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?
Items from 6-23-10 Conf Call
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.
Tuber PO:0004543 (tuber)
On the 6-23 conference call, everyone agreed that tuber is_a stem,not a shoot.
proposed def'n: A swollen or enlarged storage stem with determinate growth.
This would encompass both subterranean and aerial tubers.
- Tuber epidermis (PO:0025046): proposed def'n: A portion of stem epidermis that is part of a tuber.
- 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
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
Can we close these items? We will work on the definitions of stem and shoot tomorrow morning.
hypodermis and endodermis
During the POC conference call on 6-23-10, it was decided that endodermis and hypodermis should be part_of cortex, but we needed to change the definition of cortex to allow this. Barry suggested that we define the parent terms as the maximal portion of a tissue, then the child terms can be part_of.
cortex (PO:0005708): A maximal portion of ground tissue between the vascular system and the epidermis in a plant.
hypodermis (PO:0005051): 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)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, for instance: embryo cortex, stem cortex, and several others then must also be defined as is_a ground tissue that is part_of cortex.
