POC Conf. Call 1-11-11

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POC meeting, Webex Conference Call; Date: Tuesday Jan 11th, 2011 10am (PST)

In attendance:

POC members:

Absent:

Collaborators:


Acceptance of the minutes from the POC Conf. Call 1-4-11?


Timeline and Plan for Upcoming Release:


We have completed all the changes discussed last week and the merged plant_ontology.obo file was loaded on the *Beta* browser (Thanks Justin E!)


* Internal review before full release: Beta browser is working, so everyone in the group should go over file before the release.


* Annotations that need to be moved: We have obsoleted or renamed/redefined about 10 terms that may impact annotations from TAIR, MaizeGBD, Gramene and SGN These annotations are going to need to be reassigned/moved to new PO terms as a result of the changes that have been made.

See: The Obsoleted and new terms Jan 2011 page on our wiki that you can visit to review the changes, with links to the annotation pages. There are also our suggestions as to where the annotations should be moved to.


We have requested that each group look after the reassignment and submit updated files to the SVN. Justin E is helping can set that up for whoever is responsible for doing that if someone there does not already have access.



List of things to fix:

Minor: -typo in the 'root hair cell' comment.

Priorities for the Next Round of Revisions

We need to define some goals for the next round of revisions:

From 10-6-10 meeting:

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

-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.

-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.

  • 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...
  • Last week, DWS commented that we should review what we planned to do in the original grant proposal, and make sure we are not forgetting anything. All agreed it was a good idea and we will put it on the agenda for next time.

From Project Summary:

This proposal seeks funding to support a pilot project to develop a common set of controlled vocabulary terms describing anatomical structures and developmental stages of both the flowering and non-flowering plants. These terminologies will be applied to the task of annotating the spatial and temporal aspects of gene expression and observed phenotypes of mutants, natural variants and associated quantitative trait loci. The annotations will be carried out in collaboration with the participating plant genomics databases and large repositories of sequence datasets and seed stocks. We will map the ontology terms developed in this project to similar vocabularies developed and used in annotation by various national and international projects working on plant genomics and phenotyping of germplasm seed stocks. In this way the Plant Ontology (PO) developed in this project will serve as a common reference point, allowing comparative analysis of these datasets.


From body of proposal:



  • Target date for the next release?

TIPS proposal

An abstract/proposal was been submitted to Trends in Plant Science on Dec 31st, 2010. It was sent out to everyone by email. Any news??

Upcoming meetings 2011:

  • Plant and Animal Genome XIX Conference January 15-19, 2011 PAG 2011

Laurel, Ramona, DWS and Justin Preece are attending. PJ will attend for the weekend only as he is teaching. Alejandra cannot attend.

PO Activities at PAG:

Saturday - Early Afternoon, January 15, 2011 -- 1:30 pm - 3:00 pm (third in series of seven)

Outline for PAG2011 Computer Demo

" The Plant Ontology: Linking phenotypes and genomics across plant taxa"

Sunday Morning, 16 January 2011 -- 8:00 am - 10:10 am

Sunday Late Morning:

Time: 10:30-1:00 pm (to include lunch, will wrap up in time to get to 1:30 sessions)

PO Workshop Reg'n site and Survey

  • Outreach Booth being organized by MaizeGBD- More info TBA


  • 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)? 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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