR WORKSHOP AND TUTORIAL PROPOSALS: The deadline for workshop and tutorial proposals for the ICBO conference is February 1, 2011

We discussed the advantages of the PO organizing a workshop. LC will talk with PJ about it

BS suggested we might want to submit a short paper which could be published in longer form later

* 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.