POC Conf. Call 9-20-11

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

In attendance:

POC members:

Absent:

Collaborators: none

Acceptance of the minutes from the POC Meeting at NYBG; Sept 10th-11th, 2011?

Tech issues:

Adding Dbx Refs

need to fill in the details here

OWL version stamp

Request from Gavin Kennedy:

"Would it be possible to add an owl:versionInfo attribute to the OWL Plant Ontology so that we can track the changes in versions. This could be the version number or a date stamp, etc."

filter translation

from Mary Schaeffer at MaizeGDB

comments: It would help to have a link to what the filters mean from all pages where one can set the filters. A click on the help box seemed to missing this information, or require reading pages of stuff to find out it wasn't there.

For example - most folks will not know that MGCSC refers to the maize mutant stock collection at Illinois.

these have been posted on the POC_Technical_Issues_Page

Edits for release: PGDSO

Edits requested by MS for MaizeGDB

We don't need to fix the definitions of coleoptile emergence PO:0007045 before this release, because Mary decided she should use "radicle emergence" (PO:0007015) instead.

PGDSO terms without is_a parents

As discussed at the NYBG meeting, we can fix the three remaining PO terms without is_a parents: shoot emergence, seedling growth and imbibition.

Shoot emergence is part_of seedling growth, but has no is_a parent, and seedling growth has no is_a parent. Imbibition (sibling of shoot emergence) also has no is_a parent.

current structure:

Shoot emergence (stage) should be is_a seedling growth (stage). Seedling growth (stage) should be is_a vegetative growth stage.

Imbitition (stage) should be is_a germination (stage). Will deal with definitions of imbibition and germination later.

current and proposed terms and definitions

0 germination (PO:0007057): rename "(0) germination stage".

imbibition (PO:0007022): rename "imbibition stage" and make is_a child of "germination stage".

NOTE: RW tried the parentheses around the zero, and they display fine in the dev browser. Will leave it up so we can look at it, but should remove them before release until we are ready to change them all.

current: seedling growth (PO:0007131): Growth of embryo after imbibition up to the development of the first adult leaves. part_of germination

new proposed name and def.: seedling development stage: A vegetative growth stage that has as a participant a whole plant during the interval between germination and development of the first adult leaves.

Comment: This terms is used only for seed plants, although non-seed plants may have a comparable phase during which they produce juvenile or transition leaves.

Note: After the PGDSO is revised, the parent of seedling growth stage will be sporophyte vegetative development stage, so definition will change slightly. Also, the numbering of the children of vegetative growth stage is messed up now. Should we renumber the stages?

shoot emergence (PO:0007030): Shoot or leaf breaks through the soil surface.

Propose that we rename shoot emergence stage and make it is_a seedling growth stage, instead of part of seedling growth stage. Can work on definition when we revise the PGDSO.

Upcoming meetings and Presentations 2011/2012:

* 2011 CGRB Fall Conference Oregon State University, on Sunday-Monday, September 18-19, 2011.

Two posters related to the Plant Ontology will be presented.

JP will present a poster at the regarding the development of a semantic web application for annotation curation. This web application makes use of PO data via a newly created web service, and includes an initial data set built from PO GAF (.assoc) files for Oryza sativa.

Additionally, he and PJ will host a web presentation for Syngenta employees on the same topic on Sept 26.

LC will present the poster: Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa.

PAG 2012

January 14-18, 2012, San Diego, California

Registration and Abstract submissions open on Sept 22nd

LC is presenting in the Plant Phenotypes workshop

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

Other activities?

*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 

From the Instructions page: For authors wishing to submit to DATABASE for the 2012 BIOCURATION VIRTUAL ISSUE:

• Submission deadline: October 15, 2011
• First decisions: November 15, 2011
• Revisions deadline: December 15, 2011
• Final decisions: January 10, 2012
• Conference: April 2-4 2012

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

Call for Symposia, Colloquia and Workshops:

Submission site now open