POC Conf. Call 10-13-10

POC meeting, Webex Conference Call; Date: Oct 13th, 2010 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the 10-6-10 meeting?

Status and Update of Progress: PO Release

An announcement will be sent directly to the direct user groups.

• TAIR email: curator@arabidopsis.org
• NASC ??? email: bioinfo@arabidopsis.info (not really clear who to send it to here)
• Gramene email: gramene@gramene.org
• MaizeGDB Carolyn Lawrence
• VirtualPlant
• SoyBase Rex Nelson
• Genevestigator
• SGN Lukas Mueller+Naama Menda ?
• OryzaBase Yukiko Yamazaki?
• PlantTribes
• TraitNet
• Generation Challenge Program, CIMMYT, Mexico Rosemary Shrestha
• BRENDA
• UniProt

We will send the email to the 'contact' email address at each of these groups, or the contact people at these groups, if we do not have a generic email.

Open SF tracker items Plant Structure Ontology

Oldest tracker items

These items have been on the SF tracker between 8 months and two year. None of them are controversial. Suggest that all curators take a look at each SF item and comment on whether or not they agree with the suggestions below. That way, we can devote our meeting time to more difficult terms.

dispersed meristematic cell (2007-02-14, donghui) – see proposed solution on SF

pericarp vascular bundle (2007-03-16, cwtung) – okay to add

rhizome internode (2007-08-03, cmungall) – okay to add

peripheral vein or tertiary vein (2008-02-07, anon) – reject and close

adaxial vs. abaxial structures (2008-02-18, rdidonat) – suggest adding the terms

shoot vascular system (2008-11-14, donghui) – suggest adding

ovary septum vs. carpel septum (2009-04-27, donghui) – add as synonym of carpel septum, maybe open new tracker item for carpel septum develops_from carpel wall

create chickpea related terms (2009-05-19, cwtung) – These are actually terms for types of branches or shoot systems; first deal with re-organizing shoot system

trichome parentage (2009-12-17, cmungall) – need to come back to this when we figure out how to deal with trichomes

terms without definitions (stylar ridges) (2010-02-26, rwalls) – part of meristem – We need to deal with the organization of meristem first, then come back to these terms

Newer tracker items

We need to prioritize the following items:

• Adding Musa terms requested by Rosemary Shrestha (July 2010)

• Root terms

-Adding/modifying the root terms submitted by Rich Zobel (Nov 2009).

We (sort of) dealt with the upper level root terms that Rich requested: basal root, primary root (taproot), shoot-borne root, but we still need to deal with the rest. Includes 3 new terms: internode root, non-pericyclic lateral root, non-pericyclic basal root.

He also suggested modifications to the definitions of the following additional 14 terms: List of root terms

-adventitious root- this was flagged for consideration during the revision of shoot-borne root (PO:0000042)

• Adding Legume terms submitted by Austin Mast*

Taproot Stem Hair Prickles Fascicle Bristle (used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure) Phyllode Banner (as in a legume flower) Wing (as in a legume flower) Keel (as in a legume flower) Anther pore and anther slit Locule

New terms requested by reviewers (from Ahrestani, Kramer and Rudall)

• Elena Kramer suggested that we add the term spur to the PSO and consider dealing with common primordia in the PGDSO.

• Paula Rudall commented that the current definition of central cell has a different meaning in gymnosperms.

• TraitNet requested several new terms for the PSO: corm, spine, podarium, pneumatophore, stele, diaspore, cone, sorus, and tendril.

Primordium

Right now, we don't have a general term for primordium. Do we want one?

Also, different types of primordia are defined consistently. Currently, there are two different types of definitions:

1. anther primordium (PO:0006089): An organized group of cells that will differentiate into anther.

2. carpel primordium (PO:0004703): The very first appearance of a carpel. It initiates from the carpel anlagen region of the floral meristem.

There are multiple examples of each type.

As it is, each type of primordium is a child of what it is the primordium of. For example, carpel primortium is_a carpel, anther primordium is_a anther. These relationships make sense with definition type 2, but not with defintion type 1.

We may also want to link these to stages in the PGDSO, where appropriate.

For example, ovule primordium (PO:0000018) participates in ovule primordium visible (PO:0007620) or ovule primordium visible (PO:0007620) has_participant ovule primordium (PO:0000018).

reorganization of shoot system

We started working on this during the last round of revisions (with bud, and terms like reproductive shoot system), but it still needs some tweaking. Need to discuss vegetative shoot system.