POC Conf. Call 10-4-11

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POC meeting, Webex Conference Call; Date: Tuesday Oct 4th, 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_9-27-11?


Issues and status reports for the Upcoming Release

For more details of the changes in the upcoming release, see: Summary of Changes to PO September 2011

Updating of Dbxrefs

We got the details on how to add dbxref to AmiGO: our version of AmiGO has a built-in set of db xrefs, in a Perl file, and it is not reading the current GO file.

In order to update these, this file has to be so will have to be editted manually by JE (or JP).

We decided on the POC_Conf._Call_9-27-11 to use the PO_DBXref.txt file on the SVNto store the updated dbxrefs stanzas.

An older version of this file is also available through the documentation page on the PO website:

LC: Do we really need to have this file PO_DBXref.txt on our website, since it is just for our internal use? If so, it should be updated.

Status of Dbxrefs that need to be fixed:

  • Link to SF trackers (OB_SF_PO):

Link is currently in the PO_DBXref.txt file on SVN, appears to be working on beta, but not dev browser.

For example see thallus, PO:0030027

  • MaizeGDB Links:

These look like they are working ok on the beta browser


  • Gramene links:

The ones on the beta browser are working, not sure if the ones that were broken are there- need to load some test data on beta to make sure.

The current ones are (as of 9-29-11, #152):

abbreviation: GR 105 database: Gramene: A Comparative Mapping Resource for Grains. 106 object: Protein 107 example_id: GR:P93436 108 generic_url: http://www.gramene.org/ 109 url_syntax: http://www.gramene.org/db/protein/protein_search?acc=[example_id] 110 url_example: http://www.gramene.org/db/protein/protein_search?acc=P93436 111 112 abbreviation: GR_REF 113 database: Gramene: A Comparative Mapping Resource for Grains. 114 object: Reference 115 example: GR_REF:659 116 generic_url: http://www.gramene.org/ 117 url_syntax: http://www.gramene.org/perl/pub_search?ref_id=ID number 118 example: http://www.gramene.org/perl/pub_search?ref_id=659 119 120 abbreviation: GR_MUT 121 database: Gramene: A Comparative Mapping Resource for Grains. 122 object: Mutants 123 example_id: GR_MUT:GR:0060198 124 generic_url: http://www.gramene.org/ 125 url_syntax: http://www.gramene.org/db/genes/search_gene?acc=[example_id] 126 url_example: http://www.gramene.org/db/genes/search_gene?acc=GR:0060198 127

abbreviation: GR_QTL

database: Gramene: A Comparative Mapping Resource for Grains.

object: Mutants

example: GR_QTL:CQA11

generic_url: http://www.gramene.org/

url_syntax: http://www.gramene.org/perl/mutant/search_mutant?id=ID number

example: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=CQA11




  • Solanaceae Genome Network (SGN) links:



  • Links to the non-standard refs:

RW Created a PO_references page on the wiki and added a few of the PO_REF definition dbxrefs to the ontology file, for testing. 

 For example see thallus, PO:0030027

Annotation files

Gramene: From last meeting: New annotations should be coming from Gramene in the next 1-2 weeks- do we wnat to wiat for these, or go ahead with the release?

Upcoming meetings and Presentations 2011/2012:

Plant Genomes & Biotechnology: From Genes to Networks, CSHL

Dates: November 30 - December 3, 2011 Abstract Deadline: September 9, 2011...

Academic/Student No-Housing Package $720

RW registered and submitted abstract. Will need to present a preliminary data analysis for the talk/poster.

PAG 2012

January 14-18, 2012, San Diego, California

  • Registration and Abstract submissions: open on Sept 22
  • Early Pre-Registration Deadline: October 31
  • Travel Grants Deadline: November 1
  • Abstract Submission Deadline: November 11

Our proposal for an Ontology workshop for PAG has been approved. It will be on Saturday January 14th from 10:20am-12:30pm

Use of Ontologies for Organizing Plant and Animal Genomics Data


LC is presenting in the Plant Phenotypes workshop on Sunday Morning, 15 January 2012 -- 8:00 am - 10:10 am.

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

Other activities?

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.

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,

PJ: we should ask MS, and possibly SR, to contribute to the abstract and the annotation guide. See notes above

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

Call for Symposia, Colloquia and Workshops:

Submission site now open. Deadline for submissions is Saturday, October 15th, 2011 at 11:59 PM PST.

RW, DWS and MAG will 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.


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. RW will put the draft plant PATO on the SVN.

  • We need to have a section sponsor for the workshop proposal, DWS suggested the structural section (Head: Bruce Kirchoff), paleo section or systematists.


From meeting website:

When you submit your proposal, you will be asked for the following information:

  • What Societies and Sections will be sponsoring the session. Please provide contact information for any persons who have approved the sponsorship
  • The societies participating in Botany 2012 of which you are a member
  • The names, email and street addresses of the organizers, and which of them will lead the session
  • A title and description of the session
  • Keywords and web links that are relevant
  • Requirements, such as room type, food, special equipment or transportation, depending on the type of proposal
  • An estimate of anticipated attendance
  • A list of invited speakers or leaders, if relevant.


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.

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