POC Conf. Call 12-20-11

POC meeting, Webex Conference Call; Date: Tuesday Dec 20th, 2011 10am (PST)

In attendance:

POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_12-13-11?

Back to POC Meetings Minutes

PSDSO Revisions: Whole plant development stages

Continued from last week

Trichome terms

Need to address outstanding issues and wrap this up.

References:

Arabidopsis leaf trichomes: http://www.nature.com/nrm/journal/v5/n6/full/nrm1404.html (consistent with existing definitions of leaf trichome stage)

Alvin F. Reeves II. (1977) Tomato trichomes and mutation affacting their development. Amer. J. Bot. 64(2): 186-189. http://www.jstor.org/stable/2442106

Status of New Annotation Files for data release in Dec:

Physcomitrella Annotations

LC has been working with DL and SR to get the Physcomitrella annotations added

Updates: XXX annotations on three PO terms: spore, protonema and gametophore

Cotton (Gossypium)

LC has been working with collaborators at AgBase to add these on our new trichome development terms

Updating the Gramene Annotations

During the last release cycle, LC worked with the Gramene collaborators to get their files updated. They were also going through a release as well. Have not received any new annotations, even though they said they should be coming from Gramene in the next 1-2 weeks

Updates?

Others

Strawberry

• Strawberry is on SVN: strawberry

Potato Annotations

LC has been in contact with the group who published the potato genome paper and they are interested in collaborating with us to assign ontology terms to the annotations.

From Dr. Richard Finker (Wageningen, The Netherlands):

"We are also interested to use trait ontologies to assist in candidate gene selection within regions of interest, I'm eager to discuss with you on the efforts of cross linking ontologies to biological relevant entities. e.g. a metabolite content trait to its e.g. chebi ontology ID, form which we could obtain info about the pathway."

This will go in the next release, do they have expression data- RNA Seq?

Status of new DbxRefs:

• Need links for Physco (Cosmoss page), Gossypium and strawberry

• Things that still need to be fixed from last release: see PO_Release_SOP_Page

Annotation Guidelines

Comments from PJ from previous meeting (9-27-11): Ask MS if she can write up a small blurb on how she created the Maize annotations. Maize probe ids => gene ids methods and cut-offs, a guide for other collaborators and a page for the info. Maybe co-author it with SR

-This will also be helpful when applying for new grants

-it would be helpful to have a detailed guide on our wiki for collaborators

Wood Anatomy and Forest Trees

Wood anatomy Ontology Development: PO will work with a group of scientists to develop ontology terms to describe wood anatomy.

Please see the Wood_Anatomy and the Wood anatomy ontology meeting, 2012 at NYBG, agenda wiki pages for more information.

Three Goals:

• Develop terms for wood structure in the PAO
• Develop terms and ontology structure for wood formation,the time course of development
• Terms to describe wood quality and phenotype, traits- go into TO?

Update and status: Plan is hold the meeting at the NYBG during the first 2 weeks of Feb.

Invitation letter went out (date?) from DWS, to these experts (below) signed by all three Co-PIs, along with Jill Wegrzyn of the TreeGenes Database at UCDavis (Bioinformatics) and Andrew Groover Geneticist, USDA Forest Service, Institute of Forest Genetics, Davis CA.

Deadline for their response: Dec 31st 2011

• Frederic Lens: (new faculty at Netherlands Centre for Biodiversity Naturalis)
• Barb Lachenbruch link
• Elisabeth Wheeler (paleobotanist and wood anatomist at NC State
• Rachel Spicer Connecticut College
• John Carlson (jec16@psu.edu) link
• Meg (Margeret) Staton (mestato@yahoo.com) Clemson University (the lead on both the hardwoods website and the Fagaceae Genomics Web

Personal follow ups with the individual experts should be done to answer questions etc:

• DWS: Fredich Lens
• MAG: Elizabeth Wheeler
• LC: Barb Lachenbruch
• RW: Rachel Spicer

We should ask Jill Wegrzyn to follow up with: John Carlson and Meg (Margeret) Staton

FNA

See previous minutes for details of the mappings (POC_Conf._Call_11-1-11#FNA)

We had a conference call with FNA on Nov 18th, 2011.

Next steps:

• add 364 synonyms to existing terms - many of these are plural forms
• fix several errors that were discovered while doing the mappings (minor things, like definitions of ariloid versus strophiole).
• add 143 unique new terms, plus their synonyms

-FNA provides definitions, so this will be relatively easy

• work with FNA to create an official mapping file

-FNA will provide unique IDs for their terms. This is needed especially for FNA terms that have the same name but different meaning.

-FNA terms that map to >1 PO term should have multiple lines in the mapping file. Whenever the FNA term matches a general term plus its subtypes, should only map to the general term. They can use reasoner to infer mapping to more specific subtypes. We can create some new general terms like "organ apex".

-Some of their terms that are just too general for PO. For these, when HC does the next round of text mining, she will pull out more meaning from context, e.g., use the term leaf base instead of just base.

• begin work on phenotype/character terms, including the 101 from this list plus all of the FNA character terms

Upcoming meetings and Presentations 2011/2012:

PAG 2012

January 14-18, 2012, San Diego, California

PO will be represented at the following events:

• Ontology workshop, Saturday January 14th from 10:20am-12:30pm: Use of Ontologies for Organizing Plant and Animal Genomics Data. We have 5 speakers and time at the end for a panel discussion.

PJ will give the introductory remarks at the Ontology workshop, and hopefully take part in the Panel Discussion.

For more info, see the PAG 2012 Ontology workshop wiki page.

• LC is also presenting in the Non-Seed Plant Workshop on Saturday, Jan 14th, (3:50pm-6pm) and in the Plant Phenotypes workshop on Sunday, Jan. 15th, (8:00am - 10:10am).

• We will also do a computer demo Monday pm (tentatively) for the PO, perhaps JP would like to do this.

• The PO will also take part in an Outreach booth organized by MaizeGDB- schedule TBA

-Do we want to host the wiki page for the booth again?

Phenotype RCN meeting, 23-25 February 2012

The dates: February 23-25, 2012 (Thursday, Friday, 1/2 Saturday) have been confirmed for the next annual Phenotype RCN meeting.

It will be held again at NESCent (Durham, NC).

RW has a friend there she can stay with and is interested in going.

Any news??

Maize Genetics Meeting, March 15-18, 2012

The maize meetings are being held in Portland, OR this year.

For more info see: Maize Genetics Meeting 2012

Registration Link: 2012 Maize Genetics Conference Registration Page will open on December 30, 2011.

Deadlines: Advance meeting registration is due by January 31, 2012.

5th International Biocuration Conference

April 2-4, 2012, Washington DC

• Abstract was submitted December 9, 2011 for consideration for a talk (or else a poster). MS was co-author.

See link: File:Abs Biocuration 2012 (LC 12-9-11).pdf

• Notification date: February 3, 2012

From 9-27-11: PJ is planning to attend and will be running a biocuration workshop- is this happening?

SPNHC 2012

Annual meeting of the Society for the Preservation of Natural History Collections

Yale University, New Haven Connecticut June 11-16, 2012

Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).

The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).

From PJ: If we can show progress in the FNA work or Morphobank yes we should

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

Call for Symposia, Colloquia and Workshops:

RW, DWS and MAG put together a proposal for a half day hands-on workshop. The goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.

Proposal was submitted, waiting for news.

PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrixes.

exhibitor's booth

We should also consider hosting an outreach booth.

Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)

• 2 months of Rotating Banner Ads in the online American Journal of Botany

• A Rotating Banner Ad in one edition of the online Plant Science Bulletin

• A Rotating Banner Ad on the Botany 2012 abstract submission site

• A Rotating Banner Ad on the 2012 Conference Registration site.

PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.

Annotation wiki

JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.

ASPB Plant Biology 2012

July 20 - 24, 2012 - Plant Biology 2012, Austin, TX

Registration scheduled to open first week in January.

Early Bird Registration: by May 11

Advance Discounted: May 12-June 15

ICBO 2012

International Conference on Biomedical Ontologies (ICBO 2012), July 22nd-25th, Graz, Austria

co-located with the 7th International Conference on Formal Ontologies in Information Systems (FOIS 2012)

Relevant dates

• Jan. 31st, 2012: Paper submission deadline
• Feb. 28th, 2012: Notification of paper acceptance
• March 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
• April 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance
• June 30th 2012: Deadline for all camera-ready copies for the proceedings

We have until Jan. 31 to submit a paper. Do we want to try to prepare a manuscript for this?

Possible topics: finding commonality in development stages across the plant kingdom (revisions of PGDSO), plant phenotypes in ontologies, community driven annotation efforts (new application from JP and others), others?

BS would like to collaborate on a preliminary paper on Plant Disease Ontology. RW will review IDO and summarize what is there already for plants, what is needed, how it will link to PO. LC will also collaborate.

BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts