POC Conf. Call 8-30-11

POC meeting, Webex Conference Call; Date: Tuesday Aug 30th, 2011 10am (PDT)

In attendance:

POC members:

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_8-23-11?

Update on addition of new MaizeGDB Annotations

• This was discussed on the conference calls: [POC Conf. Call 8-2-11] and [POC Conf. Call 8-23-11], as well as the webex meeting with Mary Schaeffer on Aug. 11th, see: Submission of Association files for the Kaeppler gene expression data from MaizeGDB- Aug 2011

Loading annotation files

Any updates?

Merging maize-specific terms and other changes to the ontology

PGDSO terms

IL.03 full infloresecence length reached

Add two related synonyms:

3.4 late vegetative (maize)

VT (maize)

Also add to the comment: In US cornbelt maize, the tassel fully emerges about 2-3 days prior to silk emergence from husk leaves. At this time the ear and husk may still be enclosed within its leaf sheath depending on the variety and environmental conditions.

LP.18 eighteen leaves visible

Under synonyms add: related: VT vegetative transition in maize (US cornbelt)

3 infloresence visible - rework the tree, add a term

Current structure:

From Mary: Humble suggestions for reworking this part of the ontology so that very early stages of all species can be lumped, and to make it easier to annotate.

(1) “PO:0007047 3 inflorescence visible” should be redefined to include early stages where it may be visible (eg booting) but not yet emerged. One might rename the visible to ‘detectable’ and define appropriately.

current definition: The stage at which plant is producing inflorescence(s). is_a B reproductive growth

proposed definition, 3 inflorescence detectable phase: A reproductive growth phase during which one or more inflorescences is detectable.

Comment: This includes the time when inflorescence may be developing (e.g. booting in Zea) but not yet emerged. Includes times when inflorescences are detectable only by assay or with a microscope.

(2) PO:0007006 IL.00 inflorescence just visible should include the booting stage, etc. Perhaps rename to - IL.00 inflorescence just detectable. This will permit lumping with similar stages in Arabidopsis for example. Basically, all the developmental programs are in place and the structure is growing, even if only visible as a bulge in the sheath, or by stripping off the vegetative parts to view.

RW: What Mary describes is still visible (if the structure is actually growing), with manipulation of the plant or aid of a microscope. Use of the word detectable includes times when it could be detected by assay, but not visible. I think if we want a phase that describes that, we should add a separate phase: "inflorescence just detectable", for times when the inflorescence can be detected, but not seen, but only if people need it.

current definition: Inflorescence just visible to the naked eye.

proposed definition, IL.00 inflorescence just visible phase: An inflorescence detectable phase during which one or more inflorescences is just visible to the naked eye but not yet developed.

Comment: Includes the time when the inflorescence can be seen by removing outer leaves or bracts, or when the inflorescence is detectable as a swelling of the outer leaves or bracts, such as booting in Zea.

(3) PO:00070411 inflorescence emergence from flag leaf sheath would now have a direct is_a relationship with ‘3 inflorescence visible’.

Additional comment from Mary: "the term 'emergence from flag leaf sheath' be made more global and be called something like inflorescence emergence (eg from flag leaf sheath, from leaf sheath) with appropriate definition. This way all terms save 2 (per above) would be retained."

current definition, inflorescence emergence from flag leaf sheath: The stage at which the inflorescence emerges from the flag leaf sheath.

proposed definition, inflorescence emergence phase: An inflorescence visible phase during which an inflorescence emerges from sheathing leaves or bracts.

Comment: Includes emergence of a Zea inflorescence from a flag leaf.

(4) PO:0007014 booting would be merged to the term PO:0007006 inflorescence just detectable.

Suggest merging PO:0007014 booting with PO:0007006 IL.00 inflorescence just visible phase. All children of booting would stay under PO:0007006 (inflorescence just visible, with synonym booting).

(5) Obsolete PO:0007012 Poaceae inflorescence visible as would no longer be required.

Suggest merging PO:0007012 into inflorescence detectable stage, rather than obsoleting it. Descendants of PO:0007012 (booting and inflorescence emergence from flag leaf sheath) are already moved to other parents, see above.

coleoptile emergence -- definition

If we have time to discuss this, details are at Items_for_future_meetings#coleoptile_emergence_--_definition

5 fruit formation; FF.00 fruit size 10%

If we have time to discuss this, details are at Items_for_future_meetings#5_fruit_formation.3B_FF.00_fruit_size_10.25