POC Conf. Call 4-12-11

POC meeting, Webex Conference Call; Date: Tuesday April 12th, 2011 10am (PDT)

In attendance:

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

Absent: Dennis Stevenson (NYBG), Justin Elser (OSU), Chris Mungall (Lawrence Berkeley National Lab), Justin Preece (OSU)

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_4-5-11? There were no changes additions or deletions.

Items arising from last week's meeting:

plant cell:(PO:0009002)

Current def’n: A cell that is part of a plant and that has as its parts a plant cell wall. [source: GO:0005623, ISBN:0471245208, POC:curators]

Comment: Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid). Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". See definition of plant-type cell wall GO:0009505. Egg and sperm cells lack the cell wall.

Proposed def’n: 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. [source: POC:curators, GO:0005623]

Comment: Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid). Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". See definition of plant-type cell wall GO:0009505. Egg and sperm cells lack the cell wall.

-By using 'plant structure' we cover any cells are are or were parts of a plant, plus it makes it in the g-d format.

Proposed new def’n: A cell which is a plant structure. [source: POC:curators, GO:0005623]

Add to the comment: Includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall.

plant-type cell wall: GO:0009505 exact: cellulose and pectin-containing cell wall

Def'n: A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances.

There was an extensive discussion about how to define the plant cell and we decided to continue the use of the GO term "cell" as the genus term, and add the differentia, "which is a plant structure". We looked at the GO def'n of plant type cell wall to ensure it was not introducing circularity. We agreed to remove" Egg and sperm cells lack the cell wall." from the comment. This definition should work well for cultured cells, as well.

portion of plant tissue (PO:0009007)

current definition: A plant structure that has as its parts multiple cells and is a proper part of an organ. [source: POC:curators, TAIR:lr]

Comment: These cells are organized into a structural unit, and may include an intercellular matrix.

There are several problems with this definition:

-It does not exclude cardinal organ parts.

-Saying that it is a proper part of an organ does not work for cultured callus or for tissues in plants that don't have any organs (like a protonema or thallus).

Also: it is not consistent with our definition of plant structure which is "an anatomical structure that is or was part of a plant."

From FMA: "...consists predominantly of similarly specialized cells, with or without cells of other types and intercellular matrix"

From CARO:0000043 (also used by TAO): "Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships."

Proposed definition: A plant anatomical structure that has as its parts multiple cells of the same type(s) aggregated according to genetically determined spatial relationships.

Comment: A portion of plant tissue may contain one or several types of cells. These cells are organized into a structural unit and may include an intercellular matrix. May include other types of isolated cells, such as idioblasts in parenchyma tissue.

There was an extensive discussion about this class and how to include the requisite features and also differentiate it from the cardinal organ part.

new proposed def'n: A multicellular plant structure which consists predominantly of similarly specialized cells of one or more types.

-Should add disjoint_from cardinal organ part.

-Need to remove the part_of whole plant relation, so we can include cultured callus (see below).

In vitro plant structures

We agreed last week that the in vitro structures should be children of their respective plant structure parents (cell, tissue, and embryo). This required a little revision on some of the terms (see below). Also, removed part_of relationships to whole plant between plant cell and portion of plant tissue.- redundant

After much searching and discussion with developers of the other ontologies (details are available, but don't want to take up the whole meeting with them), we decided it was better to just keep "in vitro plant structure" and use a textual definition and assert dual parentage to it. This was after consultation with PATO, OBI, and GO, specifically CM.

* in vitro plant structure(PO:0000004):

Current definition: A plant structure that was derived from part of a plant and involves microbe-free growth in a sterile environment.

Proposed new def’n: A plant structure that is grown or maintained in vitro.

Comment: In vitro growth is defined as microbe-free growth in a sterile, culture environment, usually in the laboratory. An example of a sterile culture environment is growth on or in a nutrient medium in a Petri dish, culture flask or test tube. Microbes may be intentionally added to the culture environment, such as in co-culture with Agrobacterium.

All were in favor of the proposed definition and comment. Accepted and closed

• cultured protoplast(PO:0000006):

Current Def’n: In vitro isolated cells from which the entire cell wall has been enzymatically removed.

Propose renaming: plant protoplast (PO:0000006) ('cultured' is redundant here)

Proposed def’n: A cultured plant cell from which the entire plant cell wall has been removed.

-is_a cultured plant cell, (based on the revised plant cell definition above), and is_a in vitro plant structure

Comment: The cell wall is generally removed using polysaccharide-degrading enzymes such as cellulase, pectinase and /or xylanase.

Note: The cultured plant cell may be in suspension culture or from callus culture on solid media

We discussed whether or not it made sense to have two terms "cultured plant protoplast" and "plant protoplast" to differentiate protoplasts that were maintained for long periods of time in culture, but we decided that this probably was covered by the definition as written. Plus, it would be difficult to distinguish between them on a temporal basis (ie: at what point does one become the other?). Maybe could add "cultured plant protoplast" later as needed.

PJ supplied a couple of citations as evidence of longer term culture of plant protoplasts for our reference: Cultured Equisetum protoplasts and Kaur et al, 2006

Comment from DWS on SF: "Ok. I just wanted to be sure that we do not want to include gametes. I do (not) know for sure but I do not think sperm have a plasmalemma. Eggs do have a plasmalemma and cytoplasm. However, for plants the notion of naturally occurring makes sense to me.

* callus (PO:0005052)

We need to revise the definition of this term as it currently covers the cultured callus as well. Current definition: A tissue formed as a result of wounding, or a tissue developing in a tissue culture. [source: GR:pj]

parentage: >> parenchyma >> portion of ground tissue >> portion of plant tissue

We discussed this on last weeks POC conference call 4-5-11 POC_Conf._Call_4-5-11

Renamed "plant callus". Discussed the proposed new definition should refer to the generic case of the callus and the "cultured plant callus" should be a child of it. Will make it only a child of "is_a portion of plant tissue", rather than specifying parenchymatous tissue

Proposed new def'n: A portion of plant tissue that consists of mass of undifferentiated plant cells

* cultured plant callus (PO:0000009):

Current Def’n: In vitro grown cell aggregates that originated from isolated protoplasts, cell suspensions, or from callus that was induced in sterile medium supplemented by plant growth regulators.

Comment: None

cultured callus (PO:0000009): (Rename cultured plant callus?) yes

Proposed def’n: An in vitro plant structure consisting of a mass of undifferentiated plant cells.

Comment: Cultured callus may originate from isolated protoplasts, cell suspensions or from callus that was induced in sterile medium supplemented by plant growth regulators. Plant cell calluses may be made to differentiate into the specialized tissues of a whole plant, with the addition of a number of hormones or enzymes.

has_part cultured plant cells, is_a in_vitro plant structure

Proposed new def’n: A plant callus grown or maintained in vitro.

is_a plant callus, is_a in_vitro plant structure, has_part cultured plant cells

proposed slightly modified existing comment: Cultured plant callus may induced to form from plant protoplasts or cultured plant cells in suspension culture. After supplementation with the appropriate plant growth regulators, further differentiation may lead to the development of plant tissues and ultimately a whole plant.

---

Tabled for discussion at the next meeting, please see: POC_Conf._Call_4-14-11 for details

Cultured cells

* cultured cell (PO:0000005):

* cultured root cell (PO:0000008): Proposed new name: root-derived cultured plant cell

* cultured leaf cell (PO:0000007); Proposed new name: leaf-derived cultured plant cell:

Cultured embryos

*cultured plant embryo (PO:0000010):

*cultured somatic embryo: (PO:0000011): Child of cultured plant embryo

Children of embryonic plant structure:

coleoptile (PO:0020033): A tubular embryonic plant structure developed at the junction of the cotyledonary sheath with the seedling axis, and surrounding the plumule of a monocot embryo or seedling.

embryo proper(PO:0000001): An embryonic plant structure that is the body of a developing embryo attached to the maternal tissue in an ovule by a suspensor.

scutellum (PO:0020110): An embryonic plant structure that is a more or less shield-shaped and absorptive portion of an embryo of Poaceae.

suspensor (PO:0020108): An embryonic plant structure at the base of an embryo that develops from a basal cell and connects an embryo proper to the wall of a megagametophyte.

New definitions for embryonic plant cells and tissues

embryonic plant cell (PO:0025028): A plant cell that is part of an embryo.

apical cell (PO:0004000)

basal cell (PO:0002002)

hypophysis (PO:0020109)

(portion of) embryonic plant tissue(PO:0025233): A portion of plant tissue that is part of an embryo.

New inferred children of embryonic plant tissue:

coleorhiza (PO:0020034), embryo cortex (PO:0005014), embryo epidermis (PO:0005015), embryonic shoot apical meristem (PO:0006362), epiblast (PO:0020036), scutellar epithelium (PO:0008048), and scutellum epidermis (PO:0006049)

Proposed changes/questions for structures that were is_a embryonic plant structure:

embryonic leaf (PO:0006338): One of the first few leaves to develop from the embryonic shoot apical meristem [GR:pj].

embryonic root(PO:0000045): An embryonic plant structure that is a root that is initiated in a developing embryo. [TAIR:ki]

radicle (PO:0020031): The radicle is the basal continuation of the hypocotyl in an embryo and gives rise to the root system of the adult plant; sometimes more or less abortive.

hypocotyl (PO:0020100): The part of the stem below the cotyledonary node and transitional to a root, found in a young sporophyte. [APWeb:Glossary]

epicotyl (PO:0020035): The first internode of a stem above the hypocotyl. In literature also used for the entire embryonic axis, consisting of several internodes, above the cotyledonary node. [APWeb:Glossary]

mesocotyl (PO:0020037): The internode between the cotyledon or cotyledons and the leaf or leaves at the next node of a young sporophyte.

hypocotyl-root junction (PO:0004724): A cardinal organ part that is the part of an embryonic axis where the radicle joins the hypocotyl.

plumule(PO:0020032): A somewhat differentiated terminal bud in several embryo types above the cotyledonary node, in which one or more internodes and leaves or scales can be discerned in a primordial stage.

scutellar node (PO:0004708): The region in of an embryo axis between the primary root (enclosed in the coleorhiza) and the plumule (enclosed in the coleoptile) to which the scutellum is attached. [MaizeGDB:lv]

Other items:

*Changing the namespace from Plant Structure Ontology (PSO) to Plant Anatomy Ontology (PAO) This was discussed at the POC_Conf._Call_3-29-11

Action taken: -LC talked with CM, we all agreed that it would not be too much of an issue to do so.

-Change was made in the plant_ontology.OBO development file, version #1068 and on the SourceForge term tracker "group"

-Still needs to be changed on the PO webpage and in other spots where the individual files are linked to (such as Bioportal)- so it should also change in those places.

-Will also need to be changed on the AmiGO Browser (eg search page)- how difficult is this?

Upcoming meetings 2011:

2011 Semantic Web Workshop June 6th and 7th, Santa Fe, NM.

Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.

-JE and JP will be attending

-JE has already worked with Damian to implement a SSWAP web service for PO terms, so further collaboration with him and iPlant will benefit the POC going forward.

For more Workshop details: Semantic web.

* ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York

ICBO

LC is coorganizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.

Full-Day Workshops Schedule:

July 26 9am-6pm The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies

July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability

July 26 6.30pm-9pm Evening Workshop: Common Logic

July 27 4pm-8pm Evening Workshop: Doctoral and Post-Doctoral Consortium

- LC will attend and represent the PO. Invite other plant people?

*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn

Plant Biology 2011

Early-bird registration ends May 13.

Gramene will be putting together a workshop again, focusing on pathways. PJ will present a PO poster.

For inclusion on the program memory stick and in the program book, abstracts must be submitted by May 27.

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30.

Dennis, Alejandra, Pankaj and Ramona are planning to attend.

See IBC 2011 Bio-Ontologies Symposium wiki page for more details