POC Conf. Call 11-17-10

POC meeting, Webex Conference Call; Date: Wednesday Nov 17th, 2010 10am (PST)

In attendance:

POC members:

Absent:

Collaborators: none

Acceptance of the minutes from the POC Conf. Call 11-10-10?

Review of Changes discussed at the previous meetings:

Trichomes (Approval of changes from 11-5, 11-6, and 11-10)

We currently have the term trichome (PO:0000282), but it is problematic, because trichomes can be plant cells or portions of tissue (multicellular trichomes).

At the POC meeting on 11-10-2010, we decided to keep this term, but it will be an abbreviation (sort of synonym) for both unicellular trichome and multicellular trichome. is_a parent will be plant structure for now.

Proposed definition: A unicellular or multicellular plant structure that forms a non-sclerified outgrowth from the epidermis. Comment: This class is the union of unicellular trichome [synonym of trichome cell (PO:0008030)] and multicellular trichome (PO:newterm).

The term trichome cell (PO:0008030) currently has no is_a parent. Suggest is_a plant cell.

Proposed def: A plant cell that is part of a trichome. develops_from epidermal cell, part_of epidermis

unicellular trichome will be a narrow synonym of this trichome cell (can't have unicellular trichome is_a trichome cell -- will lead to circularity)

comment: A branch of a unicellular trichome is a GO sub-cellular component (put in dbxref after we request the term).

Will also add new term multicellular trichome.

Proposed def: A portion of plant tissue that forms a non-sclerified outgrowth from the epidermis. Comment: Can vary in size and complexity. May contain a secretory gland. is_a portion of plant tissue, develops_from epidermal cell.

Should it also have an is_a relation to trichome (PO:0000282)? This will lead to multiple parentage. Have an xp relation or put in comment?

Suggest that we obsolete the term trichome branch (PO:0008031), request term unicellular trichome branch in GO (see above), and add new term multicellular trichome branch cell

suggested def: A trichome cell that forms a branch of a multicellular trichome. is_a trichome cell

Comment: For branches of a unicellular trichome, see unicellular trichome branch (GO:xxxxxxx).

NOTE: Is it okay to say trichome is part_of epidermis (most people think of it that way)?

-Epidermis is currently defined as 'A portion of plant tissue composed of epidermal cells that develops from the protoderm and covers the surface of a plant structure.' -May need to tweek this definition slightly to allow trichomes to have part_of relation to epidermis. Maybe just add comment that epidermis can contain trichomes and stomatal pores.

Related terms that require some changes:

Secretory trichome (PO:0004509): A trichome that secretes or sequesters a substance, should be redefined as: A multicellular trichome that secretes or sequesters a plant body substance.

Non-secretory trichome (PO:0004510) should be made obsolete, as it is synonymous with unicellular or multicellular trichome. Make it a synonym of trichome.

Root hair (PO:0000256) currently is_a epidermal cell. Shoud it be is_a trichome or is_a trichome cell?

We have terms for leaf trichome (PO:0006504), seed hair (PO:0004511), and shoot axis trichome (PO:0005003). If we keep the bin term trichome, then each of these terms can be a child of that, rather than having to create unicellular and multicellular children.

Related terms without is a parents:

coma (PO:0020061): A tuft of hairs at one end of a seed. [APWeb:Glossary], synonym: brush RELATED []

suggested definition: A portion of epidermal tissue composed of unicelluar or multicellular trichomes at the end of a seed.

papillae (PO:0002001): A soft protuberance on an epidermal cell of the stigma." [ISBN:0471245208], subset: reference

Several suggestions: 1. should not only be defined as on stigma, since such protuberances can occur on other organs. 2. should be single (papilla). 3. Is a part of a cell, so outside the domain of PO. Request term in GO.

We can also add the following new terms that have been requested by Austing Mast (legumes) and/or Traitnet, or are related to trichomes:

[https://sourceforge.net/tracker/index.php?func=detail&aid=3040048&group_id=76834&atid=835555 prickle: suggested def: A portion of epidermal tissue that is a pointed, sclerified outgrowth of the epidermis. Comment: often found on stems and leaves.

thorn: Could add as narrow synonym of branch, with comment that a thorn is a short, pointed woody structure, derived from a branch.

Alternatively, could add new phenotype term (xp with PATO) thorn: A branch that is short (PATO:0000574), woody (need to request term), and pointed (PATO:0002258).

spine: leaf spine is_a leaf, stipule spine is_a stipule. Could add as synonyms, or make new phenotype terms.

leaf spine: A modified leaf that is short (PATO:0000574), roughly cylindrical (PATO:0001873), and pointed (PATO:0002258).

stipule spine: A modified stipule that is short (PATO:0000574), roughly cylindrical (PATO:0001873), and pointed (PATO:0002258).

Pores (Approval of changes from 11-5)

New top level term (sibling to plant structure) called plant anatomical space. This term would be parent to pore and slit. This would allow us to add new terms for slits or fissures as they come up.

Suggested definitions:

plant anatomical space: An anatomical space (CARO:0000005) that is part of a plant.

Ref. anatomical space (CARO:0000005): Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.

pore: A plant anatomical space that is roughly circular and forms an opening in a plant structure.

slit: A plant anatomical space that is roughly linear and forms an opening in a plant structure.

This will allow us to create is_a parents for the following terms:

micropyle (PO:0020025): "A small canal or opening through the integument(s) at the apex of an ovule." [APWeb:Glossary] comment: In a mature seed the micropyle may remain visible as an occluded pore or may be obliterated. The micropyle originates as an opening in the integuments of an ovule through which the pollen tube usually enters the embryo sac. subset: reference

Suggested def: A pore that forms an opening in the integuments at the apex of an ovule. part_of integument. Comment: The micropyle originates as an opening in the integuments of an ovule through which the pollen tube usually enters the embryo sac. In a mature seed the micropyle may remain visible as an occluded pore or may be obliterated.

seed micropyle (PO:0006334): "A pore on the seed coat which is a remnant of the ovular micropyle." [GR:pj] relationship: develops_from PO:0020025 ! micropyle. Part_of seed coat

Current definition is okay

stomatal pore (PO:0008032): "The space of variable size controlled by stomatal guard cells in response to environmental clues." [GR:cwt] synonym: "stomatal aperture" RELATED [] relationship: part_of PO:0002000 ! stomatal complex

Suggested def: A pore in an epidermis, flanked by two guard cells. Comment: The size of the stomatal pore is variable and controlled by movement of the guard cells in response to environmental cues. part_of stomatal complex

floral stomatal pore (PO:0008046): "The space of variable size controlled by floral stomatal guard cells in response to environmental clues." [GR:cwt] relationship: part_of PO:0008044 ! floral stomatal complex

Suggested def: A stomatal pore that is part of a floral stomatal complex. part_of floral stomatal complex

stomium (PO:0020101): "A fissure or pore in the anther lobe through which the pollen is released." [GR:pj] subset: reference, relationship: part_of PO:0005011 ! anther dehiscence zone

Suggested def: A slit in an anther lobe formed from when a dehiscence zone dehisces. Comment: Pollen may be released through the stomium. part_of anther

anther pore (requested by TraitNet)

Suggested def: A pore at the apex of an anther. Comment: Pollen may be released through the anther pore. part_of anther

These items were tabled for next week's discussion

Plant body substance/portion of plant substance

Last week, we discussed adding a new upper level term for plant body substances. Perhaps a more consistent name would be portion of plant substance. Possible children: Latex, xylem sap, phloem sap, resin, mucilage, oil, cuticle, cutin, sporopollenin. We can add the upper level term now, but suggest waiting to populate it, as this is not a priority for this release.

Suggested definition: plant body substance: A portion of organism substance that is or was part of a plant.

Ref.: portion of organism substance CARO:0000004): Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.

These items were tabled for next week's discussion

Upcoming meetings 2010-2011:

• Infectious Disease Ontology Workshop

Dallas, Dec. 8th and 9th, 2010

Organized by Lindsay Cowall (Duke University) and others, under the auspices of the National Center for Biomedical Ontology. IDO Workshop December 2010. Note that relations between the IDO and other ontologies is one of their provisional goals.

Pankaj will represent the PO with regard to plant infectious diseases. This is especially relevant to the PO as infectious disease agents (viruses and bacteria) are widely used in plant genetic research.

For additional information on the IDO see http://www.infectiousdiseaseontology.org/Home.html

• Plant and Animal Genome XIX Conference

January 15-19, 2011 PAG 2011

PO Activities at PAG: -PAG_2011_Collaborators_Workshop and meeting with collaborators

-Computer demonstration and poster

-Outreach booth being organized by MaizeGBD.

-Plant Phenotypes panel discussion (Laurel)

Laurel, Ramona, DWS and Justin Preece are attending. PJ may attend for the weekend only as he is teaching. Alejandra cannot attend.

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Dennis and Alejandra are planning to attend IBC2011 and speak in other symposia.

Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the genetics, genomics and bioinformatics theme.

Ramona contacted the organizers about whether or not it is possible to get a room with Internet for outreach activities, but hasn't gotten a response yet. Is this something we still want to pursue?

Pankaj, Ramona, and Angelica Cibrian (Harvard and ANMH, Genomics of Seed Plants) are scheduled to give talks. Three additional speakers will be chosen from abstracts that are submitted.

Pankaj will give the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona will present the talk on the Plant Ontology, and abstracts have been submitted.

Next meeting scheduled for Weds, Dec. 1st, 2010 at 10am PST

Have a wonderful Thanksgiving!