POC Conf. Call 11-15-11

POC meeting, Webex Conference Call; Date: Tuesday Nov 15th, 2011 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_11-8-11?

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PGDSO revisions

sub-types of whole plant development stage: vegetative, reproductive, senescent, and dormant stages

Continued from POC_Conf._Call_11-8-11.

other gametophyte stages

proposed definition, gametophyte dormant development stage: A gametophyte development stage that has as a participant a whole plant during the interval between a suspension of physiological activity and the reactivation of physiological activity.

proposed definition, gametophyte vegetative development stage: A gametophyte development stage that succeeds spore germination and ends with the formation of gametangia.

proposed definition, gametophyte reproductive development stage: A gametophyte development stage that is initiated with the development of a gametangium and terminated with fertilization.

Comment: Some gametophytes may die before fertilization.

Plant structure development stages (other than whole plant)

Need to get these in order so we can deal with user requests.

Need to look at seed and leaf dev stages, see where trichomes will fit in; add tuber dev stages (under plant organ dev stage).

Status of New Annotation Files for data release in Dec:

This content below needs updating: Copied from 9-27-11 meeting

Physcomitrella Annotations

From 9-20-11 meeting: PJ will reply to SR about the Physco annotations- re: they should be using the actual gene ids rather than the microarray probe ids

What link do we need to use for these and how do we get AmiGO to recognize it?

Need to set up SVN access for SR or whoever will be sending the files.

PJ will contact SR about the files

Gramene Annotations

Regarding the following tech section from today's mtg agenda:

Two of the Gramene dbxrefs in PO_DBXref.txt are not working:

GR: http://www.gramene.org/perl/protein_search?acc=P93436

GR_MUT: http://www.gramene.org/perl/mutant/search_mutant?id=GR:0060198

Don’t know if it is because the urls are wrong, or if it is because the ids are bad. If someone from Gramene can provide the correct urls, we can write new stanzas for the dbxref file.

JP hunted down the correct link templates and confirmed them with Ken:

http://www.gramene.org/db/protein/protein_search?acc=# (e.g. P93436)

http://www.gramene.org/db/genes/search_gene?acc=GR:# (e.g. GR:0060198 ...yes, Ken says mutant searches should be processed via the gene search)

JP and JE and I will work to get these implemented in the AmiGO codebase. RW will update the xref file.

New annotations should be coming from Gramene in the next 1-2 weeks

Grape and Strawberry

• LC working on grape file, see sample

• Strawberry is on SVN: strawberry

What links do we need to use for these and how do we get AmiGO to recognize them?

See notes above

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?

Comments from PJ about Annotation Guidelines

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

Upcoming meetings and Presentations 2011/2012:

Plant Genomes & Biotechnology: From Genes to Networks, CSHL

Dates: November 30 - December 3, 2011

RW registered and submitted abstract (Media:PO_abstract_PGBatCSHL2011.pdf). This presentation should involve the larger analysis for the PO paper with the data from Physco and grape etc.

Will be a poster. Can also set up laptop in the poster room to give demo.

Sematic web conference focused on life science

JP will attend the SWAT4LS meeting in December. Folks such as TW from NCBO will be there.

PAG 2012

January 14-18, 2012, San Diego, California

Please see the PAG 2012 Ontology workshop wiki page.

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 may be tied up on Sat am, so we will not plan on him giving a talk at the Ontology workshop, but hopefully he can take part in the Panel Discussion.

• LC is also presenting in the Non-Seed Plant Workshop} (Saturday, Jan 14th, 3:50-6pm) and in the [http://pag.confex.com/pag/xx/webprogrampreliminary/Symposium56.html Plant Phenotypes workshop on Sunday, Jan. 15th, (8:00am - 10:10am).

• LC will also do a computer demo for the PO, unless one of the Justins is there and wants to do it.

• The PO will take part in an Outreach booth organized by MaizeGDB.

Important Dates:

• Abstract Submission Deadline: November 11

Who is attending: LC, PJ (weekend), maybe JP, JE?

Abstract deadline is November 11. Will need abstracts for plant phenotype workshop, computer demo, non-seed plant workshop, and any talks going into the Ontologies workshop.

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.

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

Call for abstracts is now open: Need to clarify the deadlines

There are three submission categories for abstracts:

1. Talk or Poster (with consideration for oral presentation)

2. Poster only

3. Workshop only

• Submission deadline November 30, 2011

• Notification of acceptance February 3, 2012

Instructions

There are seven topic sessions from which submitters are invited to select:

  1. Ontologies, standards and best practices, including gold standard datasets.
  2. Protein annotation; sequences, structures and pathways.
  3. Community annotation and Wikis.
  4. Genomics and metagenomics data curation.
  5. High throughput proteomics data (focus on NGS and MS data) curation and presentation.
  6. Literature collection, text mining and curation.
  7. Tools to assist curation, including automated pipelines. 

There are four submission tracks:

  1. Paper, with consideration for oral presentation
  2. Talk
  3. Workshop
  4. Poster 

PJ planning to attend and will be running a biocuration workshop, LC and RW can go, DWS will be away,

'From 9-27-11: PJ: we should ask MS, and possibly SR, to contribute to the abstract and the annotation guide.

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.

ICBO 2012

International Conference on Biomedical Ontologies (ICBO 2012)

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

22-25 July 2012; Graz, Austria.

Conference Web site: http://purl.bioontology.org/ICBO/

We also have the opportunity to organize an anatomy workshop as well along with CM and MH- need to decide about this soon

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

Could also consider organizing a phenotype ontology workshop.

Relevant dates

31 December 2011: Workshop and tutorial proposal submission deadline

25 January 2012: Notification of acceptance of workshops and tutorials

31 January 2012: Paper submission deadline

28 February 2012: Notification of paper acceptance

15 March 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline

15 April 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance

30 June 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.