POC Conf. Call 11-17-10

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

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG)

Absent: Alejandra Gandolfo; (Cornell University), Barry Smith (University at Buffalo, NY), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: none

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

There were no additions, deletions or changes to the minutes of the last meeting.

Review of Changes discussed at the previous meetings:

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

• trichome (PO:0000282), is problematic, because trichomes can be plant cells or portions of tissue (multicellular trichomes).

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

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.

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

Proposed def'n: 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).

• multicellular trichome- will be added as a new term

Proposed def'n: 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.

Definitions above were approved.

Question: Should multicellular trichome (PO:newterm) also have an is_a relation to trichome (PO:0000282)? This will lead to multiple parentage.

A unicellular trichome is also a trichome, but we can't put an is_a relation between trichome cell and trichome, because not all trichome cells are trichomes, but we could put part_of relation. That way all annotations would group under trichome. Have an xp relation or put in comment?

Will add is_a relation for multicellular trichome, part_of relation for trichome cell. We decided that in this case the dual is_a parentage was biologically necessary.

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'n: 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).

Above changes were approved. RW: Added comment: 'consider multicellular trichome branch cell' to obsolete trichome branch.

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 tweak 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.

yes. Add comment to epidermis. LC added comment: "Epidermis can also include 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 portion of plant substance.

Change primary name to glandular trichome, secretory trichome is synonym.

Glandular trichome (PO:0004509): new def'n: A  trichome that secretes or sequesters a portion of plant substance.

added synonym: secretory trichome (narrow)

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

Merge with trichome, made non-secretory trichome a synonym of trichome (PO:0000282), added narrow synonyms 'unicellular non-secretory trichome' and 'multicellular non-secretory trichome for trichome cell and multicellular trichome.

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

No. Should be is_a root epidermal cell. (made new terms root epidermal cell (PO:0025164) and shoot epidermal cell (PO:0025165)).

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.

Okay

Note: make seed trichome primary name for PO:0004511, seed hair as exact synonym; add pubescence as related synonym of seed trichome.

The more specific sub-terms can be post-compositionally created or we can add them as needed by our users

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 plant tissue that contains multiple trichomes and is located at the end of a seed.

proposed new def'n: A portion of seed coat epidermis that consists of multiple seed trichomes at the micropyle.

(add seed epidermis as synonym of seed coat epidermis)

• 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

Create new PO term papilla cell, with child stigma papilla cell (analogous to root hair cell and epidermal cell). (RW: should also add leaf papilla cell, since papilla are common there). Request papilla and stigma papilla to GO.

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

• prickle

suggested def'n: A portion of epidermal tissue that is a pointed, sclerified outgrowth of the epidermis.

new def'n: A portion of epidermis that is a sclerified outgrowth.

Comment: often found on stems and leaves.

new children: root prickle and shoot axis prickle- define accordingly

• 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).

def'n: A branch that is a sclerified, pointed outgrowth. Comment A thorn is a short, pointed (PATO:0002258) woody structure, may be branched.

• spine:

leaf spine is_a leaf, stipule spine is_a stipule.

Could add as synonyms, or make new phenotype terms.

spine leaf: is_a leaf new def'n: A leaf that is a sclerified and pointed (PATO:0002258) and lacks a lamina.

comments: none

spine stipule: A stipule that is sclerified and pointed (PATO:0002258).

stipule (PO:0020041): new def'n: A phyllome that is one of (usually) a pair of appendages at a leaf base.

Comment: take out the existing one about monocot leaves

Pores and anatomical space (Approval of changes from 11-5)

Postponed for future meeting

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.

At the last meeting, Barry suggested that we have only two branches in the ontology (one for independent continuants and one for occurants). Should we make a new tope level term plant anatomical entity, which would be parent to plant structure, plant anatomical space, and portion of plant substance (see below)? See dev browser for proposed structure.

Suggested def: An anatomical entity that is or was part of a plant. [source: CARO:0000000, POC:rw]. Comment: Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces.

Children of plant anatomical space:

• pore (PO:0025118): A plant anatomical space that is roughly circular and forms an opening in a plant structure.

• slitNew term,

proposed def'n: 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'n: 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

Proposed def'n: 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

Proposed def'n: 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)

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

Plant body substance/portion of plant substance

Postponed for future meeting

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.

Primordium, approval of changes from 10-5-10

Postponed for future meeting

At the POC meeting on 11-5-2010, we agreed to add the new term primordium, child of portion of plant tissue.

Proposed def: A portion of plant tissue that differentiates and develops from meristem tissue into a new plant structure.

There was some discussion of whether or not we should keep the comment "A visible primordium of an organ is the first distinct stage of the respective organ development.

Have deleted is_a relations between primordia and the structures they develop into and replaced with develops_from relations (e.g., leaf develops from leaf primordium).

Although we have the term adventitious root primordium, can’t add adventitious root develops form adventitious root primordium, b/c adventitious root is a synonym for several terms.

Also added new term: phyllome primordium, which is parent to leaf primordium, petal primordium, etc.

Parts of root tip (continued from meeting on 10-26-10)

Postponed for future meeting

Proposed new parent term: root parenchyma (PO:0025095): A portion of parenchyma tissue that is part of a root system.

root cap: PO:0020123

original def: "A group of cells that covers the apical meristem of the root." [APWeb:Glossary], subset: reference

Suggest: is_a root parenchyma

Proposed definition: A portion of root parenchyma tissue that is part of the root tip and covers the root apical meristem. Comment: Often composed of living and dead parenchyma cells. Protects the root apical meristem.

central root cap: PO:0020130

original def: "The central part of a root cap in which the cells are arranged in longitudinal files." [GR:pj], synonym: "columella cells" RELATED [] plus columella root cap, relationship: part_of PO:0020123 ! root cap

Suggest: is_a root parenchyma

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

lateral root cap: PO:0020131

original def: "The part of the root cap that is parallel to the sides of the axis." [ISBN:0122151704], synonym: "peripheral cells" RELATED [], relationship: part_of PO:0020123 ! root cap

Suggest: is_a root parenchyma

Proposed definition: A portion of parenchyma tissue that is part of a root cap and is parallel to the sides of a root axis. comment: This is the general term for the lateral portion of any root cap and not the term for a root cap of lateral root (PO:0003018) or lateral root cap of lateral root (PO:0003020).

quiescent center: PO:0020149

original def: "Hemispherically shaped aggregation of mitotically and metabolically inactive cells positioned behind the root cap." [ISBN:0122151704]

Suggest: is_a meristem, part_of root apical meristem

Proposed definition: A hemispherically shaped portion of meristem tissue consisting of mitotically and metabolically inactive cells that is part of the root apical meristem and is positioned behind the root cap.

differentiation zone: PO:0020135, alt_id: PO:0003002

original def: "The portion of the root located behind the elongation zone containing cells that are differentiating into their final form and function." [GR:pj], subset: reference, synonym: "maturation zone" RELATED [], synonym: "specialization zone" RELATED []

Suggest: is_a cardinal organ part, part_of root

Proposed new name: root differentiation zone; Proposed definition: A cardinal organ part 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.

Comment: Most of the primary tissues of a root mature in the differentiation zone. This zone is where root hairs are produced.

Could add new parent term "shoot axis differentiation zone" to be parent to this term and to stem internode differentiation zone (PO:0008042)

elongation zone: PO:0020125

original def: "The portion of the root that includes small, densely cytoplasmic cells that are dividing and expanding in size." [GR:pj], subset: reference, synonym: "region of cell elongation" RELATED [], synonym: "region of radial enlargement" RELATED []

Suggest: obsoleting this term, because the definition is wrong, and making a new term, root elongation zone; is_a cardinal organ part, part_of root tip

Proposed definition: A cardinal organ part that is part of a root that is located directly behind a root apical meristem, in which the cells are undergoing longitudinal expansion.

Comment: The elongation zone is only a few millimeters in length and is the only portion of the root in which cell elongation generally occurs. Root hairs are not yet produced in this region. Primary root tissue begin to differentiate in the root elongation zone.

Could add new parent term "shoot axis elongation zone" to be parent to this term and to stem internode elongation zone (PO:0008041)

Other items

Collaboration with Physco group to cover mosses in PO

Email from Stefan Rensing:

"We have now completely reworked the mapping of bryophyte terms to the new version of the PO. We would be happy to make this mapping available to you on the condition that we will be co-authoring the eventually resulting publication. Would that be ok for you?

Of course, we are willing and interested to continue discussion on this topic, e.g. on how to broaden term definitions that to our opinion are currently too narrow to accommodate bryophytes."

MossOntology wiki

Action: Pankaj will respond to Rensing (copy to po-internal). Lol will invite Rensing or someone from Physco group to present at the PO workshop at PAG. We will not do a meeting at this time.

Pankaj will send email

PlantSystematics.org - follow-up from discussion at NYBG

Postponed for future meeting

Early priorities:

-ask Kevin Nixon to pull out keywords and list of captions and we will map to the PO terms

-Identify missing PO ids or issues in the keywords, such as typos

-correct any problems

-ask KN to add a field to the PS.org data entry page for PO:ID

JE create a script for linking

Searches at PO site as well as PS.org

-add PO id to each term in the PS.org database, add new field, start with new images, work on backlog of images on the site.

If adding lost of images for PO creates data storage issues, we could mirror PS.org database at OSU.

Later priorities:

-set up PO search page. Wait until there are enough PO images populating the site.

-Have a 'public comment' or feedback link on the image page, needs to be moderated.

-create xml files for images, so users can scroll over images or select from menu to see different structures that are part of the same image. Create layers so that only a part of the image is highlighted for each structure. Consider buying a tool for the computer to draw outlines freehand.

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!