POC Conf. Call 6-29-10

POC meeting, Webex Conference Call; Date: June 29th, 2010 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the 6-23-10 meeting? All in favor?

Workshop page: [Corvallis Workshop June 29th and 30th, 2010]

Agenda for June 29th Conference Call:

The main goals of the meeting will be ontology development and preparation for a release, along with focused training on annotating genes and mappings.

*Curators discussion: Determine priorities for next release of PO:

1. Date of next release? July 2010?

-What needs to be done before this release?

2. Is top level of Plant Structure ontology ready to go? -Review of top level terms

-Review of second level terms

-Should structures have part_of relations (to whole plant, sporophyte or gametophyte) whenever possible?

-Do we want to keep in vitro structures or send to OBI?

3. Status and goals for is_a completeness (Ramona can report)

- 136 terms without is_a parents

Based on definitions:

-73 of these terms have obvious parents (many of them some kind of portion of plant tissue)

-11 more terms could be assigned parents if new terms were created

-15 terms could be assinged parents with some consideration

-36 terms need discussion to determine parent terms (no obvious parent)

4. Should we aim to complete one branch of the ontology? For Example: leaves, in vitro terms or plant cells, specific type- axial cells for example hydroids and leptoids?

5. Changing lower-level terms to include cross products and genus-differentia definitions.

-How much can be done before release

6. Goals and timetable for the next release:

fall 2010?

1.bud (PO:0000055)

All of the grand-children of bud . See SF tracker item for explanation and suggestions. This issue came up while working on the terms for tuber eye.

At 6-23-10 conference call, we decided to make only 'axillary bud' and 'terminal bud' direct children of bud to eliminate the problem of dual parentage.

Added new terms: terminal reproductive bud (PO:0025071) and axillary reproductive bud (PO:0025072).

This will allow annotations of reproductive buds from non-flowering plants and 'terminal floral bud' and 'axillary floral bud' will be children of these terms Therefore, the terms 'floral bud', 'vegetative bud' and 'inflorescence bud' were obsoleted.

2. Tuber PO:0004543 (tuber is a what?)

Current def'n: Swollen storage shoot with determinate growth.

6-23 It was agreed by all present that tuber is_a stem,not a shoot.

From SF after the call: proposed def'n: A swollen or enlarged storage stem with determinate growth.

This would encompass both subterranean and aerial tubers.

• Aerial tuber epidermis (PO:0025047): A portion of tuber epidermis that is part of an aerial tuber.

• Subterranean tuber epidermis (PO:0025048): A tuber epidermis that is part of a subterranean tuber.

Comment: The skin of young potatoes is epidermis while the skin of mature potatoes is periderm. Related syn.: potato skin

LC: I am leaving this one open till we complete the tuber is_a stem discussion.

3. tuber epidermis

New terms to deal with tuber epidermis:

• Tuber periderm (PO:0025043): A portion of stem periderm that is part of a tuber.

• Aerial tuber periderm (PO:0025044): A portion of tuber periderm that is part of an aerial tuber.

• Subterranean tuber periderm (PO:0025045): A portion of tuber periderm that is part of a subterranean tuber. Comment: The skin of young potatoes is epidermis while the skin of mature potatoes is periderm. Narrow syn.: potato skin

• Tuber epidermis (PO:0025046): A portion of shoot epidermis that is part of a tuber.

proposed def'n: A portion of stem epidermis that is part of a tuber.

Probably, this should read 'A portion of stem epidermis...', but right now, a tuber is_a shoot, and not a stem. Need to decide which it is: see below.

hypodermis and endodermis

should be is_a ground tissue, part_of cortex.

RW suggests that both of these terms should be is_a 'cortex', rather than part_of 'cortex' (see SF tracker item for explanation).

During the POC conference call on 6-23-10, it was decided that endodermis and hypodermis should be part_of cortex, but we will need to change the definition of cortex to allow this.

cortex (PO:0005708): The proposed new def'n will be: A maximal portion of ground tissue between the vascular system and the epidermis in a plant.

For hypodermis, endodermis, and similar terms (like perimedullary zone), Barry suggested that we define the parent terms as the maximal portion of a tissue, then the child terms can be part of.

hypodermis (PO:0005051): Current def'n: The outermost layer of a portion of cortex. A layer or layers of cells beneath the epidermis that is distinct in appearance from adjacent tissues.

Proposed def'n: A portion of ground tissue that is the outermost layer of a portion of cortex. comment:A layer or layers of cells beneath the epidermis that is distinct in appearance from adjacent tissues.

endodermis: (PO:0000252) Current def'n: The innermost layer of a portion of cortex. The layer of tissue forming a sheath around the vascular region and often having a casparian strip in its anticlinal walls; it may have secondary walls later.

Proposed def'n: A portion of ground tissue that is the inner most layer of a cortex and has a casparian strip in its anticlinal cell walls. Comment: Forms a sheath around the vascular system. It may have secondary walls later, part_of cortex

Other types of cortex, like stem cortex, then must also be defined as is_a ground tissue that is part_of cortex.

I will leave these open for now, until these changes are reviewed next week.