POC Conf. Call 4-12-11
POC meeting, Webex Conference Call; Date: Tuesday April 12th, 2011 10am (PDT)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC_Conf._Call_4-5-11?
Items arising from last week's meeting:
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.
- 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 below
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
* cultured cell (PO:0000005):
Renamed: cultured plant 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. In cell cultures, the cells are no longer organized into tissues.
Note: in order to make this is_a plant cell, I had to revise the definition of plant cell, so that it includes cell that are not part of the whole plant.
* 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 new def’n: A plant structure which has as its parts a maximally connected lumen and the contents of this lumen and any external encapsulating structures (if present) such as the plasma membrane and the plant 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.
* cultured root cell (PO:0000008): Proposed new name: root-derived cultured plant cell
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
* cultured leaf cell (PO:0000007); Proposed new name: leaf-derived cultured plant cell:
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.
Comment: 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).
May be derived from an isolated protoplast after the cell wall is re-established or from cultured callus that was induced from a segment of leaf.
*Cultured cell (PO:0000005):' Current Def’n: In vitro grown, isolated cells and small cell aggregates that proliferate while suspended in liquid sterile medium or spread on a solid agar medium. [source: TAIR:ki]
Comment: In cell cultures, the cells are no longer organized into tissues.
Rename: cultured plant cell (PO:0000005)
Proposed def’n: A plant cell that is grown or maintained in vitro.
Comment: Includes isolated cells and small cell aggregates that proliferate while suspended in liquid sterile medium or spread on a solid agar medium. In cell cultures, the cells are no longer organized into tissues. This is class is a cross-product of plant cell (PO:0009002) and in vitro growth ( requested in PATO:000XXXX).
* cultured 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).
This is class is a cross-product of plant embryo (PO:0009009) and in vitro growth ( requested in PATO:000XXXX).
*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.
* cultured callus (PO:0000009): (note:fixed typo in name)
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
Problem: cannot be a portion of plant tissue: (A plant structure that has as its parts multiple cells and is a proper part of an organ).
* Children of cultured plant cell: these are more problematic:
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).
cultured protoplast (PO:0000006):
Current Def’n: In vitro isolated cells from which the entire cell wall has been enzymatically removed.
cultured root cell (PO:0000008):
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. What about a cell from a cultured root?
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What about a whole plant or parts thereof that are grown in culture? Suppose someone had an annotation for a leaf from an in vitro grown plant. Where should they put it?
Also, we talked about using derived_from relations for in vitro structures (e.g., cultured cell derived_from plant cell). Do we still want to do that? How to assure that the derives from relations always hold?
Additional comments on today's discussions on in vitro structures:
PATO may deprecate growth quality branch. Perhaps in vitro growth should go into the Environment Ontology.
LC:Checked ENVO: not appropriate, I think
Checked EO: Has a term laboratory study, in vitro could be an is_a child?
BS pointed out that an in vitro grown plant is still a whole plant, just as fetus grown in a lab is still a fetus. However, there is some utility to distinguishing between in vitro plant structures that are growing ex situ (such as cultured cells or callus) and a plant structure that is part of a whole plant that is growing in vitro. In the latter case, annotations can be made to the plant structure in PO, plus another layer of annotation that describes the environment in which plants are grown.
There is still the grey area of, for example, a root that was induced from a callus in vitro. PJ felt that this should be annotated as a root, with the in vitro culture environment as a separate annotation.
We agreed to the new definition of in vitro plant structure proposed above in principle, but will have to work on exact definition, depending on whether or not we can use the term from another ontology.
We agreed that children of in vitro plant structure should be renamed as above and also be children of their respective plant structure. For example, cultured plant cell should be a child of plant cell (maybe parenchyma cell?).
Definition of portion of plant tissue will have to be revisited to accommodate tissues in plants without organs (like liverworts). Also, need to make sure definition of portion of plant tissue distinguishes it form cardinal organ part. Will either need to remove clause about being a proper part of a plant organ, so that cultured callus can go here, or only make cultured callus a child of in vitro plant structure.
Most in vitro plant structures could have dual parentage (is_a plant cell, tissue, whatever, and is_a in vitro plant structure). Can't use intersection_of terms b/c in vitro growth is not in PO.
We agreed that the children of cultured plant cell need to be renamed and possibly redefined to make it clearer what they are referring to. For example:
cultured leaf cell (PO:0000007) should be named leaf-derived cultured cell. Use this term if we don’t know what part of the leaf it is from. Could have, e.g., leaf-mesophyll-derived cultured cell as a child term.
Definition of cultured plant callus should say "a mass of undifferentiated parenchyma cells.
MAG supplied a definition of callus (in vivo) to insure that it is only composed of parenchyma cells:
>From Eames and MacDaniels-- Introduction to Plant Anatomy
CALLUS: Among the important functions of the cambium is the formation of "callus" or "wound tissue" When wound occur in roots or stems, masses of soft parenchymatous tissue quickly from on or below the injured surface; this tissues is known as callus. Callus may be formed by the division of parenchyma cells on the phloem and the cortex, but its most frequent source is the cambium. The outer cells of this tissue either become suberized themselves or periderm develops within them, so that a protecting bark is formed beneath which the cambium is active and in forming new vascular tissue in the normal way.
On 4/6/2011 DWS commented by email: "This is true of both the cork and vascular cambia, the former also being termed the phellogen".
BS will send paper on how to deal with carcinomas. Solution may be similar for plant callus. See this citation: Smith et al, 2005
Smith, B., Kumar, A., Ceusters, W., and Rosse, C. (2005). On carcinomas and other pathological entities. Comp Funct Genom, 6, 379-387
Need to keep in mind callose, (note: distinct from 'callus') as a substance that is associated with sieve elements.
Callose: definition: A complex branched carbohydrate that is a common wall constituent associated with the sieve areas of sieve elements; may develop in reaction to injury in sieve elements and parenchyma cells. (Raven, Evert and Eichhorn, 4th edition)
From DWS by email: "Callose is not a structure, but rather a compound that occurs in the cell wall as a ring that surrounds the sieve pores. It is electron translucent in TEM. It also occur in the walls of pollen tubes. The plugs in the sieve pores are protein that becomes occlusive as the result a drastic changes in pressure a dure to wounding. The are actually artifacts."
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).
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 idoblasts in parenchyma tissue.
Should add disjoint_from cardinal organ part.
Need to remove the part_of whole plant relation, so we can include cultured callus. Also, it is not consistent with our definition of plant structure which is "an anatomical structure that is or was part of a plant."
removing the part_of relationships to whole plant?
In the current development version of the PO, LC proposed removing the part_of relationships to whole plant, as this seems redundant based on the definition of plant structure (PO:0009011):
Definition: 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. CARO:0000003 anatomical structure is defined as: 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 (new def'n of 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.
*PO:0000003 : whole plant part_of children:
PO:0025007 : collective plant structure: def'n: 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.
PO:0009002 : plant cell: proposed def'n: A plant structure which has as its parts a maximally connected lumen and the contents of this lumen and any external encapsulating structures (if present) such as the plasma membrane and the plant cell wall.
PO:0009008 : plant organ: def'n: 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.
PO:0009007 : portion of plant tissue Old def'n: A plant structure that has as its parts multiple cells and is a proper part of an organ. (see proposed def'n above)
*PO:0000003 : whole plant is_a children:
PO:0009010 : seed
PO:0000034 : vascular system
PO:0009009 : embryo
PO:0020092 : megagametophyte
PO:0020091 : microgametophyte
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:
Haploid 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.
We could add zygotic and haploid embryo as children of embryo.
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:
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
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:
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? Can these leaves persist after germination?
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.
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.
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. Should they be synonyms?
made is_a stem internode
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. Is this accurate? The hypocotyl-root junction remains after germination.
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.
Proposed definition: A stem node that is the part of an embryo axis where the scutellum is attached.
Comment: A scutellum is attached to an embryo axis between the primary root (enclosed in the coleorhiza) and the plumule (enclosed in the coleoptile).
is_a stem node, part_of embryo axis
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.
-JE and JP will be attending Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.
-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
LC contributed to the workshop proposal "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" Authors: Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland and Laurel Cooper (Accepted)
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?
-BS suggested we might want to submit a short paper which could be published in longer form later- see above
*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn
Early-bird registration ends May 13.
Gramene will be putting together a workshop again, focusing on pathways. PJ will present a PO poster.
Abstract deadlines: Your abstract must be submitted by March 11 if you want it to be considered for a minisymposium talk.
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 proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme.
Dennis, Alejandra, Pankaj and Ramona are planning to attend.
Early bird registration deadline - Extended 1 March 2011 Deadline for registration by presenters 1 March 2011
See IBC 2011 Bio-Ontologies Symposium wiki page for more details
