POC Conf. Call 1-10-12

POC meeting, Webex Conference Call; Date: Tuesday Jan 10th, 2012 10am (PST)

In attendance: POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Dennis Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell University), Pankaj Jaiswal (OSU), Justin Elser (OSU), Justin Preece (OSU), ,

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

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_1-3-12? No additions, deletions, or changes.

Back to POC Meetings Minutes

Term Requests from Agron-Omics

At the recent EBI Crop Ontology meeting PJ met with Sean Walsh

Arabidopsis GROwth Network integrating OMICS technologies

please see: Items_for_future_meetings for more info.

Anatomical spaces:

Requests:

• mesophyll and/or spongy mesophyll intercellular space: A space between adjacent (spongy) mesophyll cells.

• substomatal cavity: Cavity located immediately proximal to the stoma.

We suggest creating new a general term for intercellular space, plus one for leaf mesophyll intercellular space. Then spongy mesophyll intercellular space and substomatal cavity can be specific subtypes.

proposed new term: intercellular space (PO:0025379): A plant anatomical space that is located inside a portion of plant tissue between two or more cells.

Does GO have a term for intercellular space? They have extracellular space (GO:0005615): def'n: That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. Related synonym: intercellular space.

comment: Often located in mesophyll tissue. This term does not include spaces on the surface of a plant structure, like a stomatal pore, stomium, or micropyle, nor larger cavities or canals that are surrounded by tissue, such as an archegonium neck canal.

proposed new term: leaf mesophyll intercellular space (PO:0025380): An intercellular space that is part of a leaf mesophyll.

Comment: Includes the air spaces in the spongy mesophyll and substomatal cavities.

proposed new term: spongy mesophyll intercellular space (PO:0025381): A leaf mesophyll intercellular space that is part of a spongy mesophyll.

Could modify definitions to say "...space located between two or more cells of the spongy mesophyll...". Could mirror general definitions, and say, e.g., "An intercelluar space that is located inside a leaf mesophyll between two or more leaf mesophyll cells, but this is not necessary to repeat "between two or more cells" since it is stated in the definition of the intercellular space

Should also add a term for 'palisade mesophyll intercellular space' too, because cell walls are not necessarily touching.

proposed new def'n, substomatal cavity: A leaf mesophyll intercellular space that is located directly below and contiguous with a stomatal pore.

Can have stomata in many kinds of organs. Should add general term for substomatal cavity, and phyllome substomatal cavity, add subtype for leaf for now, can add others (like petal) later. Can mirror hierarchy of stomatal complex.

revised def'n: substomatal cavity: An intercellular space that is located directly below and contiguous with a stomatal pore. adjacent_to stomatal pore

Do we need to set up leaf mesophyll intercellular space as a cross product of is_a intercellular space and part_of leaf mesophyll, so that leaf substomatal cavity will be an inferred subtype?

leaf sinus

suggested def'n: Part of leaf margin. A small depression between two projecting lobes of a leaf.

Suggest adding the new term as parent: phyllome sinus (PO:0025383): A plant anatomical space that is a phyllome marginal embayment, incision or indentation between marginal projections of any sort, typically lobes, teeth, or the base of cordate phyllomes.

part of phyllome margin,

Revised def'n for requested term: leaf sinus (PO:0025384): A phyllome sinus that is a marginal embayment, incision or indentation between marginal projections of any sort, typically lobes, teeth, or the base of cordate leaves.

leaf sinus (new term) is a phyllome sinus (new term), part of leaf margin (rather than leaf lamina margin)

definition of leaf sinus from 'Manual of Leaf Architecture' (Ellis et al,2009): A marginal embayment, incision, or indentation between marginal projections of any sort, typically lobes, teeth, or the base of cordate leaves. (ISBN: 978-0-8014-4)

Anything that has a lamina can have a sinus.

Leaf lamina - now it is defined as any lamina that is part of a leaf, so petiole lamina is a subtype of leaf lamina. We should redefine this that the leaf lamina is a part exclusive of the petiole, because this is how most people think of it. Could add general term for "leaf part lamina" that would include leaf lamina and petiole lamina.

We can add terms for lobe or tooth as well, later as needed.

Portions of plant substance:

requested term:

• epicuticular wax: The plant cuticle is covered by epicuticular wax. It consists of a mixture of organic compounds. Epicuticular wax forms an above ground boundary layer between a plant and its environment.

Does this conflict with GO? No, they don't have terms for this. They have cuticle development, which can be used for either a plant or animal. We need to have a discussion with GO about whether or not they should include extracellular deposition.

* Existing term: cuticle (PO:0000022)

current def'n.: A layer of fatty material, cutin, rather impervious to water, located on the outer walls of epidermal cells. (ISBN:0471245208).

The cuticle is composed of a cuticular membrane, which is which is made mostly of cutin, adjacent to the epidermis, and the layer of epicuticular wax on top.

Image from: PMID:12467640: Kunst, L. & Samuels, A.L. Biosynthesis and secretion of plant cuticular wax. Prog. Lipid Res. 42, 51-80 (2003).

proposed revised def'n., cuticle (PO:0000022): A plant anatomical substance composed of a polyester matrix of hydroxy- and hydroxy epoxy fatty acids C16 and C18 long (cutin), embedded and overlayed with cuticular wax and forming a layer on the surface of a plant epidermis.

comment: The cuticle is produced in and secreted by epidermal cells of leaves, stems, fruits, and other aerial plant structures. It has as parts an inner cuticle proper and an outer layer of epicuticular wax.

is_a portion of plant substance, adjacent_to epidermis

ref: PMID:12467640

We should name this plant cuticle to avoid conflicts with cuticles in animals, which are different, and prefix other terms. Not needed for cutin, since it only occurs in plants (animals have chitin).

Reword this to say "..polyester matrix of hydroxy- and hydroxy epoxy C16 and C18 fatty acid chains (cutin)..."

Should start adding PO ids to comments whenever we refer to them. This will create automatic hyperlink and serve as a check that we actually have the terms in the PO.

proposed new term: cuticle proper (PO:0025387): A portion of plant substance that is the inner layer of a cuticle, composed primarily of cutin, embedded and overlayed with cuticular wax.

synonyms: cutin matrix; adjacent_to epidermis

ref: PMID:12467640

This should be called "plant cuticle proper"

proposed new term: cutin (PO:0025385): A portion of plant substance that is composed of a polyester matrix of hydroxy- and hydroxy epoxy fatty acids C16 and C18 long (Need to check on other components; may want to work on wording a little)

Comment: Cutin is the insoluble, covalently cross-linked polymer that forms an electron dense layer over the epidermal cells of an aerial plant structure.

ref: PMID:12467640

Reword as per definition of cuticle, only in plants so we don't have to call it "plant cutin".

proposed new term: cuticular wax (PO:0025386): A portion of plant substance comprised predominantly of very long chain aliphatic lipids and is part of a cuticle.

Comment: Also includes triterpenoids and minor secondary metabolites, such as sterols and flavonoids. May be embedded within or external to the layer of cutin of the cuticle proper. Phenotypically, wax is distinguished as the glaucous or whitish bloom on a part of a plant shoot system that corresponds to crystalloid epicuticular wax with light scattering capacity.

ref: PMID:12467640, PO_REF:00010

Revised def'n for requested term, epicuticular wax(PO:0025388): A portion of cuticular wax that forms crystalloids or a smooth film on the exterior of a cuticle.

comment: Epicuticular waxes may take a variety of forms, such as plates, ribbons, tubes, and rods.

adjacent_to cuticle proper

ref: PMID:12467640, PO_REF:00010

ok

proposed new term: intercuticular wax (PO:0025389): A portion of cuticular wax that is an amorphous mixture of lipids embedded in the cutin of a cuticle proper.

part_of cuticle proper, adjacent_to cell wall (but cell wall is not a PO term)

ref: PMID:12467640, PO_REF:00010

ok

These terms will be a good opportunity for us to add links to ChEBI.

e.g., CHEBI:33653 aliphatic compound

Meristems:

adaxial meristem

Suggested def'n: adaxial meristem: A meristematic tissue on the adaxial side of a young leaf primordium that contributes to the increase in the thickness of a leaf.

From Fahn: A meristematic tissue on the adaxial side of a leaf primordium that contributes to the thickness of the petiole and midrib (also called ventral meristem).

There are two types of adaxial meristems: One that occurs early in leaf development, and contributes to the thickness of the entire leaf, as in unifacial leaves, and one that occurs later in development and contributes to the thickness of the petiole and midrib. The later is a 'Rundingsmeristem' in German, or an 'adaxial rounding meristem'.

Propose revised def'n, new term: leaf adaxial meristem (PO:000xxxx): A portion of meristem tissue that is found on the adaxial side of a young leaf.

Comment: Contributes to the thickness of a leaf. There are two types of adaxial meristems. In leaves with a petiole and lamina, an adaxial rounding meristem occurs later in development, is separated from the apical meristem, and contributes to the thickness of the petiole and midrib. In unifacial leaves, the an adaxial meristem occurs earlier in development, is close to/adjacent to/part of the apical meristem, and contributes to the the thickness and cross-sectional shape of the entire leaf.

is_a meristem, part_of leaf, participates_in leaf expansion stage (PO:0001052)

synonym: ventral meristem

We could create two new terms:

leaf adaxial rounding meristem - the first type described above, as found in A.t..

leaf adaxial unifacial meristem - the second type described above, as found in Acacia

We decided that it would be better to just keep them in the comment for adaxial meristem at this point. Concerned that people will end up using the wrong type, and the separate terms are not widely used. Also, most of our annotations will be on the first type. Can add both as synonyms to adaxial meristem. Put in reference for the leaf adaxial rounding meristem from DWS

Should we also add a term for leaf abaxial meristem? Yes

Should have generic phyllome abaxial/adaxial/plate meristem, with specific subtypes for leaves, etc., only add for leaves at this point. This should be part_of vascular leaf, not leaf.

marginal meristem

From Agron-Omics: A region of meristematic tissue located along the edges of a leaf primordium. Repeated divisions of initials in this area give rise to the mesophyll and epidermal tissues of the blade.

From Fahn: The meristem along the edge of a developing leaf.

From Steves and Sussex: Marginal meristem consists of both marginal and submarginal initials. They then go on to describe how these meristems have been shown not to contribute to lamina formation in some leaves, using clonal analysis of leaf formation. However, there could be meristematic tissue at the margins of leaves in some species and not in other.

proposed definition, leaf marginal meristem: A portion of meristem tissue on the edge of a young leaf that has as parts marginal and submarginal initials.

Comment: Marginal meristems develop at the two lateral sides of a leaf primordium and may contribute to expansion of the lamina. Marginal initial may give rise to epidermal tissue while sumarginal initial may give rise to the mesophyll. May be of limited duration.

is_a meristem, part_of leaf, participates_in leaf expansion stage

synonym: leaf marginal blastozone

Discussion of how this compares to L1, L2, L3. Cannot necessarily generalize and say that L1 gives rise to epidermis and L2 and L3 give rise to ground tissue across all species.

We don't want to say that these meristems are part_of primordium, because primordium ends when leaf form starts differentiating, and that is when these meristems are active.

We will need to work on leaf expansion stages more in the future.

Need to add terms for marginal initials and submarginal initial.

Usually called "marginal meristem", can add "margin meristem" as a synonym.

plate meristem

From Agron-Omics: Meristem established inside the leaf primordia. The plate meristem is a meristematic tissue consisting of parallel layers of cells dividing anticlinally (perpendicular to leaf surface) and contributes to the major part of leaf growth.

From Evert (Esau's Plant Anatomy): A meristematic tissue consisting of parallel layers of cells dividing only anticlinally with reference to the wide surface of the tissue. Characteristic of ground meristem of plant parts that assume a flat form as a leaf.

of Musa: After cessation of marginal growth, further growth of the lamina is brought about by cell division in the various cell layers of the lamina. These divisions are mostly anticlinal, and thus a plate meristem is formed. A plate meristem is one in which the planes of cell division in each layer are perpendicular to the surface of the organ in which the meristem occurs. The activity of such a meristem results in increase in the surface area but not thickness of an organ.

proposed def., leaf plate meristem: A portion of leaf meristem tissue in which the planes of cell division in each layer are perpendicular to the surface of the leaf.

comment: The activity of a leaf plate meristem results in increase in the surface area but not thickness of a leaf.

is_a meristem, part_of leaf, participates_in leaf expansion stage

Should add a comment to leaf intercalary meristem to make it clear that it does not include plate meristems.

Definition should say "...are anticlinal..." instead of "...are perpendicular to the surface...".

Just like the marginal meristem, plate meristem is not part_of primordium, because it is present after the primordium stage.

...anlagen

Agron-Omics has requested several new anlagen terms. We have the existing term:

carpel anlagen (PO:0006005): A portion of meristem tissue that is a presumptive region on a floral meristem where carpel primordia would initiate.

This term is been used in the literature, showing differential patterns of gene expression in this area, prior to primordium formation. e.g., PMID:21547450 uses "organ anlagen".

We can general term for root anlagen and phyllome anlagen.

root anlagen: A portion of pericycle tissue that will give rise to a root primordium.

comment: Only detectable by gene expression, not morphology.

phyllome anlagen: A portion of meristem tissue that will give rise to a phyllome.

comment: Only detectable by gene expression, not morphology.

cotyledon anlagen

From Agron-Omics: A portion of meristem tissue that is a presumptive region on the embryo meristem where cotyledon primordia would initiate.

Proposed definition: A phyllome anlagen that will give rise to a cotyldon primordium and is part of a plant embryo.

is_a meristem, part_of embryo

We could say more about the embryo here, and where the cotyledon develops from in different taxa.

Can add cotyledon primordium develops_from cotyledon anlagen.

leaf anlagen

From Agron-Omics: A portion of meristem tissue that is a presumptive region on a vegetative meristem where leaf primordia would initiate.

Proposed definition: A phyllome anlagen that will give rise to a leaf primordium and is part of a peripheral zone of a vegetative shoot apical meristem.

is_a meristem, part_of peripheral zone, part_of vegetative shoot apical meristem

Can add leaf primordium develops_from leaf anlagen.

PMID:14732442

Can add comment that this is the region where you have the maximum concentration of auxin in the SAM (at least in a few species that have been studied). This lets people know to look for it in other species.

new definition for carpel anlagen: A phyllome anlagen that will give rise to a carpel primordium and is part of a peripheral zone of flower meristem.

is_a meristem, part_of peripheral zone, part_of flower meristem

Flower meristem should be is_a reproductive shoot apical meristem.

Ok to add these terms.

New terms and changes arising from last week's discussion

Postponed until a future meeting. See POC Conf. Call 1-24-12

Upcoming meetings and Presentations 2011/2012:

PAG 2012

January 14-18, 2012, San Diego, California

PO will be represented at the following events:

• Ontology workshop, Saturday January 14th from 10:20am-12:30pm: Use of Ontologies for Organizing Plant and Animal Genomics Data. We have 5 speakers and time at the end for a panel discussion.

PJ will give the introductory remarks at the Ontology workshop, and hopefully take part in the Panel Discussion.

For more info, see the PAG 2012 Ontology workshop wiki page.

• LC is also presenting in the Non-Seed Plant Workshop on Saturday, Jan 14th, (3:50pm-6pm) and in the Plant Phenotypes workshop on Sunday, Jan. 15th, (8:00am - 10:10am).

• We will also do a computer demo Monday 12:50 pm for the PO.

• The PO will also take part in an Outreach booth organized by MaizeGDB- schedule TBA

-Do we want to host the wiki page for the booth again?

Phenotype RCN meeting, 23-25 February 2012

The dates: February 23-25, 2012 (Thursday, Friday, 1/2 Saturday) have been confirmed for the next annual Phenotype RCN meeting.

It will be held again at NESCent (Durham, NC).

RW has a friend there she can stay with and is interested in going.

This meeting will focus on bringing in new people and training them on how to develop and use anatomy ontologies. RW offered to help with the training.

The projects of the Plant Working Group that we started in CO will be worked on during the next meeting.

Eva said that they can cover RW's plane fare from NY.

Maize Genetics Meeting, March 15-18, 2012

The maize meetings are being held in Portland, OR this year.

For more info see: Maize Genetics Meeting 2012

Registration Link: 2012 Maize Genetics Conference Registration Page will open on December 30, 2011.

Deadlines: Advance meeting registration is due by January 31, 2012.

5th International Biocuration Conference

April 2-4, 2012, Washington DC

• Abstract was submitted December 9, 2011 for consideration for a talk (or else a poster). MS was co-author.

See link: File:Abs Biocuration 2012 (LC 12-9-11).pdf

• Notification date: February 3, 2012

From 9-27-11: PJ is planning to attend and will be running a biocuration workshop- is this happening?

SPNHC 2012

Annual meeting of the Society for the Preservation of Natural History Collections

Yale University, New Haven Connecticut June 11-16, 2012

Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).

The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).

From PJ: If we can show progress in the FNA work or Morphobank yes we should

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

Call for Symposia, Colloquia and Workshops:

RW, DWS and MAG put together a proposal for a half day hands-on workshop. The goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.

Proposal was submitted, waiting for news.

PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrixes.

exhibitor's booth

We should also consider hosting an outreach booth.

Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)

• 2 months of Rotating Banner Ads in the online American Journal of Botany

• A Rotating Banner Ad in one edition of the online Plant Science Bulletin

• A Rotating Banner Ad on the Botany 2012 abstract submission site

• A Rotating Banner Ad on the 2012 Conference Registration site.

PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.

Annotation wiki

JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.

ASPB Plant Biology 2012

July 20 - 24, 2012 - Plant Biology 2012, Austin, TX

Registration scheduled to open first week in January.

Early Bird Registration: by May 11

Advance Discounted: May 12-June 15

ICBO 2012

International Conference on Biomedical Ontologies (ICBO 2012), July 22nd-25th, Graz, Austria

co-located with the 7th International Conference on Formal Ontologies in Information Systems (FOIS 2012)

Relevant dates

• Jan. 31st, 2012: Paper submission deadline
• Feb. 28th, 2012: Notification of paper acceptance
• March 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
• April 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance
• June 30th 2012: Deadline for all camera-ready copies for the proceedings

We have until Jan. 31 to submit a paper. Do we want to try to prepare a manuscript for this?

Possible topics: finding commonality in development stages across the plant kingdom (revisions of PGDSO), plant phenotypes in ontologies, community driven annotation efforts (new application from JP and others), others?

BS would like to collaborate on a preliminary paper on Plant Disease Ontology. RW will review IDO and summarize what is there already for plants, what is needed, how it will link to PO. LC will also collaborate.

BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts

Next meeting scheduled for Tuesday, Jan. 17th, 2012 at 10am PST/1pm EST

Although LC will be at the PAG meeting, the rest of the group will meet to work on new definitions for vascular terms that are needed for the Wood Ontology meeting.