POC Conf. Call 9-22-10

POC meeting, Webex Conference Call; Date: Sept 22nd, 2010 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators: none

Acceptance of the minutes from the 9-15-10 meeting?

Status and Update of Progress: PO Release

Flower PO:0009046

Proposed def'n (from 9/15/10 mtg): A determinate reproductive shoot system that has as part at least one carpel or at least one stamen and does not contain any other determinate shoot system as a part.

Comment: may have as part one or more petals, sepals or tepals. May contain pistillode or staminode or other aborted organs that don't show up in mature form.

From SourceForge tracker: RW:Having the word reproductive in the definition is redundant, because it is already implied by the presence of a carpel or stamen. Also, some flowers are sterile, and not involved in reproduction. Instead we can keep the original comment: "The characteristic reproductive structure of angiosperms."

secondary xylem PO:0009046

New proposed def: A portion of xylem tissue that develops from a vascular cambium.

Comment:It is absent in some dicots and most monocots; the "wood" of dicot angiosperm trees, shrubs, and lianas.

Exact synonym: wood

• From SourceForge tracker:

RW: Should also apply to gymnosperms. Need to reword comment slightly.

basal root (PO:0025002)

Proposed def'n (from 9/15/10 mtg): A root that arises from a part of the hypocotyl.

We will deal with synonyms and child term (non-pericyclic basal root) of basal root in next round of revisions.

primary root (PO:0000042) to 'taproot'

Current def'n: A root that develops directly from a embryonic radicle. Tap root is given as a related synonym.

We will leave this as is for now. Tap root may be a type of primary root or may be an exact synonym. Will get more feeback from others.

Comment: Often is the central axis of the root system.

shoot-borne root (PO:0000042)

Current Def'n: A post-embryonic root that develops from shoot tissue. [source: GR:pj, TAIR:ki]

Hyphen was added to the name, as suggested.

• From SourceForge tracker:

RW: Adventitious root is already a related synonym of shoot-borne root in the PO. If we remove it, it won't show up in searches. Rather than removing it, I suggest following Rich's suggestion of making it a broad synonym of both shoot-borne root and basal root (it's okay for multiple terms to share a broad synonym).

subterranean tuber axillary shoot (PO:0025081)

Proposed def'n: An axillary shoot that develops from a subterranean tuber axillary bud.

New term for tuber sprout (exact synonym)

From 9-15-10 meeting: Can have 'swollen eye' as synonym of tuber axillary bud. (note there is no term 'tuber axillary bud', it should go on 'subterranean tuber axillary vegetative bud' or the new term 'subterranean tuber axillary shoot' ). We will ask Naama if it is more like a bud or a shoot.

Annotations that have no term associated with them

-There are 10 terms that have been obsoleted from this version of the PO.

PO:0025003 compound plant organ

PO:0025002 simple plant organ

(These two were never in the live version, so they were actually destroyed, not obsoleted)

PO:0009014 dermal tissue

PO:0000057 inflorescence bud

PO:0000058 vegetative bud

PO:0008034 leaf whorl

PO:0008037 seedling

PO:0009004 gametophyte

PO:0009003 sporophyte

PO:0000056 floral bud

Only the last 5 of them are problematic: leaf whorl, seedling, gametophyte, sporophyte and floral bud.

PO:0008034 leaf whorl

• Annotations: 15,802, from 'po_anatomy_gene_arabidopsis_tair.assoc'

Source: TAIR

These ones are pretty straightforward- we decided at the 4-27-10 meeting that leaf whorl would be 'replaced-by' 'collective leaf structure' PO:0025022

Laurel changed the consider relation to 'replaced_by 'collective leaf structure'(PO:0025022)'.

PO:0008037: seedling

• 16 annotations from 'po_anatomy_gene_arabidopsis_tair.assoc'

Source: TAIR

-Recommended to TAIR that they should be moved to seedling growth stage (PO:0007131) in PGDSO and also to whole plant (PO:0000003)in PSO.

Laurel will add the consider relation to seedling growth stage in the PGDSO

PO:0009003: sporophyte

• 1 annotation from: 'po_anatomy_gene_arabidopsis_tair.assoc'

Source: TAIR

-Recommended to TAIR that they should be moved to sporophytic growth phase (PO:0028002) in PGDSO and also to whole plant (PO:0000003)in PSO.

Laurel will add the consider relation to seedling growth stage in the PGDSO, but we need to clarify whether or not this works for TAIR's script.

Yes -- these annotations should also be attached to whole plant.

TAIR (Tanya Berardini 9/16/10): -suggested that we handle moving these annotations for now, since we want to include them in the new release. Laurel is working on getting the updated files from TAIR, since the ones on the SVN are about 18 months old.

• 116 annotations from 'po_anatomy_gene_oryza_gramene.assoc' and 'po_anatomy_qtl_oryza_gramene.assoc'

Source: Gramene

Suggested that the associations for genes be moved to PO:0000003 whole plant, plus sporophytic growth phase (PO:0028002) for genes;

Seedling vigor QTLs are already associated with PO:0007131 seedling growth, suggested adding association to whole plant PO:0000003 as well, if appropriate

Laurel is working on getting the updated files from Gramene, since the ones on the SVN are about 18 months old.

PO:0009004 gametophyte

• 1 annotation from 'po_anatomy_gene_oryza_gramene.assoc'

Source: Gramene

Suggested that this association be moved to male gametophyte (PO:0020091) or female gametophyte (PO:00290092) or to gametophytic phase (PO:0028003) and/or to to whole plant PO:0000003

Note: It is already associated with the megagametophytic stage (PO:000721)Note: This appears to be an error and pollen developmental stage (PO:0001007) in the PDGSO.

Note: This annotation is concerning rice anthers so it should be moved to male gametophyte (PO:0020091) and to gametophytic phase (PO:0028003).

In the ontology, LC -Added replaced_by 'gametophytic phase' (PO:0028003)' relation -Added the consider 'whole plant'(PO:0000003) relation -Added consider 'male gametophyte (PO:0020091)' relation -added consider 'female gametophyte' (PO:0020092)'

PO:0000056: floral bud

• 54 annotations from: po_anatomy_gene_arabidopsis_tair.assoc

Source: TAIR

Question from TAIR (Tanya Berardini@ TAIR 8/16/10)

"Why was 'floral bud' removed as a parent term for both 'axillary floral bud' and 'terminal floral bud'? I'm not sure I understand why this potentially useful grouping term was deemed no longer useful. I am not sure that we'll be able to move all our annotations to the more specific terms as the publications do not always specify whether axillary or terminal flower buds were used or whether the DNA/RNA/protein sample was obtained from a mixture of both."

This was discussed at the 9-8-10 meeting. All those present felt it was preferable to keep the current structure for floral bud. For more detailed information and graphics, please see the [Summary of Changes] page We were concerned about instituting a policy of changing the ontology, unless the change is biologically appropriate.

Response: TB: "The PO suggestion "...to move the annotations to both axillary floral bud and terminal floral bud, if that is appropriate. " is not necessarily practical as this information is not always available and I would be reluctant to move the annotations to the child terms if I wasn't sure that these were correct."

In order to get a better understanding of the issue, Laurel went through the annotations associated with the term 'floral bud' and looked at each paper to see how they describe the plant tissue samples. Most of them refer to "floral bud", "flower bud", or simply "buds". In a few cases they seem to be referring to the whole inflorescence.

In light of this, we need to reopen the discussion of the bud structure and will reexamine these terms.

We had some discussion of bud terms. Since all floral buds are at the end of a shoot (since they are determinate) they should all be terminal buds, but then those terminal buds can arise either at the end of a shoot or in an axil. Pankaj and Lol will work on sketching new structures for bud terms that includes the categories reproductive bud and floral bud. Will re-open SF tracker so we can work on this more.

Priorities for the Next Round of Revisions

-Merging the plant structure and plant developmental stages ontologies

-Adding Musa terms requested by Rosemary Shrestha

-Root terms- Rich Zobel

-Legume terms submitted by Austin Mast

-New terms requested by reviewers (from Ahrestani and Kramer)

-is_a parents for remaining terms (will require work on upper level structure for non-material entities)

-convert to intersection_of relations?

-work on PGDSO

-tuber growth and development stages, open on SF since 6/2009

-add links to more images

-Others??- PJ: Lol and Ramona will focus more on adding annotations (~50% of time)

-What is the target date for the next release?