POC Conf. Call 11-10-10

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

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Barry Smith (University at Buffalo, NY), Justin Preece (OSU), Alejandra Gandolfo, (Cornell University), Justin Elser (OSU)

Absent: Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab),

Collaborators: none

Acceptance of the minutes from the Friday, November 5th and Saturday, November 6th meeting?

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

Minutes are in italics below each agenda item.

Agenda:

Review of Changes discussed at the NYBG Meeting:

Restructuring of PGDSO

The goal here was to fix the top level terms and their definitions so we can incorporate all plants

Issues:

• Definition of top-level term: plant growth and development stage

• Where should gametophytic phase and sporophytic phase be? Should there be a class 'plant life cycle phase'?

• How to add plant structure and whole plant growth stages for non-angiosperms:

Friday Nov. 5th: - Barry gave a brief presentation of the structure of the Basic Formal Ontology (BFO), and how it is divided into occurants and continuants, with dependent and independent continuants. (see ppt File:BFO for Plants.pdf

-In the PSO, plant structures (plant anatomical entities) are Independent Continuants (corresponding to the GO cellular component) and the plant processes (plant life cycle process) are the occurrents, corresponding to the GO Biological processes. He felt that the current structure, based on stages as continuants, was not correct.

Points of discussion:

-What is a whole plant?

We decided that zygote and spore were also whole plants, however, if we are going to remove other whole-plant phases of the plant life cycle (like seedling and gametophyte), it may be inconsistent to include structures like zygote, embryo or spore.

-Splitting the PSO into adult and embryonic plant structures:

Other anatomy ontologies (such as FMA) have dealt with the problem of embryonic or developing structures by only including adult structures. There are special problems with plants, in that the same plant can contain both adult and embryonic structures.

-Creating a separate branch of the PSO for reproductive plant structures and vegetative plant structures:

We felt it might be better to leave those divisions at lower ontology levels, like we currently have for reproductive shoot system. Could add new terms like reproductive organ or reproductive cell. Still under consideration.

-Do we need to include a term like 'whole plant collective structure' (may not be best name) to deal with structures like seeds that contain parts of multiple individuals?

-Adding a category for embryonic growth stages to the PGDSO:

Suggested New "working" Structure of the PGDSO:

• The root term, plant growth and development stage, would be renamed 'plant life cycle process' (an "Occurrent").

The top level structure would have three branches, as below

-Add corresponding phases for each of the developmental processes.

For example: gametophytic phase corresponds to gametophyte development and leaf development phase could correspond to leaf development.

Then it would be possible to move the developmental processes to GO, but keep the phases in PO.

We reviewed this proposed structure, and decided to experiment with how it will work for existing PGDSO terms. Barry suggested that his goal was to have all PO terms in one of two branches: plant structures (plant anatomical entity = independent continuant) and plant processes (plant life cycle process = occurent)

Lol and Ramona will work on moving all of the ~120 terms from the PGDSO into one of the three new plant life cycle process branches, to see where they can fit. Can delete existing relations for those terms, but will still be able to compare to old structure by comparing dev to live browser. Will schedule a meeting with Barry next week to go over any problems or issues that may come up, then present the results to the whole group on our meeting on Dec. 1

Note from BS: Keep in mind where there might be potential overlaps with the GO- we will need to figure out how to split the process terms, ie: will they reside in the PO or in GO? Make a list as we go along.

-Stage term names need to be rewritten as nouns, for example: "whole plant in the phase where 1 leaf is visible'

-Complex terms could be rendered using post coordination; ie: 'on the fly' for users, but some may need to have actual PO IDs in order to accommodate annotations.

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

We will add two new terms: unicelluar trichome, is_a epidermal cell, and multicellular trichome, is_a portion of epidermal tissue

These terms will replace the existing term trichome (PO:0000282), which should be made obsolete.

We will 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.

We have the term trichome cell (PO:0008031), part_of trichome, has no is_a parent.

Suggest that it is_ a epidermal cell. It can have the child unicellular trichome, but then we could also use trichome cell to describe individual cells that are part of a multicellular trichome.

To deal with the term trichome branch (PO:0008031), we will need the new term multicellular trichome branch cell, is_a trichome cell. We will put a comment under unicellular trichome that the branches of a branched unicellular trichome are part of GO.

Suggested definitions:

trichome cell (PO:0008030): An epidermal cell that is part of a unicellular or multicellular trichome.

New def'n: A plant cell that is part of a trichome.

trichome cell is a plant cell that develops from an epidermal cell, not is_a epidermal cell.

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.

Having trichome cell defined as a cell that is part of a unicellular trichome, and unicellular trichome as a trichome cell creates a circularity. Instead, we will make unicellular trichome a narrow synonym of trichome cell.

unicellular trichome: An trichome cell that forms an outgrowth from the epidermis. Comment: Can vary in size and shape and may be branched. See unicellular trichome branch (GO:xxxxxxx). Synonyms: hair, scale

Won't use this term (see above)

multicellular trichome: A portion of epidermial tissue that forms an outgrowth from the epidermis and is not sclerified. Can vary in size and complexity. May contain a secretory gland.

new def: A portion of plant tissue that forms an outgrowth from the epidermis and is not sclerified.

Can't use epidermal tissue, instead develops from an epidermal cell. (could not find a term similar to trichoblast for shoot trichome development)

multicellular trichome branch: A trichome cell that forms a branch of a multicellular trichome. Comment: For branches of a unicellular trichome, see unicellular trichome branch (GO:xxxxxxx).

The items below were postponed until next week's discussion

This structure will require some reorganization of existing trichomes:

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.

We have terms for leaf trichome (PO:0006504), seed hair (PO:0004511), and shoot axis trichome (PO:0005003). We will need to split each of these into unicellular and multicellular terms, children of unicellular or multicellular trichome.

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: The items below were postponed until next week's discussion

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

Other Items: Open Source forge tracker items, user requests

See the minutes from Friday, November 5th for details of the discussion on the following items:

-embryo:

-egg cell and sperm cell

-Reorganization of shoot system: vegetative shoot system and how it overlaps with shoot-borne shoot system (PO:0004545)

-Musa terms requested by Rosemary Shrestha (July 2010)

- See discussion of bud

These items were tabled for next week's discussion

New Item: 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

How do we want to proceed? Should we set up a Webex or Skype meeting?

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.

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

Registration is open, abstract deadline Nov 1, 2010.

-We will have a PAG_2011_Collaborators_Workshop and meeting with collaborators. We will also present a computer demonstration and poster. We will also be part of an Outreach booth being organized by MaizeGBD.

-Laurel has been invited to take part in the Plant Phenotypes panel discussion.

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, Nov. 17th, 2010 at 10am PST

Alejandra gone from Nov 19-Dec 9th.