POC Conf. Call 11-10-10

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

In attendance:

POC members:

Absent:

Collaborators: none

Acceptance of the minutes from the 11-5-2010 and 11-6-2010 meeting?

Agenda: In progress...

Restructuring of PGDSO

On 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. The PSO covers independent occurents. He suggested that the life cycle of a plant is a continuant that contains phases, and that the current structure, based on stages as continuants, was not correct.

There was some discussion of what is a whole plant, and 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.

There was a discussion of 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. We discussed the possibility of creating a separate branch of the PSO for reproductive plant structures and vegetative plant structures, but 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.

We discussed the possible 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.

We need to add a category for embryonic growth stages to the PGDSO

There was a discussion of a major restructuring of the PGDSO:

The root term, plant growth and development stage, would be renamed plant life cycle process (a continuant).

The top level structure would have three branches, as below (this is an example, not a final, agreed-upon structure):

Plant life cycle process

>plant life cycle phase (phases in a plant life cycle)

>>gametophytic phase

>>sporphytic phase

>>>embryonic phase

>>>vegetative growth phase

>>>reproductive phase

>plant life cycle phase transition (the landmarks that mark the transitions from one phase to another)

>>>meiosis

>>>fertilization

>>>etc.

>plant structure development (these are biological processes, and may be better in GO, or maybe only put top level terms in GO with more detail in PO)

>>plant organ development (e.g. leaf or root development)

>>plant tissue development (maybe)

>>collective plant structure development (e.g. flower or inflorescence development)

>>whole plant development

>>>gametophyte development

>>>sporophyte development

(See also dev browser)

It should be possible to add corresponding phases for each of the developmental processes. For example, gametophytic phase corresponds to gametophyte development, and leave 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.

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?

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 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.

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

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 be contain a secretory gland.

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).

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.

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.

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:

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

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.

Next meeting

Weds Nov 10th- Barry cannot attend

Next meeting scheduled fro Nov. x 2010 at xx