POC Conf. Call 4-14-11

POC meeting, Webex Conference Call; Date: Thursday April 14th, 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), Justin Preece (OSU), Justin Elser (OSU)

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

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_4-12-11? There were no changes additions or deletions.

Issues arising from the last meeting:

portion of plant tissue (PO:0009007)

proposed def'n (from 4-12-11 meeting):A multicellular plant structure which consists predominantly of similarly specialized cells of one or more types.

Comment: A portion of plant tissue may contain one or several types of cells that 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.

Suggested revisions: Proposed new def'n: A plant structure that consists predominantly of similarly specialized cells of one or more types in a specific spatial arrangement.

Comment: A portion of plant tissue may contain one or several types of cells that are organized into a structural unit (which includes a mass of callus) and may include an intercellular matrix. May include other types of isolated cells, such as idioblasts.

- On dev: Added disjoint_from cardinal organ part, removed the part_of whole plant relation, so we can include cultured callus (see below)

We discussed whether or not it was necessary/correct to specify "a specific spatial arrangement". BS suggested that based on the FMA definition, it was not. We decided to put it in the comment instead

Proposed revised def'n: A plant structure that consists predominantly of similarly specialized cells of one or more types.

Comment: A portion of plant tissue may contain one or several types of cells that are organized in a specific spatial arrangement into a structural unit (which includes a mass of callus) and may include an intercellular matrix. May include other types of isolated cells, such as idioblasts.

Note: we will create the term idioblasts, since we are referring to it

Removing the part_of relationships to whole plant?

We are proposing removing the part_of relationships to whole plant, as it is redundant based on the definition of plant structure and excludes any plant structures that are no longer part of the whole plant (such as plant cells in wood, eyes in a potato tuber, tissue in a cut flower, etc).

What are the advantages/disadvantages to having these all rooted in whole plant?

We discussed whether or not having the part_of relationship to whole plant was incorrect and/or redundant. Consensus was that the definitions were sufficient as stated. Since not every instance of plant cell, plant tissue, etc. is part of a whole plant, it is not correct to use the part_of relation.

plant structure (PO:0009011): An anatomical structure that is or was part of a plant, or was derived from a part of a plant. [source: CARO:0000003, POC:curators]

Comment: 'Part' includes both proper parts and the whole plant.

Anatomical structure (CARO:0000003): Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome.

All the children of plant structure are defined (except for plant cell*) as " A plant structure...." so therefore they are already part of a plant and can also include entities that were derived from a plant (such as the in vitro structures) or plant material such as wood, which is no longer part of a whole plant.

part_of children of whole plant

collective plant structure (PO:0025007): A plant structure that is a proper part of a plant and is composed of two or more organs and any associated portions of plant tissue.

collective organ part structure (PO:0025269): A plant structure composed of two or more cardinal organ parts from adjacent organs and any associated portions of plant tissue.

plant organ (PO:0009008): A plant structure that is a functional unit, is a proper part of a plant, and includes portions of tissues of at least two different types that derive from a common developmental path.

portion of plant tissue (PO:0009007)(proposed def'n from above): A plant structure that consists predominantly of similarly specialized cells of one or more types in a specific spatial arrangement.

plant cell (PO:0009002) (Revised def'n: 4-12-11): A cell which is a plant structure. maybe this should be "A plant structure which is cell"?

vascular system (PO:0000034): A plant structure that includes the totality of the portions of vascular tissue in their specific arrangement in a whole plant or in a constituent part thereof.

Should vascular system stay as part of whole plant? Maybe not. what about the vascular system in a cut flower in a vase?

• removed part_of relationship between plant cell and POPT in dev version #1066

add comments on vascular system and other plant systems

*PO:0000003 : whole plant is_a children:

PO:0009010 : seed

PO:0009009 : embryo

PO:0020092 : megagametophyte

PO:0020091 : microgametophyte

PO:0030027 : thallus

Adding mutual disjoint from relations among top-level PAO terms

RW: Based on recent internal email exchange in the POC, I suggest that we add mutual disjoint_from relations among the following top-level terms of the PAO:

PO:0025001 : cardinal organ part

PO:0025007 : collective plant structure

PO:0025269 : collective organ part structure

PO:0009002 : plant cell

PO:0009008 : plant organ

PO:0009007 : portion of plant tissue

Note: intentionally left out: PO:0025099: embryonic plant structure, PO:0000282: trichome, PO:0000034: vascular system and in vitro plant structure

I don't think PO:0025007: whole plant should be in the list, because there are times when a plant cell or an in vitro plant structure is a whole plant. Perhaps whole plant should be disjoint_from cardinal organ part, collective plant structure, plant organ and portion of plant tissue.

All agreed to adding the disjoint relations. BS said that it was best practice to add any disjoint relations that are always true, and we should be adding them as we go along.

Continuation of in vitro plant structures from the last meeting:

From the POC Conf call 4-12-11:

plant callus (PO:0005052): A portion of plant tissue that consists of mass of undifferentiated plant cells.

revised comment: Consists primarily of parenchyma cells but may contain other cell types as the callus begins to differentiate. May be formed as a result of wounding or may develop in in vitro culture.

cultured plant callus (PO:0000009): A plant callus grown or maintained in vitro.

revised comment: Cultured plant callus consists primarily of parenchyma cells, but may contain other cell types as the callus begins to differentiate. After supplementation with the appropriate plant growth regulators, further differentiation may lead to the development of plant tissues, plant organs and ultimately a whole plant.

Do we need a term such as in planta callus as parallel/sibling to the cultured one?

children of cultured plant callus

* embryogenic callus (PO:0006091)

current def'n: A type of cultured callus that form embryo-like structures such as somatic embryos. [source: POC:curators]

proposed def'n: A cultured plant callus that forms somatic embryos.

*organogenic callus (PO:0006090)

current def'n: A type of cultured callus that has competence to form any organ such as root, leaf, shoot, leafless shoot or bare stem, etc.

proposed def'n: A cultured plant callus that forms plant organs.

The problem I see with both of these terms is how do you determine when and if a 'cultured plant callus' is an embryogenic callus or a organogenic callus? I think these are redundant, based on the new def'n of cultured plant callus. But these are terms used in the literature.

The cultured plant callus is induced to form plant organs by externally applied plant growth regulators.

Proposed solution: Merge these two terms into cultured plant callus

Cultured plant cell and its children

*cultured plant cell (formerly cultured cell) (PO:0000005)

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

is_a plant cell, is_a in vitro plant structure

Comment: Includes isolated plant cells and small plant cell aggregates that proliferate while suspended in sterile liquid medium or spread on a solid agar medium.

*leaf-derived cultured plant cell (formerly cultured leaf cell) (PO:0000007):

Current Def’n: In vitro grown isolated cells and small cell aggregates that originated from isolated leaf protoplasts (after they re-established cell wall, or from callus that was induced from leaf tissue).

Proposed def’n: A cultured plant cell that was derived from leaf tissue.

proposed Comment: May be derived from cultured plant callus or plant protoplast induced from a segment of leaf. In the case of the plant protoplast, after the re-establishment plant cell walls.

is_a cultured plant cell, derives_from leaf mesophyll

problem: we do not have the term leaf cell, should it be leaf-mesophyll-derived cultured plant cell ?

*root-derived cultured plant cell (formerly cultured root cell) (PO:0000008):

current def’n: In vitro grown isolated cells and small cell aggregates that originated from isolated protoplasts after they re-established cell wall, or from callus that was induced from segment of root

Proposed new def’n: A cultured plant cell that was derived from root tissue.

Comment: The root-derived cultured plant cell may be derived from isolated protoplasts after the cell wall is re-established or from callus that was induced from a segment of root.

Currently has 3 annotations to it

Note: Made root-derived cultured plant cell (PO:0000008) derives_from root parenchyma and leaf-derived cultured plant cell derives_from leaf mesophyll.

plant embryo (PO:0009009)

current definition: A whole plant in the post-zygotic stage that does not yet consist of fully differentiated tissues.

Comment: Adventitious embryos and somatic embryos do not arise from zygotes. Cultured embryos (PO:0000010), including haploid embryos, are in vitro plant structures. Embryos occur prior to germination in vascular plants.

This is not really consistent with the fact that we have tissues like embryonic epidermis and embryonic cortex.

Logically, an embryo could be treated like a sporophyte or gametophyte, that is, a whole plant in the embryonic life cycle phase. However, since we don't have embryonic phase yet, and so much research is done on embryos, it seems appropriate to pre-compose the term embryo and use that for now.

Proposed definition of plant embryo: A whole plant in the early part of a sporophytic phase after the first cell division.

Comment: An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. In seed plants, the embryonic phase ends with germination. In non-seed plants and cultured embryos of seed plants, the end of the embryonic phase is less clearly defined and varies among taxa.

Other issues:

Adventitious embryos, somatic embryos, embryos that arise through apogamy, and cultured haploid embryos, embryos cannot be considered in the sporophytic phase (as it it defined now), since they are not the product of fertilization.

Suggest that we rework the definition of sporophytic phase with a comment about apogamy. see below:

• PJ suggested we could add zygotic and haploid embryo as children of embryo.

adventitious embryo (PO:0004537): Embryo derived directly from nucellus cells without involving embryo sac cells

cultured embryos

*cultured plant embryo (PO:0000010):

Current Def’n: In vitro isolated and maintained mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte). [source: TAIR:ki]

Comment: None

Rename: cultured plant embryo (PO:0000010)

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

Comment: Includes isolated and maintained mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte).

parentage: is_a plant embryo (PO:0009009) and is_a in vitro plant structure

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

Current Def’n: An embryo arising from previously differentiated somatic cells in vitro, rather than from fused haploid gametes, i.e., zygote.

Proposed def’n: A plant somatic embryo that is grown or maintained in vitro.

is_a: plant somatic embryo??

If cultured plant embryo is to be a child of embryo, we will need to adjust definition of embryo. Should talk to Melissa Haendel about how they handle haploid and diploid embryos in Zebrafish.

See new proposed definition of embryo below.

embryonic plant structures

Definition of embryonic plant structure:

embryonic plant structure (PO:0025099): A plant structure that is part of an embryo.

Comment: Includes organs, tissues and cell types that are unique to embryos, not plant structures that can occur in both embryos and mature plant structures.

Changed definition from "proper part of" to "part of", so it would be consistent with the intersection of term. Think part_of is better anyway, because technically an embryo is an embryonic plant structure.

Some terms were left as is_a children of embryonic plant structure:

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

Both now have cross-product definitions, and no asserted is_a children

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

is_a embryonic plant structure, intersection_of: is_a plant cell, intersection_of: part_of embryo

Made apical cell (PO:0004000, now embryonic apical cell) is_a apical cell part_of embryo (still dev_from zygote). Should probably obsolete and replace with new term to avoid confusion

Made basal cell (PO:0002002, now embryonic basal cell) is_a plant cell, part of embryo (still dev_from zygote)

Made hypophysis (PO:0020109, now embryonic hypophysis) is_a plant cell, part_of embryo.

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

is_a embryonic plant structure, intersection_of: is_a portion of plant tissue, intersection_of: part_of embryo

Should we add the portion of prefix to the name?

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) are now inferred children of embryonic plant tissue.

Technically, we could get rid of the is_a embryonic plant structure relation for both, because it would be inferred, but is makes it easier to work with the reasoner off when the relations are there.

Here is a picture of some plant tissues, to show how it works:

Proposed changes/questions for structures that were is_a 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. [APWeb:Glossary]

We do not have the term cotyledonary sheath in the PO, and, according to Beentje (the Kew Plant Glossary), the coleoptile is the cotyledonary sheath. Also, the coleoptile persists after germination, so it is not an embryonic plant structure. According to Esau, the coleoptile has stomata, which means it has an epidermis, and this consists of two or more tissue types. This makes it a plant organ, even though many authors casually refer to it as a tissue.

Proposed definition: A plant organ (phyllome?) that surrounds the plumule of an embryo or the emerging shoot apex of a seedling. [ISBN:9781842464229, ISBN: 0471244554]

Comment: Found in grasses. Develops at the first node above the scutellum, and thus is often thought to be the first leaf. Protects the emerging shoot system as it grows through the soil.

coleorhiza (PO:0020034): A portion of plant tissue surrounding the radicle in the embryo or seedling of some monocots. [APWeb:Glossary]

Currently part_of embryo, but it is also part of the seedling. It develops in the embryo, but persists after germination to protect the embryonic root. Suggest removing part_of plant embryo relation. The coleorhiza, like the coleoptile, has an epidermis (and root hairs), and thus should be classified as a plant organ, even though many authors casually refer to it as a tissue.

Proposed definition: A plant organ that surrounds the radicle in the embryo and seedling.

Comment: Found in grasses and some other monocots. Protects the emerging embryonic root.

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

currently is_a cardinal organ part, propose is_a stem internode (we didn't have this term before but do now)

Proposed definition: A stem internode that is the part of a stem below the cotyledonary node and transitional to a root.

is_a stem internode

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]

currently is_a embryonic plant structure, propose is_a stem internode (PO:0005005). Also, the second part of the current definition only adds ambiguity. Need to define it more precisely.

Proposed definition: The first stem internode above a hypocotyl. [Esau]

Comment: The epicotyl is the first internode of the stem above the cotyledons.

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

This definition sounds like the same thing as an epicotyl. Esau says the mesocotyl is the plant axis between the scutellum and the coleoptile and that in grasses, the scutellum is generally thought to represent the cotyledon and the coleoptile to represent the first leaf. In that case, the mesocotyl (as the axis between the scutellum and the coleoptile), is analogous (or homologous) to the epicotyl in dicots and other monocots. In grasses, the hypocotyl is not visible, except perhaps as the scutellar node.

For a picture, see http://www.agry.purdue.edu/ext/corn/news/timeless/GerminationEvents.html

Proposed definition: A shoot internode that is the part of an embryo axis or the stem of a seedling above the scutellum and below the coleoptile. [Easu]

Comment: Occurs in grasses. In grasses, the hypocotyl and cotyledon may not be visible and may be represented by the scutellar node and scutellum, making the mesocotyl similar to the epicotyl in other taxa. Elongation of the mesocotyl during seedling growth pushes the coleoptile above the soil surface.

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

Moved to is_a cardinal organ part. Will automatically be is_a embryonic plant structure b/c it is part of embryonic axis. May want to remove this relation. The hypocotyl-root junction remains after germination.

Proposed definition: A cardinal organ part that is the part of a plant axis where the radicle joins the hypocotyl.

Proposed synonym: transition zone (Bell and Bryan 2008, and others)

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.

made is_a terminal bud, part_of embryo

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]

Sounds like it should be is_a stem node. Also, the region between the primary root and the plumule contains the mesocotyl as well as the scutellar node.

Proposed definition: A stem node that is the part of an embryo axis directly above the radicle where the scutellum is attached.

Comment: Found in grasses, where no hypocotyl is present. The scutellar node may represent a reduced hopocotyl and cotelydonary node.

is_a stem node, part_of embryo axis

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

Propose that this should be is_a root instead of is_a embryonic plant structure, b/c it is not necessarily part of an embryo.

Proposed definition: A root that is initiated in a developing embryo.

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. is_a embryonic root [APWeb:Glossary]

Proposed definition: An embryonic root that is the basal continuation of a hypocotyl in an embryo and may develop into the root system of an adult plant.

Comment: Sometimes abortive.

remove part_of embryo axis, because it persists after germination.

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

Is this an embryonic plant structure, that is, is it always part of the embryo?

Proposed definition: A vascular leaf that is one of the first few leaves to develop from the embryonic shoot apical meristem and is part of an embryo.

is_a vascular leaf,

Should this really be part_of embryo? Do these leaves persist after germination?

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