Minutes and Agenda 2-23-10

Agenda for the POC Conference Call 2-23-10

Items for discussion: 1.Discuss the Plant Structure parent terms that were defined at the meeting in Ithaca- these have been posted on Sourceforge for people to comment:

• plant cell

def: An anatomical structure that is or was part of a plant and that has as its parts a maximally connected lumen, the contents of this lumen and the surrounding cell wall.

New def: ...is a cell, which is the basic functional unit of a plant, and that has as its parts a maximally connected lumen, the contents of this lumen and the surrounding plant cell wall. Comments: applies to living or dead cells

Note: There is no "lumen" term in GO- so it should be added. Raven, Evert and Eichhorn define the lumen as: "the space bounded by the cell wall". Def: maximally connected lumen ?? is there a simpler way to word this?

• plant organ

def: "A maximal anatomical structure which is a proper part of a plant and which derives from a single ontogenetic event and includes as parts portions of tissues of at least two different types. Examples: stem, leaf, root."

New def: -is an anatomical structure that is a functional unit, is a proper part of a plant and includes portions of tissues of at least two different types which derive from a common developmental path.

(reworded slightly for readability)

Comments: May include individual cell types that are not part of tissues. example: stomatal cells which are part of the leaf, "proper" refers to not being the whole plant Examples: stem, leaf, root

Note: in 2-11-10 talk, Barry Smith suggested having child terms of plant organ: simple, compound and complex plant organs- tabled for next discussion.

• portion of plant tissue

def: "An anatomical structure in a plant that consists of cells and intracellular matrix." comment: See Esau on simple and compound tissue. **This still needs to be fixed.

New def: -is an anatomical structure in a plant that consists of one or more cell types, organized into a structural and functional unit, and may include an intercellular matrix.

Comment: intercellular matrix- def: middle lamella- "layer of intercellular (between the cells) chiefly, pectic substances, cementing together the primary walls of contiguous cells ( ref: Evert, 3rd ed 2006)

2. Whole plant was redefined as "A plant structure which is a whole organism." and gametophyte and sporophyte were moved under it.

There was much discussion about this one and several good points were raised: -Does this include single-celled plants? Can something be a plant cell and a whole plant? (Chris made a comment about disjoints in OBO-Edit- not too sure about this) - PJ- problem of having some terms that should be under both gametophyte and sporophyte- example is a leaf like structure- phyllome. Also, root-like structures eg. rhizoids -also the problem of having term inflation if all the plant structures have to be qualified as either gametophytic or sporophytic - gametophyte and sporophyte are really phases of development not plant structures, although botanists are used to referring to the "gametophyte and sporophyte" -should gametophyte and sporophyte actually be siblings of 'whole plant', so that terms like microphyll can have multiple parentages. - there was discussion about actually dissolving the gametophyte and sporophyte terms, but we decided not to disrupt the ontology right now and do the following: -move all terms that are currently under gametophyte and sporophyte under whole plant, - then worry about populating gametophyte and sporophyte with specific terms - figure out how to cross reference between the PO Structure and Development ontologies.

Note: Make sure that gametophytic stage and sporophytic stage are defined in the developmental stage ontology.

3. in vitro cultured cell, tissue and organ was moved out the Plant Structure class and made a separate class. def: "Isolated and grown plant protoplast, cell, tissue and organ, involving, as a common factor, growth of microbe-free plant material in sterile environment, such as sterilized nutrient medium in a test tube or petri dish." -tabled for next discussion.

4. New parent terms proposed by Ramona:

• cardinal organ part

def: A plant structure that is a direct or immediate part of an organ that is often maximal(?) but is smaller than the organ itself. Examples include lobe, operculum, neck, petiole?, leaflet. -tabled for next discussion.

• collective plant structure

A plant structure that is composed of multiple organs but is not an organ. (Maybe something about a bona fide boundary, some way to distinguish it from whole plant). Examples: flower, perianth, inflorescence. collective structure or compound organ? -tabled for next discussion.

5. Term request from TAIR for "gamete"- proposed (RW): add gamete to the ontology (is_a parent, plant cell), with sperm cell and egg cell as siblings under a common parent 'gamete'. -tabled for next discussion.

6 Assignment of Term numbers:

We need a set of numbers for the POC curators ( Lol and Ramona, mostly)- existing:

Group identifier range (from-to) TAIR 0000001-0005000 Gramene 0005001-0010000 IRIS-IRRI 0010001-0015000 MaizeGDB 0015001-0020000 UMSL 0020001-0025000

Proposed: 0025000-0030000 PO curators 0030001-0035000 NYBG

7. Next conference call- Tues Mar 2nd at 11 am PST