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". Question: BS 'Does that plant structure term imply a 'specific spatial arrangement' He suggested that based on the FMA definition, it was not necessary to have it in the def'n. We decided to put it in the comment instead. The FMA parent term specifies genetically determined spatial relationship

We should check how PS is defined in terms of the "genetically-determined spatial relationships"

BS: Is it true that the POPT is such that the surrounding boundaries are not genetically determined, but the POPT is going to be filling out the space left by the surrounding structures whose boundaries are genetically determined? And the spatial boundaries are not genetically determined. After reconsidering, BS stated that the FMA specifies a determinate shape and inherent boundaries in the named (maximal) portion of tissues. Tissue has its own shape and boundary, according to the FMA

We agreed that this was true in general, although we would probably have to look at each instance as there are a long list of is_a children

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

From FMA: "A portion of plant tissue is an anatomical structure that has as its parts cells of predominantly one type...and consists predominantly of similarly specialized cells, with or without cells of other types and intercellular matrix"

We agreed that in plants the POPT often is composed of more that one type of cells, such as xylem and phloem, with varying composition, depending on their position in the plant.

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

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.

For the terms in the list below, we will remove the part_of relations to whole plant, since "Plant structure already gives you the info you need and it is part of the definition, so you do not need to assert this relationship, it can be inferred (BS)

RW: We wouldn't infer the part_of whole plant relations for things like plant cell or plant tissue, because they are not true for every instance, but we could infer that they are, were, or were derived from a whole plant.

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"?

We will leave it as it is, for now

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?

Comments about the VS: BS: Are there other systems in plants: No, plants do not have analogous systems to the skeletal or integumentary systems in animals,

There are shoot system and root system, which are both collective plant structures (composed of two or more organs and any associated portions of plant tissue).

VS is defined differently than the other structures "includes the totality of of vascular tissue in their specific arrangement in a whole plant or in a constituent part thereof. Contains other types of cells, (covered in comment) and also includes the "holes" or connections to the exterior environment.

PJ: should VS be a sibling of the root system or shoot system? (No, not a collective plant structure), but we should have shoot VS and root VS etc.

Response: We have 14 direct is_a children of vascular system: for anther, cotyledon*, embryo*, filament, hypocotyl*, leaf lamina, petiole, phyllome, root, scutellar*, shoot axis, shoot system*, stigma. (I think filament vs should be part_of anther VS).

Do all of these satisfy the part_of whole plant rule? What if these organs are no longer part of a whole plant?

From PJ: shoot VS- parts of vascular system, do we have all the lower terms such as shoot system xylem, SS phloem etc? Do we need them? shoot xylem and shoot phloem and all the lower terms: - is this the current situation?

We decided that the VS would have to stay as a part of the whole plant, as a result of the way it is defined.

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

*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

PO:0000034:vascular system (should also be included in this list)

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 between the upper level terms above and we should also include the vascular system. Whole plant should be disjoint_from all the above, except for plant cell, in vitro plant structure and embryonic plant structure (since it includes embryo).

BS: You should add the disjoints where ever you are sure of it. Owl does not assume any disjointness, so it is 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.

new revised comment: 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.

PJ: callus parenchyma cells are different from regular parenchyma cells, so we should have separate terms for them. All agreed; will be is_a parenchyma cell; part_of plant callus

These definitions were accepted.

- Do we need a term such as in planta callus as parallel/sibling to the cultured one? We decided that any annotations for in planta callus should go to plant callus.

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

Is this a phenotypic descriptor or a developmental stage?

PJ: A callus is made competent by addition of PGR

These two terms might be better described as growth stages of a callus in the PGDSO, but since they aren't there yet, we will keep them in the PAO for now. Need to add comment that makes it clear that it is the treatment of the callus that determines whether or not they are organogenic or embryogenic.

add comment: a plant callus that has been treated to form an organ/ an embryo

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 ?

Definition okay. Should use derived_from leaf, since there is no way of knowing what kind of cell it came from, if the whole leaf was ground up.

*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.

Definitions okay. Should be derived_from root.

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:

• on 4-12-11 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

need to revise the def'n: Proposed revised def'n: A plant embryo derived directly from nucellus cells without involving embryo sac cells

is this always true? Will check on it

Comments on plant embryo: BS: The word 'early' is quite vague, can we say pre-seedling stage?

PJ: need to have terms for: zygotic embryo- the one in the seed and also haploid embryo- child of cultured embryo. Do they ever form in nature? Check on

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] Italic text 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

PJ: We should we have a cultured zygotic embryo, any annotation to cultured ZE should go there

*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.

new proposed def’n: A plant embryo arising from previously differentiated somatic cells in vitro, rather than from the zygote or from gametes.

is_a: plant embryo

from 4-12-11: 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 above.

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.

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

embryo proper (PO:0000001)

scutellum (PO:0020110)

suspensor (PO:0020108)

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

(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

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

coleoptile (PO:0020033)

coleorhiza (PO:0020034)

hypocotyl (PO:0020100)

epicotyl (PO:0020035)

mesocotyl (PO:0020037)

hypocotyl-root junction PO:0004724

plumule(PO:0020032)

scutellar node (PO:0004708)

embryonic root (PO:0000045)

radicle (PO:0020031)

embryonic leaf (PO:0006338)

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