POC Conf. Call 12-15-10

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POC meeting, Webex Conference Call; Date: Wednesday Dec 15th, 2010 10am (PST)

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG), Justin Elser (OSU), Justin Preece (OSU)

Absent: Alejandra Gandolfo; (Cornell University), Barry Smith (University at Buffalo, NY), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: none


Acceptance of the minutes from the POC Conf. Call 12-1-10? There were no additions, deletions or changes to the minutes of the last meeting.


Remaining terms without is_a parents

current def: An opening pore on the epidermis of leaves and stems bordered by two guard cells and serving in gas exchange.

Suggested definition: a portion of shoot epidermis that has as parts two guard cells and a stomatal pore. May also contain subsidiary cells.

is_a portion of shoot epidermis (had a conversation with Barry at an earlier meeting, in which he said it was okay for a portion of tissue to include an anatomical space as a part).

Right now stomatal complex has part_of relations to leaf adaxial epidermis, leaf abaxial epidermis, leaf lamina adaxial epidermis, leaf lamina abaxial epidermis, and petiole epidermis. This is problematic, because not every stomatal complex can be a part of all those structures.

Suggest that stomatal complex be a general term, without part_of relations, and we create new child terms for each of the different portions of leaf epidermis - leaf abaxial stomatal complex, leaf lamina abaxial stomatal complex, petiole stomatal complex, etc. - that can have part of relations to the corresponding portion of epidermis.

We agreed to make stomatal complex the general term, with specific children such as leaf stomatal complex, etc. Suggested definition is okay.


  • Leaf trichome and pavement cell have a similar problem (it is part of leaf adaxial epidermis, leaf abaxial epidermis, leaf lamina adaxial epidermis, and leaf lamina abaxial epidermis). Suggest similar solution.

This would also address a user request on an open SF tracker for Abaxial vs Adaxial

We will keep the current terms as general terms, and add specific children for leaf lamina, leaf petiole, leaf abaxial and leaf adaxial epidermis. Won't add children of leaf lamina adaxial and abaxial epidermis and petiole adaxial and abaxial epidermis until users request them.

Note from DWS: need to look at the use of the term pavement cell in embryology.


  • Also need to sort out leaf epidermis children. This is the current structure:

LeafEpidermis.jpg

Suggest that we get rid of leaf abaxial epidermis and leaf adaxial epidermis. Each of them only has a few annotation, and they could probably be moved to the terms for lamina abaxial and adaxial epidermis and/or petiole abaxial and adaxial epidermis.

Although the group agreed that it is not good to have multiple parentage, we decided to keep leaf abaxial epidermis and leaf adaxial epidermis, because users need it to annotate general patterns of abaxial/adaxial expression. Will assert is_a relations between leaf lamina ab/adaxial epidermis and petiole ab/adaxial epidermis and leaf ab/adaxial epidermis.


current def: An opening pore on the epidermis of floral organs bordered by two guard cells and serving in gas exchange.

Right now, we have a term floral epidermis, and floral stomatal complex is part of it.

I suggest that we obsolete floral epidermis, since it doesn't really make sense to refer to the epidermis of a flower as a whole. We already have the floral parts organized as organs or cardinal organ parts. Instead, we should use the term phyllome epidermis (which we already have) and make petal epidermis, sepal epidermis, etc., children of phyllome epidermis. There is only one direct annotation to floral epidermis, and it could probably be moved to the more specific parts of the flower.

I also suggest that we obsolete floral stomatal complex, and replace it with terms like petal stomatal complex, etc. (for example, petal stomatal complex is a stomatal compelx that is part of a petal epidermis).

We agree to the changes described above.


shoot apex: PO:0000037

current def: "The topmost part of the shoot, situated at the distal extremity of the shoot axis, consists of apical meristem and the youngest leaf primordia." [TAIR:ki]

subset: reference

Proposed definition: A shoot axis that is the most distal part of a shoot and has as parts a shoot apical meristem and the youngest leaf primordia."

is_a shoot axis

PJ suggested adding the term 'apical plant structure' on the top somewhere and shoot apexcbecomes is_a of this item. This will be your place to hold leaf/shoot/inflo/root/etc apex terms.

RW: this could be problematic, because the apices leaf/shoot/inflo/root/etc are different types of structures.

PJ: Also we should have vegetative and reproductive shoot apex and phyllome/leaf primordia is part of the vegetative shoot apex/meristem

We agreed that the idea of grouping different shoot apices was useful, but decided against it because we don't want to create too many upper-level catch-all terms that encompass different kinds of structures. Will make shoot apex is_a shoot axis, defined as above. Will add children reproductive shoot apex and vegetative shoot apex.


More terms w/o parents

current def: "Enlargement or swelling on the roots of plants, particularly in the Fabaceae, inhabited by nitrogen-fixing bacteria." [ISBN:0471245208]

Proposed definition: A cardinal organ part that is an outgrowth of a root and is inhabited by nitrogen-fixing bacteria.

Comment: Root nodules are a symbiosis between a plant (often, but not exclusively, of the Fabaceae) and bacteria of the genus Rhizobium, Bradyrhizobium, or Azorhizobium.

is_a cardinal organ part, part_of root

We may want to add the term root nodule meristem, is a root meristem, referred to in dbxref: PMID:1809347

Suggested definition was approved. Will add root nodule meristem. May also want to add sister term for coralloid roots (as in Cycads), which contain N-fixing cyanobacteria.


current def: "The angle between the petiole of a leaf and the stem to which it is attached." [GR:cwt] relationship: part_of PO:0020040 ! leaf base xref: SF: 3007368

Suggested parent: is_a axil, part_of shoot system


  • Should the PO have a generic term axil and, if so, how it should be defined?

See also older tracker item leaf base vs. axil?

Suggested def. for axil: A plant anatomical space that is the space between a shoot axis and a leaf, bract or branch that branches from the shoot axis.

Either we should keep the term leaf axil and make a parent term axil is_a plant anatomical space, or delete the term leaf axil and move it's annotations to axillary bud meristem.

We will add leaf axil as a child of plant anatomical space, make leaf axil, branch axil and bract axil children of it.


current def: "A group of four haploid cells that remained joined together shortly after meiosis. Each cell will give rise to the male gametophyte." [TAIR:ki] subset: reference

Proposed definition: A portion of plant tissue consisting of four haploid cells that remained joined together shortly after meiosis. Each cell will give rise to a male gametophyte.

is_a portion of plant tissue, develops_from microsporocyte

Suggested definition was accepted, expect remove word haploid. Will also add new term tetrad of megaspores, with comment that usually only one of the four megaspores develops and the other three die.


current def: "Portion of an organ that is fragmented; in capsule, the portions into which the pericarp splits at maturity." [APWeb:Glossary]

subset: Arabidopsis

-In Arabidopsis, the fruit is composed of two fused carpels, so when it dehisces, each valve is developed from a carpel, which makes it an organ, unless only part of the carpel develops into the valve, in which case it would be a cardinal organ part.

-Technically, part of something can include the whole thing, so it is safer to use cardinal organ part and explain that sometimes the valve develops from the whole carpel.

In other dehiscent fruits such as legumes, each part that splits apart is from the same carpel, so it would be a cardinal organ part. However, I only found one paper on WOS that referred to the dehisced pod segments as valves.

The term valve has also been used to refer to dehiscent sections of an anther, which I think is synonymous with locule (maybe the locules become valves after they dehisce?), but perhaps it would be better to restrict our definition of valves to parts of a fruit; call it fruit valve for clarity.

Suggested definition for fruit valve (new name): A cardinal organ part that is a part of a fruit that splits apart when the fruit dehisces.

Comment: A fruit valve may develop from an entire carpel (as in Brassicaceae) or from part of a carpel (as in Fabaceae).

We will make valve (PO:0000033) a general term, for the portions of any plant structure that splits apart (is_a a cardinal organ part), and add fruit valve and moss capsule valve as children of valve.

Definition of valve: A cardinal organ part that is a part of a plant structure that splits apart when the structure dehisces.

Definition of fruit valve: A valve that is a part of a fruit that splits apart when the fruit dehisces.


current def: "Central axis of the fruit." [POC:curators] subset: Tomato

Suggested def: A portion of plant (parenchyma?) tissue that forms the central axis of a fruit.

portion of plant tissue or portion of parenchyma tissue

Should just be portion of plant tissue, because it may contain non-parenchymatous tissue.

Will add general term columella, with children fruit columella and moss capsule columella.


current def: "A leaf like structure often found enclosing the grass fruit, caryopsis. It is derived from the dried lemma (PO:0009037) and palea (PO:0009038) floral bracts found in the grass floret (PO:0006318)." [GR:pj] subset: Maize, subset: Poaceae, subset: Rice

Suggest changing name to Poaceae hull (in our effort to get rid of sensu terms).

Suggested def: A collective phyllome structure that encloses a fruit of the Poaceae (caryopsis) that develops from the dried lemma and palea.

is_a collective phyllome structure

Changes suggested above were accepted.

More terms w/o parents

current def: "A tubular cell extension formed by the germinating pollen grain; carries the male gametes into the ovule." [ISBN:0471245208] subset: reference

The pollen tube is a cellular extension, and will be requested in GO.

Will obsolete PO:0006345 and add new term pollen tube cell

Suggested def: A plant cell that develops from a vegetative cell and forms a tubular extension of the pollen grain.

Comment: carries the male gametes to into or near the ovule. May be branched in gymnosperms. See GO:xxxxxx (waiting for number) for pollen tube and GO:xxxxxx (waiting for number) for pollen tube tip.

  • Suggest we add tube cell as a related synonym to vegetative cell (PO:0020099). Also suggest rewording definition of vegetative cell to include non-angiosperms.

Current def. of vegetative cell: The larger cell of the male gametophyte of angiosperms that does not divide further.

Suggested def. of vegetative cell: A plant cell that is the larger cell of a male gametophyte in seed plants. It does not divide further and develops into a pollen tube cell.

These changes were accepted.


current def: "A cell layer found in basal endosperm transfer cell." [GR:cwt] part_of basal endosperm transfer cell

This definition and relationship is wrong. The basal endosperm transfer layer is a layer of cells (composed of basal endosperm transfer cells) which is part of the endosperm.

basal endosperm transfer layer:

Proposed def'n: A portion of plant tissue that is part of an endosperm and is composed of basal endosperm transfer cells. Comment: Involved in transferring nutrients to an embryo.

Note: comment should be 'transferring nutrients to an 'embryo'.


basal endosperm transfer cell:

Current def'n: A transfer cell found in endosperm, responsible for passing through all nutrients entering the seeds by symplastic or apoplastic methods.

Proposed def'n: A transfer cell that is part of a basal endosperm transfer layer. Comment: Responsible for transferring nutrients to an embyo by symplastic or apoplastic methods.

Should be is is_a transfer cell, Note: comment should be 'transferring nutrients to an 'embryo'.

Will obsolete the existing ID (PO:0009019) and create new ID for 'basal endosperm transfer layer'. Proposed definitions are okay.


current def: "In a grass floret, one of two or three tiny scales or flaps of tissue outside the stamens, possibly representing reduced perianth segments." [APWeb:Glossary], subset: reference

Parent and definition will depend on whether it is truly composed on one type of tissue (as current definition implies) or has multiple tissues.

(1) If only one tissue type, is_a portion of plant tissue.

Proposed definition 1: A portion of plant tissue that is part of a grass floret and is one of two or three tiny scales or flaps of tissue outside the stamens.

Comment: May represent a reduced perianth segment

(2) If two or more tissues, is_a phyllome.

Proposed definition 2: A phyllome that is part of a grass floret and is one of two or three tiny scales or flaps of tissue outside the stamens.

Comment: May represent a reduced perianth segment

Use definition #2. Change comment to "May represent a reduced floral structure" because it may actually represent a reduced stamen, rather than a perianth segment.


current def: "A structure associated with and often partly or wholly covering a seed and developed from the funicle or raphe." [APWeb:Glossary]

comment: Also used more generally to refer to a similar structure derived from any part of the ovule - there has been much and sometimes acrimonious debate over the correct definition of the term, so when used the origin of the aril should generally be given for clarity. subset: reference


Suggested def: A cardinal organ part that is a fleshy outgrowth of the funicle or raphe, covering all or most of the seed (ISBN-13:978-0-88192-850-1, Bell and Bryan)

Comment: A fleshy outgrowth from another part of a seed is an arilloid.

is_a cardinal organ part, part_of seed

The aril actually only grows out of the funicle, but when the ovule is bend over, it presses against the funicle and forms a raphe, so it may appear that the aril is growing from the raphe. Change definition to reflect this:

New definition: A cardinal organ part that is a fleshy outgrowth of the funicle, covering all or most of the seed. Comment: A fleshy outgrowth from another part of a seed is an arilloid. If the ovule is pressed against the funicle to form a raphe, it may appear that the aril is growing from the raphe.


note: check with Chris about putting the PO IDs in the def'ns


current def: "An outgrowth from parts of the seed other than from the funiculus or raphe." [ISBN:0080280293]

Suggested def: A cardinal organ part that is a fleshy outgrowth of a seed and does not cover the entire seed and develops from a part of the seed other than the funicle or raphe. (ISBN-13:978-0-88192-850-1, Bell and Bryan)

is_a cardinal organ part, part_of seed, narrow synonyms: strophiole (an arilloid on the raphe) and caruncle (an arilloid near the micropyle)

Accepted, except change definition to say "... other than the funicle" instead of "... other than the funicle or raphe"


current def: "An inpushing of the anther wall." [APWeb:Glossary] subset: reference

Suggested def: A cardinal organ part that is an inpushing of the anther wall.

is_a cardinal organ part, part_of anther wall

>>During the last revision, I made anther wall a portion of plant tissue (it had no is_a parent). I think it should actually be a cardinal organ part, because it contains more than one tissue type (def. of anther wall: A multicellular layer with outer epidermis and an inner endothecium).

Okay to make anther wall a cardinal organ part.

New definition of placentoid: A portion of parenchyma tissue that is part of a connective and projects into a pollen sac. Ref. Flowering plant embryology: with emphasis on economic species By Nels R. Lersten, ISBN:9780470752685


  • root stele: PO:0020124, alt_id: PO:0003012 and stele

current def: "The central column of primary vascular tissue in the root and any tissue that it surrounds." [APWeb:Glossary]

comment: Includes the pericycle as the outermost layer of the stele. subset: reference, synonym: "root vascular cylinder" RELATED []

Suggest we add a general term stele, parent to root stele and new term shoot axis stele.

definition of stele (from Beentje 2010): a part of a plant axis made up of the primary vascular system and its associated ground tissue.

suggested parent: cardinal organ part

suggested definition of stele: A cardinal organ part that is the central column of a plant axis that consists of the primary vascular tissue and the ground tissue it surrounds.

root stele: a stele that is part of a root.

shoot axis stele: a stele that is part of a shoot axis

(could have children stem stele and branch stele)

Add parent term stele. Def: A cardinal organ part that is the central column of a plant axis that consists of the primary vascular tissue and the associated ground tissue. Comment: If a pith is present, it is part of the stele, otherwise the stele only includes the primary vascular tissue and the ground tissue that surrounds it.

Definitions for root stele and shoot axis stele are okay. Won't add branch and stem stele unless they are needed.


current def: "The egg cell and two synergids located at the micropylar end of the embryo sac." [TAIR:lr] subset: reference

suggest: is_a cardinal organ part

Suggested def: A cardinal organ part that has as parts an egg cell and two synergids and is located at the micropylar end of the embryo sac.

Comment: Found in angiosperms.

Definition is okay.

Should add new subset for angiosperms (and other taxa as needed). Later can add dbxrefs to the NCBI taxon numbers, but that can be done with a PERL script.

Sporangium

We currently have the terms nucellus (=megasporangium) and microsporangium (=pollen sac), but their definitions are angiosperm-centric, and they need is_a parents.

Suggest: Add a generic term 'sporangium', parent to mega- and microsporangium, and defining mega- and microsporangium so they are applicable to all plants.

We can then make nucellus and pollen sac children of mega- and microsporangium.


suggested def: A hollow cardinal organ part in which spores are produced (Raven et al.) Comment: may be multicellular or unicellular.

is_a cardinal organ part


suggested def: A sporangium in which megaspores are produced (Raven et al.)


current def: A portion of subepidermal tissue in the ovule surrounding the megasporocyte. [source: APWeb:Glossary]

suggested def: A megasporangium in a seed plant, composed of fleshy subepidermal tissue inside an ovule and surrounding a megasporocyte.

Comment: In seed plants, the megaspores and megagametophyte are retained within the nucellus.

Note: should there be an Angiosperm subset or cross ref to NCBI Taxonomy ID?


suggested def: A sporangium in which microspores are produced (Raven et al.)


currently, the name of this term is microsporangium, with pollen sac as synonym, but suggest that we us microsporangium as a more general term and rename this term pollen sac. It already has a part_of relation to anther.

current def: "A sporangium producing microspores, usually many in number." [APWeb:Glossary], subset: reference, synonym: "anther lobe" RELATED [], synonym: "pollen sac" RELATED []

suggested def: A microsporangium in an angiosperm that is a cavity in an anther that contains pollen grains (Raven et al.).

The above suggestions were accepted. Later, if needed, we can add other terms for microsporangia or megasporangia that may be different in other taxa besides angiosperms.

parts of embryo

BS already suggested that we separate the PSO into mature plant structures and immature plant structures. If we do this, then embryonic plant structure would be a child of immature plant structure.

If not, it would be is_a plant structure.

All of the various parts of the embryo could be children of embryonic plant structure. This would include terms like embryo axis, embryo cortex, etc. that are now classified as mature plant structures, but probably shouldn't be, because organs are not fully developed in the embryo (tissues are debatable). This term would also be parent of the terms below.

suggested def'n: "A plant structure that is a proper part of an embryo".

Comment: includes organs, tissues and cell types that are unique to embryos. Cell or tissue types that can occur in both embryos and mature plant structures are children of mature plant structure.

New term embryonic plant structure was accepted. Want to consider adding other categories like leaf structure, etc.

For now we will not add the terms mature plant structure and immature plant structure. Embryonic plant structure will be a child of plant structure. May re-address this at some point in the future.

Could have terms like embryonic parenchyma cell or embryonic epidermal cell.

Will move other embryonic structures from their current is_a parents to this term. See SF tracker for list of terms.

The suggested definitions below were accepted.


current def: "The body of the developing embryo attached to the maternal tissue in the ovule by filamentous suspensor." [TAIR:ki]

Suggested def: "An embryonic plant structure that is the body of a developing embryo attached to the maternal tissue in the ovule by a suspensor."

Comment: The embryo proper is the entire embryo exclusive of the suspensor.


current def: "A nearly always single file of cells at the base of the embryo derived from the basal cell." [GR:pj]

comment: It anchors the embryo in the embryo sac and pushes it into the endosperm.

suggest is_a embryonic plant structure

Suggested def: "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.

Comment: The suspensor often allows the embryo to penetrate deep into the endosperm. Across plant species, suspensors are morphologically diverse and may be single- or multicellular, undifferentiated or highly differentiated, and variously shaped.

Comment from DWS: Need to double check that suspensor develops from the basal cell in all taxa.


current def: "A more or less shield-shaped and absorptive portion of an embryo of grasses, probably a modified cotyledon." [APWeb:Glossary] synonym: "haustorial cotyledon" RELATED []

suggest is_a embryonic plant structure

Suggested def: An embryonic plant structure that is a more or less shield-shaped and absorptive portion of an embryo of Poaceae. Comment: Probably a modified cotyledon.


current def: "Junction point of the embryonic root and hypocotyl." [TAIR:ki] subset: reference

suggest is_a embryonic plant structure, part_of embryo axis

Suggested def: An embryonic plant structure that is the part of an embryo axis where the radicle joins the hypocotyl.

Restructuring PGDSO for Occurents

Discussion of this item was postponed to a future meeting.

Suggested New "working" Structure of the PGDSO:

  • The root term, plant growth and development stage, would be replaced by 'plant life cycle process' (an "Occurrent").

LC, BS and RW met on 11-30 to discuss this restructuring, and changed the upper level term from plant life cycle process to plant process, plus several other changes.

The top level structure would have three branches, as below

Life cycle process 2.jpg

None of the old term names or definitions have been changed yet, except to put (phase) on the end of some term names that did not have stage in their names.

Key changes:

  • Most of the terms from PGDSO went under plant structure development phase, but a few went under plant structure development process.
  • In the case of seedling development (which went under plant structure development process) we added a new phase called seedling phase. Something like imbibition is not a phase, but a developmental process, so it went under plant structure development process.
  • Could add a germination phase that begins with imbibition and ends with emergence of the radicle.

New: Barry has suggested we need a term like 'plant life' ('life of whole plant') of which all phases would form parts


From the 11-10-10 meeting:

-Add corresponding phases for each of the developmental processes.

For example: gametophytic phase corresponds to gametophyte development and leaf development phase could correspond to leaf development.

Then it would be possible to move the developmental processes to GO, but keep the phases in PO.

-We reviewed this proposed structure, and decided to experiment with how it will work for existing PGDSO terms.

Barry suggested that his goal was to have all PO terms in one of two branches:

  • plant structures (plant anatomical entity = independent continuant)
  • plant processes (plant life cycle process = occurent)

Lol and Ramona have been working on moving all of the ~120 terms from the PGDSO into one of the three new plant life cycle process branches, to see where they can fit.

  • Can delete existing relations for those terms, but will still be able to compare to old structure by comparing dev to live browser.

Note from BS: Keep in mind where there might be potential overlaps with the GO- we will need to figure out how to split the process terms, ie: will they reside in the PO or in GO? Make a list as we go along.

-Stage term names need to be rewritten as nouns, for example: "whole plant in the phase where 1 leaf is visible

-Complex terms could be rendered using post coordination; ie: 'on the fly' for users, but some may need to have actual PO IDs in order to accommodate annotations.


changes in new PGDSO version

Possible collaboration with the PRO (Protein Ontology)

Discussion of this item was postponed to a future meeting.'

Bary has asked that we spend a few minutes to discuss a possible collaboration with the PRO (Protein Ontology)

POC Conference Call Schedule for next term

We need to go through the doodle poll process again to Schedule the POC Conference Calls for next term.

Please visit the link below and fill in when you are available:

Winter term 2011 POC Conf Calls

Upcoming meetings 2010-2011:

  • Plant and Animal Genome XIX Conference

January 15-19, 2011 PAG 2011

Laurel, Ramona, DWS and Justin Preece are attending. PJ may attend for the weekend only as he is teaching. Alejandra cannot attend.

PO Activities at PAG:

Saturday - Early Afternoon, January 15, 2011 -- 1:30 pm - 3:00 pm (third in series of seven)

" The Plant Ontology: Linking phenotypes and genomics across plant taxa"

Sunday Morning, 16 January 2011 -- 8:00 am - 10:10 am

Sunday Late Morning:

Time: 10:30-1:00 pm (to include lunch, will wrap up in time to get to 1:30 sessions)

PO Workshop Reg'n site and Survey

  • Poster: link to abstract TBA
  • Outreach Booth being organized by MaizeGBD- More info TBA


* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Dennis and Alejandra are planning to attend IBC2011 and speak in other symposia.

Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the genetics, genomics and bioinformatics theme.


Pankaj will give the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona will present the talk on the Plant Ontology. Abstracts have been submitted.

No additional abstracts were submitted for our proposal, and Angelica does not think she will be able to attend because of lack of funds.

Dennis will speak in place of Angelica. PJ invited two other speakers. Gavin Kennedy will talk about the ontology application in large scale phenomics projects. Rudi Appels will speak on crop genomics and phenomics. Ramona has contacted the organizers to figure out how to nominate additional speakers, and will pass on information to the speakers. We hope to use the 6th time slot for a discussion session.

RW heard from organizers re. additional speakers. Will forward their information. Still waiting to hear about discussion session.

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