POC Conf. Call 5-22-12

POC meeting, Webex Conference Call; Date: Tuesday May 22nd, 2012 10am PDT/1pm EDT

In attendance:

POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_5-8-12?

Back to POC Meetings Minutes

Open Items from Past Meetings:

ovule

At the POC meeting on 4-17-12, we agreed to make ovule a plant organ, instead of a cardinal organ part. It may be part of carpel, which is a plant organ, but we already have other examples of organs that are part of other organs (e.g., nucellus and pollen sac).

Also, ovule is currently part_of ovary, but that is only true for angiosperms. Ovules can be found in all seed plants.

proposed def., ovule (PO:0020003): A plant organ (PO:0009008) that has as parts a nucellus (PO:0020020) containing a female gametophyte (PO:0025279), one or two integuments (PO:0020021), and a funicle (PO:0020006).

comment: A seed (PO:0009010) develops from an ovule. In angiosperms, an ovule is located in an ovary (PO:0009072). In gymnosperms, an ovule is located on an ovuliferous bract (add term).

PJ requested separate subtypes for ovarian ovule and non-ovarian ovule, to make annotation easier. Suggest using ovuliferous scale ovule instead of non-ovarian ovule. See Items_for_future_meetings#ovuliferous_scale.

Antiraphe, chalaza, integument, nucellus, and raphe are part_of ovule. Will need to add comment to each of these saying: "If you are annotating to this structure for an angiosperm, please add an additional annotation to ovarian ovule (PO:id). If you are annotating to this structure for an gymnosperm, please add an additional annotation to ovuliferous scale ovule (PO:id)."

Root primordia and roots

lateral root

lateral root (PO:0020121), current def.: A root that develops from a lateral root primordium located in the pericycle layer of a primary root.

proposed def.: A root (PO:0009005) that develops from a lateral root primordium (PO:0000016) that is part of another root.

comment: A lateral root primordium may develops on any root, including a primary root (PO:0020127), on an existing lateral root (PO:0020121), or a shoot-borne root (PO:0000042) . In seed plants, a lateral root primordium generally develops from pericycle cells (PO:0025261), but cells of an endodermis (PO:0000252) may also participate in its formation in some species. In ferns, lateral root primordia develop from the endodermis.

root anlagen

Root anlagen is_a portion of pericycle tissue, but this is not always true. Lateral roots can also develop from endodermis, and shoot-borne root develop from parenchyma cells on a stem or branch (or elsewhere).

New proposed definition for root anlagen (PO:0025433): A portion of plant tissue (PO:0009007 that is committed to the development of a root primordium (PO:0005029).

Comment: Only detectable by gene expression, not morphology. May arise in a pericycle (PO:0006203), as the lateral root of in most seed plants, an endodermis (PO:0000252), as in ferns, or from parenchyma cells (PO:0000074) that are part a shoot axis (PO:0025029), in the case of a basal root (PO:0025002) or shoot-borne root (PO:0000042).

root primordium

root primordium (PO:0005029), new def.: A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005).

Comment: Root primordia may arise from pericycle cells (PO:0025261), as in most seed plants, cells of an endodermis (PO:0000252), as in ferns, or from cells on a shoot axis (PO:0025029), in the case of basal root primordia (PO:0025479) and shoot-borne root primordia (PO:0025480). Transition from root primordium to root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147).

ref.: Steves and Sussex, ISBN:0521288959, POC:curators

added root primordium develops from root anlagen (PO:0025433).

adventitious root primordium (PO:0008038): We don't actually have a term for adventitious root. This term has been obsoleted. There are no annotations on adventitious root primordium.

basal root primordium, new term (PO:0025479): A root primordium (PO:0005029) that is committed to the development of a basal root (PO:0025002).

comment: Transition from basal root primordium to basal root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147).

synonym: adventitious root primordium (broad)

added basal root develops_from basal root primordium

shoot-borne root primordium, new term (PO:0025480): A root primordium (PO:0005029) that is committed to the development of a shoot-borne root (PO:0000042).

comment: Transition from shoot-borne root primordium to shoot-borne root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147).

synonym: adventitious root primordium (broad)

added shoot-borne root develops_from shoot-borne root primordium

lateral root primordium (PO:0000016), existing def.: A root primordium that is derived from a root pericycle and will develop into a lateral root.

lateral root primordium (PO:0000016), proposed def.: A root primordium (PO:0005029) that is committed to the development of a lateral root (PO:0020121).

comment: In seed plants, a lateral root primordium generally develops from pericycle cells (PO:0025261), but cells of an endodermis (PO:0000252) may also participate in the formation of a lateral root primordium in some species, and in ferns lateral root primordia develop from the endodermis. Transition from lateral root primordium to lateral root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147), which can occur before the lateral root penetrates the exterior of the parent root.

>Removed the relation lateral root primordium develops_from pericycle (PO:0006203), because it is not always true.

>Added relation lateral root primordium part_of root, because that is what makes it a lateral root primorodium.

ovule

At the POC meeting on 4-17-12, we agreed to make ovule a plant organ, instead of a cardinal organ part. It may be part of carpel, which is a plant organ, but we already have other examples of organs that are part of other organs (e.g., nucellus and pollen sac).

Also, ovule is currently part_of ovary, but that is only true for angiosperms. Ovules can be found in all seed plants.

proposed def., ovule (PO:0020003): A plant organ (PO:0009008) that has as parts a nucellus (PO:0020020) containing a female gametophyte (PO:0025279), one or two integuments (PO:0020021), and a funicle (PO:0020006).

comment: A seed (PO:0009010) develops from an ovule. In angiosperms, an ovule is located in an ovary (PO:0009072). In gymnosperms, an ovule is located on an ovuliferous bract (add term).

PJ requested separate subtypes for ovarian ovule and non-ovarian ovule, to make annotation easier. Suggest using ovuliferous scale ovule instead of non-ovarian ovule. See Items_for_future_meetings#ovuliferous_scale.

Antiraphe, chalaza, integument, nucellus, and raphe are part_of ovule. Will need to add comment to each of these saying: "If you are annotating to this structure for an angiosperm, please add an additional annotation to ovarian ovule (PO:id). If you are annotating to this structure for an gymnosperm, please add an additional annotation to ovuliferous scale ovule (PO:id)."