POC Conf. Call 10-26-10

POC meeting, Webex Conference Call; Date: TUESDAY Oct 26th, 2010 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the 10-20-10 meeting?

Proposed fixes for terms without is_a parents

Raphe, funicle and hilum

Raphe, antiraphe, and hilum

Seed raphe (PO:0006331), seed funicle (PO:0006332), hilum (PO:0020063), and hilum groove (PO:0004719) have no is_a parents. These are related to the open SF items for raphe and antiraphe.

Dealing with this will assign parents to 4 terms without and close 2 SF tracker items.

Current defintions:

raphe (PO:0020027): That part of the funicle that is adnate to the ovule.
[source: APWeb:Glossary], part_of funicle, no is_a parent

seed raphe (PO:0006331): The ridge along the body of the seed formed from the part of funiculus that was adnate to the ovule. [ISBN:047124529]

antiraphe (PO:0020028):The region on the other side of the ovule from the raphe. [source: APWeb:Glossary]

seed funicle (PO:0006332): Remnants of the funicle from the ovary where it attaches the ovule to the placenta. [GR:pj]

hilum (PO:0020063): The scar on a seed at the place where it was attached to its funicle. [APWeb:Glossary]

hilum groove (PO:0004719): Longitudinal groove in the testa through the prominent hilum of the seed.

funicle (PO:0020006): A stalk that attaches the ovule to the placenta. [source: APWeb:Glossary, GR:pj] is_a stalk, which is_a cardinal organ part (definition is okay, just here or reference)

Question: For all of these, are they better classified as portions of plant tissue (contain only one tissue type) or cardinal organ parts (contain more than one tissue type? Depending on the answer to this question, all of the following definitions will be portions of plant tissue or cardinal organ parts.

Proposed definitions (see SF tracker items):

raphe: A cardinal organ part that is a ridge on an ovule
where a funicle is or was fused to the ovule. is_a cardinal organ part,
part_of ovule



seed raphe: A cardinal organ part that is a ridge on a seed
that develops from a raphe. is_a cardinal organ part, part_of seed,
develops_from raphe

antiraphe: A cardinal organ part that is the
part of an ovule on the opposite side from a raphe. is_a cardinal organ part,
part_of ovule



seed funicle: A stalk that is attached to a seed and is the remnants of a funicle. is_a stalk, develops_from funicle.

hilum: A cardinal organ part that is a scar on a seed at the place where it was attached to a funicle. . is_a cardinal organ part, part_of seed

hilum groove: A cardinal organ part that forms a longitudinal groove in the testa through the prominent hilum of a seed. is_a cardinal organ part, part_of seed.

stylar ridge

The following terms have no is_a parents and no definitions:

stylar ridge of lower floret of pedicellate spikelet of ear (PO:0009024)

stylar ridge of lower floret of sessile spikelet of ear (PO:0009076)

stylar ridge of upper floret of pedicellate spikelet of ear (PO:0009079)

stylar ridge of upper floret of sessile spikelet of ear (PO:0009092)

They already have part_of relationships to their corresponding spikelets

Each of them occurs in a different structure, and has slightly different development, but they are all characterized by the following description: “The gynoecium development of the lower floret begins with the
production of a ridge on the abaxial surface of the apical meristem of the
floret, distal to the third stamen (which later degenerates). This is the
stylar ridge.” (MaizeGDB:60893)

Suggest a new parent term stylar ridge, proposed definition: A portion of meristem tissue that is part of a floret meristem and is characterized as a ridge on the abaxial surface of a floret meristem.

[FYI: Floret meristem (sensu Poaceae) (PO:0006329): Meristem that gives rise to the organs of a floret of a grass plant. [source: GR:pj]. Is_a floral meristem, which is_a meristem. Perhaps floral meristem should be is_a apical meristem instead.]

Proposed definitions for children:

stylar ridge of lower floret of pedicellate spikelet of ear: A stylar ridge that is part of a gynoecium of a lower floret of pedicellate spikelet of ear. Comment: While the development of this stylar ridge is very similar to
that of the upper florets, the development does not proceed beyond the
early ridge stage.

stylar ridge of lower floret of sessile spikelet of ear: A stylar ridge that is part of a gynoecium of a lower floret of sessile spikelet of ear. Comment: Continued overgrowth of the shoot apex (which becomes the
ovule primordium) by the ring of stylar tissue leads to the formation of
the stylar canal, which is detected as a slight protruberance on the mature
ovary.

stylar ridge of upper floret of pedicellate spikelet of ear: A stylar ridge that is part of a gynoecium of a pedicellate spikelet of ear.

stylar ridge of upper floret of sessile spikelet of ear: A stylar ridge that is part of a gynoecium of a sessile spikelet of ear.

Definitions from MaizsGDB cite Cheng & Pareddy, ID#60893 but I can’t find this reference. Not sure where the descriptions came from. Can’t actually find any references to stylar ridge on WOS. There are no annotations to these terms in the PO.

Dehiscence zone

fruit dehiscence zone (PO:0004707) and anther dehiscence zone (PO:0005011) have no is_a parents. Suggest new term dehiscence zone. New term for mosses, capsule annulus, could also go here.

Current definitions:

fruit dehiscence zone (PO:0004707): A narrow band of cells that extends along the dehiscent fruit's dehiscence region which upon fruit maturation by drying, undergoes cell separation. This allows the valves to detach from the replum and for the seeds to be dispersed. [GR:pj, TAIR. Comment: Found in deshiscent fruit.

anther dehiscence zone (PO:0005011): A narrow band of cells that extends along the entire length of the anther. This site is observed as an indentation between the locules of each theca. Upon anther maturation, cell separation within the dehiscence zone allows the anther wall to break and for pollen to be released. [PMID:15319479]

Proposed definitions:

dehiscence zone: A portion of plant tissue that is part of a plant structure and consists of a narrow band of cells that undergoes cell separation upon maturation of the structure.

fruit dehiscence zone: A dehiscence zone that is part of a fruit. Comment: Upon fruit maturation by drying, undergoes cell separation, allowing the valves to detach from the replum and seeds to be dispersed.

anther dehiscence zone: A dehiscence zone that is part of an anther. Comment: Extends along the entire length of the anther and is observed as an indentation between the locules of each theca. Upon anther maturation, cell separation within the dehiscence zone allows the anther wall to break open and pollen to be released. [PMID:15319479]

capsule annulus (new term): A dehiscence zone that is part of a capsule, located at the base of an operculum. Synonym: capsule dehiscence zone Comment: Upon capsule maturation, cell separation in the annulus allows the operculum to separate from the capsule, aiding in spore dispersal.

New children for portion of plant tissue

The following terms have no is_a parents. Suggest making them children of portion of plant tissue, with the approprate part_of relations (most part_of relations already exist).

protective layer (PO:0006212): The layer of cells in the abscission zone that have lignin and suberin depositions and are found on the axial side of the break or exposed surface of abscission. [ISBN:0122151704]

part_of abscision zone

Proposed new def: A portion of plant tissue composed of a layer in the abscission zone that have lignin and suberin depositions and are found on the axial side of the break or exposed surface of abscission.

root cap (PO:00020123): A group of cells that covers the apical meristem of the root. [APWeb:Glossary]

part_of root

Proposed new def: A portion of plant tissue composed of a group of cells that covers the apical meristem of the root.

elongation zone (PO:0020125): The portion of the root that includes small, densely cytoplasmic cells that are dividing and expanding in size. [GR:pj]

synonym "region of cell elongation" RELATED []:

synonym "region of radial enlargement" RELATED []:

part_of root

Proposed new def: A portion of plant tissue that is part of the root and includes small, densely cytoplasmic cells that are dividing and expanding in size.

central root cap (PO:0020130): The central part of a root cap in which the cells are arranged in longitudinal files. [GR:pj]

synonym "columella cells" RELATED []:

part_of PO:0020123 root cap

Proposed new def: A portion of plant tissue that is the central part of a root cap in which the cells are arranged in longitudinal files.

lateral root cap (PO:0020131): The part of the root cap that is parallel to the sides of the axis." [ISBN:0122151704]

synonym "peripheral cells" RELATED []:

part_of PO:0020123 root cap

Proposed new def: A portion of plant tissue that is the part of a root cap and is parallel to the axis.

differentiation zone (PO:20135, alt_id PO:3002): The portion of the root located behind the elongation zone containing cells that are differentiating into their final form and function. [GR:pj]

synonym "maturation zone" RELATED []:

synonym "specialization zone" RELATED []:

part_of root

Proposed new def: A portion of plant tissue that is the part of a root and is located behind the elongation zone and contains cells that are differentiating into their final form and function.

quiescent center (PO:20149): Hemispherically shaped aggregation of mitotically and metabolically inactive cells positioned behind the root cap. [ISBN:0122151704]

part_of root

Proposed new def: A portion of plant tissue that is part of a root and contains hemispherically shaped aggregation of mitotically and metabolically inactive cells positioned behind the root cap.

Other Items:

*Question from Daniel Lang <daniel.lang@biologie.uni-freiburg.de> (to Pankaj Sept 2009)

Looking for estimates of the number of cell types and the number of different tissue types in the gametophytic and sporophytic generations of the following angiosperms:

Arabidopsis lyrata, Arabidopsis thaliana, Carica papaya, Glycine max, Medicago truncatula, Populus trichocarpa, Ricinus communis, Vitis vinifera, Oryza sativa, Sorghum bicolor and Zea mays (current estimate: total 100 cell types) See details in 10-6 meeting

Has anyone responded to him? Dennis and Ramona should report back at this meeting.

• Setting up conference call with Bruce Kirchoff to discuss the Plant Ontology and the issues he raised at the Botany Meeting

See details of his comments in 10-6 meeting.

This was scheduled to be done after Sept 20th, so we should probably decide when we want to do it.

Laurel can set up a Doodle poll?? Who wants to take part?