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.

BS and MAG pointed out a few typos on the summary page (still in progress), PJ suggested we should still offer the PSO and PGDSO files separately for users. JE could create a script to parse out the two parts and post them on the svn

Download ontologies page needs to be updated- take off the links to the really old files? We should encourage users to use the merged file, though

* 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.

Update on annotations:

TAIR: We have been working with Tanya and Donghui on getting the chnges made. Tanya is creating the GO terms we requested. We will give the the 'final' (release ready) plant_ontology.obo file later today so they can update their files. Once those are done then they will commit them to the SVN.

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)


List of things to fix:

Open to discussion:

pollen tube cell (PO:0025195): A plant cell that develops from a vegetative cell and forms a tubular extension of the pollen grain. [source: POC:rw] Comment: Carries the male gametes to into or near the ovule. May be branched in gymnosperms. See GO for pollen tube and pollen tube tip.

versus:

obsolete pollen tube (PO:0006345): A tubular cell extension formed by the germinating pollen grain; carries the male gametes into the ovule. [source: ISBN:0471245208]

The curator at TAIR made the argument that pollen tube and pollen tube cell are used interchangeably in the literature.

Is it always the case the the entire cell is composed of the tube? If so, the terms are redundant.

Everyone felt that we should keep it as it is. Some of the annotations should go in both GO and PO. We should find out from Chris about how they deal with the cross ontology cross products (???)

Minor fixes:

-typo in the 'root hair cell' comment.

-add GO numbers in the comments for pollen tube tip and unicellular trichome branch (just added in GO).

Discussion about 'has_part' relation: RW, LC and JE have been working on an icon for it. JE says it may break the browser, but there are has_part relations in the live version which loaded fine, apparently

JE will run a test to see if they are a problem

Ramona will check with Chris about how it is used in GO. We should decide whether to up "Hp" or "H", most people liked the former.

Priorities for the Next Round of Revisions

  • Target date for the next release?

Lets plan for early to mid march. (Before spring break!)


Defining Goals and Priorities for the next round of revisions:

From 10-6-10 meeting:

  • 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...

Tasks set out in Grant Proposal

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 the proposal:

The specific aims of the project are as follows:

3.1 Develop and enrich the PO to describe plant anatomy and developmental stages of all plants.

3.2 Develop PO as reference ontology of plant structures and growth stages by doing mappings to similar vocabularies in use by plant databases.

3.3 (deleted)

3.4 Outreach and education activities to extend the PO usage and awareness on Plant Biology research.


"Of particular concern at this juncture, is the development of ontologies for the Assembling the Tree of Life (AToL) Angiosperm and Gymnosperm projects, where large number of morphological and anatomical data matrices covering the range of representative species and the traits observed through a plant’s life cycle are being assembled."

Examples: megagametophyte; endosperm; phyllome (ligule); parts of a moss versus multicellular algal species versus angiosperms; whole plant growth stage and plant part developmental stage ontology will also be extended to span both the lower and higher flowering and non-flowering plants

"add two new relationship types namely the contained_in and adjacent_to"

"even though we will still not integrate these (phenotypic) terms in the PO, we will mirror the Phenotype Attribute and Trait Ontology (PATO) developed by several model organism databases"


3.1.2 Ontology Deliverables:

Year-1 make PO OBO compliant, adjust the ontology for integration of non-flowering plant terms, test the integrated version with existing annotations and pilot annotations from non-flowering plants. Distribute ontology in RDF, OWL and XML formats. Customize the OBO-Edit for PO development.

Year-2 Add terms and annotations from Vitaceae, Rosaceae, Fabaceae,Gymnosperms and Pteridophytes. Also add Phenotype Attribute and Trait Ontology (PATO). Customize the Ontology browser to display mappings, cross products and annotations using PO, PATO and GO. Customize the web-accessible annotation tools.

Year-3 Add terms and annotations from Compositeae and non grass monocots including Banana and Coconut, Sorghum, Triticeae, Brachypodium and Brassicaceae

Year-4 Add terms and annotations from Malvaceae (cotton), Salicaceae (Poplar), Bryophytes and Chlorophytes.

The plan on adding annotations is described as part of the outreach activities (section 3.4). Database development and integration of annotations from collaborative projects and individuals will be a continuous activity in all 4 years.


3.2.2 Mapping Deliverables:

Year-1 Mapping software improvements and training. Mapping to Cell Type Ontology and keywords from Uniprot and Swissprot databases.

Year-2 Cross products with Gene Ontology, Plant Trait Ontology Jaiswal, Gandolfo and Stevenson; Project Description; 12

Year-3 Cross products with USDA-GRIN database and CGIAR-Generation Challenge Program descriptors

Year-4 Pilot mapping to Tree of Life (AToL) project vocabularies for Gymnosperm and non-grass monocots


3.4.1 Outreach and Education: Deliverables

Year-1 Ontology design and development workshop, 1st Open workshop for POC collaborators at PAG meeting, Image library work begins and begin web services (SSWAP) from the project website.

Year-2 1st Teachers workshop for area schools at Cornell Univ., 1st Open PO annotation workshop and 2nd collaborators workshop at PAG meeting, 1st Student workshop at NYBG and First release of the image library and continue building image library.

Year-3 2nd Teachers workshop for area schools at Cornell Univ., 2nd Open PO annotation workshop and 3rd collaborators workshop at ASPB meeting, 2nd Student workshop at NYBG and continue building image library.

Year-4 3rd Teachers workshop for area schools at Cornell Univ., 3rd Open PO annotation workshop and 4th collaborators workshop

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-

-Booth number 427, -We will be sharing with: MaizeGDB, GrainGenes, Gramene, SGN, Oryzabase, NIAS Rice Databases, SCRI, PMN/TAIR, SoyBase, PLEXdb, SoyKB, CottonDB, LIS, PlantGDB

More info about schedules: 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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