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

Adding Musa terms requested by Rosemary Shrestha (July 2010)

1. Musa leaf terms: Petiole wing, Petiole margin, Cigar leaf, Petiole canal, Petiole margin edge, Cigar leaf dorsal surface

2. Musa flower terms: Bunch, Basal flower, Free tepal, Compound tepal, Crown, Free tepal apex, Hermaphrodite flower, Compound tepal lobe, Peduncle surface, Male bud, Female flower, Peduncle hairs, Bract apex, Bract external face, Bract internal face, Bract base

3. Musa fruit terms: Hand of fruits, Flower relics

4. Musa shoot terms: Sucker, Pseudostem, Pseudostem underlayers

Laurel sent a message to Rosemary to see if there were any changes, will post the spreadsheet listing all the details of the terms.

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.

In his Root mini-ontology, he proposed the following three 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)

From 9-15-10 PJ: We also should discuss root terms with Phil Benfey (Duke) and Leon Kochian (Cornell). They are developing software for root type recognition. Should work to integrate PO with their software. Don't know if Rich is involved in discussions with them.

Adding Legume terms submitted by Austin Mast

Taproot Stem Hair (Esau's Anatomy of Seed Plants gives "hair" as a sub-category of "trichome") 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.