POC Conf. Call 5-8-12

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POC meeting, Webex Conference Call; Date: Tuesday May 8th, 2012 10am PDT/1pm EDT

In attendance:

POC members:

Absent:


Collaborators: none

Streaming recording link:

https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=64664517&rKey=a11e211fa18dda2a Download recording link:

https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=64664517&rKey=528f85d29a3d1a4c

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_5-1-12?

Back to POC Meetings Minutes

Update and Progress report from Cornell (MAG)

  • New website at Cornell for the PO project CUPAC

Comments sent by email from MAG (5-7-12):

  • Number of slides/photos:
    • We have already 340 anatomical slides photographed and a total of 6270 images. All the slides are barcoded for easy access (holotype collection).
    • Each slide is photograph in detail with magnifications from 4 to 40 X. The number of photographs per slide varies depending on the structure, tissue and cell details.
    • I selected the taxa based on the terms we are working on, so we have for example all the cell types and tissues already photographed, We also have specific structures such as prothalia, anterida and archegonia, early stages of sporophytes, ovules, sections of rhizomes, roots, stem, leaves, ovaries, seeds, and wood.
    • Kevin will provide everyone with a password, so everyone will be able to edit the information of the photo or slide.
    • Jennifer (MAG's tech) will prepare the list of the taxa for next week (currently only works 1 day per week).

Problems with some of the children of Cardinal Organ Part (COP)

LC: we need to review the classification of some of this important group of plant structures, which includes about 50 direct is_a children such as the parts of the leaf, plant axis, root, shoot axis, sporangium, archegonium, ovary, palea, petiole, etc etc

COP = cardinal organ part

CPS = collective plant structure

COPS = collective organ part structure

parts of seed (PO:0009010)

Seed is_a plant structure, but seed develops from ovule, which is now a plant organ.


COP's that are part of a seed: : hilum (PO:0020063), hilum groove (PO:0004719); arilloid (PO:0019022); seed funicle (PO:0006332)(>stalk > COP); seed raphe (PO:0006331)


Suggested solution: make seed is_a plant organ

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.

-Note: The definition of plant structure (the genus) encompasses any entity that is: "An anatomical structure that is or was part of a plant, or was derived from a part of a plant."


Issue: a seed has an embryo (and other things) as part.

However, we already have several organs that have other organs as parts (e.g., carpel), and even an ovule can have a whole plant as a part (the megagametophyte).

Suggest adding comment to plant organ saying that is may have other plant organs as parts and add comment CPS it from plant organ (see below).

parts of fruit and parts of gyneocium

Fruit and gynoecium are collective plant structures.

COP's that are part of fruit: fruit distal end (PO:0008001); fruit proximal end (PO:0008002)

The problem with fruit is that it can either develop from a single carpel or from a gynoecium that is composed of multiple carpels. Anything that is part of gynoecium or a fruit is problematic.

Problematic classes:

  • gynoecium - Right now, we have a note on gynoecium, saying that it is composed of a single carpel, the annotation should go on carpel.
  • ovary ((PO:0009072) - ovary is_a plant structure, to deal with it multiple nature
  • funicle (PO:0020006) - part of ovary. Suggest changing funicle to part of ovule. This is consistent with seed funicle being part of seed.
  • ovary wall (PO:0005022) - part of ovary. Can be either a COP (if one carpel) or a collective organ part structure (if multiple carpels), just like ovary
  • fruit (no mention of fruits from single carpels)
  • fruit distal end
  • fruit proximal end
  • fruit valve (is_a valve, which is_a COP)

other

These do not have a part_of relation to any plant organ:

receptacle (PO:0009064): A receptacle can be part_of either a pedicel or a peduncle as stated in definition. Add relation part_of shoot axis, to be more specific.

Is a receptacle part of a flower? It was orginally. It could stay part of shoot axis and also be part of flower.

lamina (PO:0025060)

Already is part of plant organ through transitivity, but should change the definition to correspond.

lamina (PO:0025060), proposed def.: A cardinal organ part (PO:0025001) that is thin and flat.

comment: Refers to PATO:0000407 (flat) and PATO:0000592 (thin).

RW will post new proposed def. on SF.


stalk (PO:0025066) - Already part of plant organ through transitivity.

Problematic subtypes are funicle and seed funicle. Suggest making funicle part of ovule (this makes sense, since seed funicle is part of seed). If seed is_a plant organ, then funicle will be fine as a subtype of stalk.

Plant organ, CPS and COPS

These classes might be a little confusing, since a plant organ can have other organs as parts, making it seem like it fits the definition of CPS (two or more organs).

plant organ (PO:0009008), current def.: 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.

comment: Examples: stem, leaf, root. May include individual cell types that are not part of tissues (e.g.: idioblasts).

plant organ (PO:0009008), proposed def.: A plant structure (PO:0009011) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path.

comment: Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual cell types that are not part of tissues (e.g., idioblasts). A plant organ may have one or more different plant organs as parts, such as sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094).


colllective plant structure (PO:0025007), current def.: 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.

comment: Organs can be of the same type or different types. Examples include: flower PO:0009046, perianth PO:0009058, inflorescence PO:0009049. See also collective organ part structure, for plant structures composed of parts of multiple organs, but no complete organs.

colllective plant structure (PO:0025007), proposed def.: A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and is composed of two or more adjacent plant organs (PO:0009008) and any associated portions of plant tissue (PO:0009007).

comment: A colllective plant structure must have as parts at least two organs that do not have a part of relation between them, that is, they must be adjacent, rather than one within the other. The organs in a collective plant structure can be of the same type, such as a corolla (PO:0009059) composed of multiple petals (PO:0009032), or of different types, such as a flower (PO:0009046). Examples include flower, perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs, but no complete organs.


cardinal organ part (PO:0025001), current def.: A plant structure that is a proper part of an organ and includes portions of tissues of at least two different types.

comment: Cardinal refers to the fact that these are biologically meaningful parts, not arbitrary. Examples include lobe (PO TBD), operculum (PO TBD), neck (PO TBD), petiole PO:0020038, leaflet PO:0020049.

cardinal organ part (PO:0025001), proposed def.: A plant structure (PO:0009011) that is a proper part of a plant organ (PO:0009008) and includes portions of plant tissue (PO:0009007) of at least two different types.

comment: Cardinal refers to the fact that these are biologically meaningful parts, not arbitrary. Examples include petiole (PO:0020038), lamina (PO:0025060), and leaflet (PO:0020049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs.

Items from older meetings

Root primordia and roots

lateral root

lateral root (PO:0020121), current def.: A root that develops from a lateral root primordium located in the pericycle layer of a primary root.

proposed def.: A root (PO:0009005) that develops from a lateral root primordium (PO:0000016) that is part of another root.

comment: A lateral root primordium may develops on any root, including a primary root (PO:0020127), on an existing lateral root (PO:0020121), or a shoot-borne root (PO:0000042) . In seed plants, a lateral root primordium generally develops from pericycle cells (PO:0025261), but cells of an endodermis (PO:0000252) may also participate in its formation in some species. In ferns, lateral root primordia develop from the endodermis.

root anlagen

Root anlagen is_a portion of pericycle tissue, but this is not always true. Lateral roots can also develop from endodermis, and shoot-borne root develop from parenchyma cells on a stem or branch (or elsewhere).

New proposed definition for root anlagen (PO:0025433): A portion of plant tissue (PO:0009007 that is committed to the development of a root primordium (PO:0005029).

Comment: Only detectable by gene expression, not morphology. May arise in a pericycle (PO:0006203), as the lateral root of in most seed plants, an endodermis (PO:0000252), as in ferns, or from parenchyma cells (PO:0000074) that are part a shoot axis (PO:0025029), in the case of a basal root (PO:0025002) or shoot-borne root (PO:0000042).

root primordium

root primordium (PO:0005029), new def.: A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005).

Comment: Root primordia may arise from pericycle cells (PO:0025261), as in most seed plants, cells of an endodermis (PO:0000252), as in ferns, or from cells on a shoot axis (PO:0025029), in the case of basal root primordia (PO:0025479) and shoot-borne root primordia (PO:0025480). Transition from root primordium to root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147).

ref.: Steves and Sussex, ISBN:0521288959, POC:curators

added root primordium develops from root anlagen (PO:0025433).


adventitious root primordium (PO:0008038): We don't actually have a term for adventitious root. This term has been obsoleted. There are no annotations on adventitious root primordium.


basal root primordium, new term (PO:0025479): A root primordium (PO:0005029) that is committed to the development of a basal root (PO:0025002).

comment: Transition from basal root primordium to basal root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147).

synonym: adventitious root primordium (broad)

added basal root develops_from basal root primordium


shoot-borne root primordium, new term (PO:0025480): A root primordium (PO:0005029) that is committed to the development of a shoot-borne root (PO:0000042).

comment: Transition from shoot-borne root primordium to shoot-borne root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147).

synonym: adventitious root primordium (broad)

added shoot-borne root develops_from shoot-borne root primordium


lateral root primordium (PO:0000016), existing def.: A root primordium that is derived from a root pericycle and will develop into a lateral root.

lateral root primordium (PO:0000016), proposed def.: A root primordium (PO:0005029) that is committed to the development of a lateral root (PO:0020121).

comment: In seed plants, a lateral root primordium generally develops from pericycle cells (PO:0025261), but cells of an endodermis (PO:0000252) may also participate in the formation of a lateral root primordium in some species, and in ferns lateral root primordia develop from the endodermis. Transition from lateral root primordium to lateral root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147), which can occur before the lateral root penetrates the exterior of the parent root.

>Removed the relation lateral root primordium develops_from pericycle (PO:0006203), because it is not always true.

>Added relation lateral root primordium part_of root, because that is what makes it a lateral root primorodium.

ovule

At the POC meeting on 4-17-12, we agreed to make ovule a plant organ, instead of a cardinal organ part. It may be part of carpel, which is a plant organ, but we already have other examples of organs that are part of other organs (e.g., nucellus and pollen sac).

Also, ovule is currently part_of ovary, but that is only true for angiosperms. Ovules can be found in all seed plants.

proposed def., ovule (PO:0020003): A plant organ (PO:0009008) that has as parts a nucellus (PO:0020020) containing a female gametophyte (PO:0025279), one or two integuments (PO:0020021), and a funicle (PO:0020006).

comment: A seed (PO:0009010) develops from an ovule. In angiosperms, an ovule is located in an ovary (PO:0009072). In gymnosperms, an ovule is located on an ovuliferous bract (add term).


PJ requested separate subtypes for ovarian ovule and non-ovarian ovule, to make annotation easier. Suggest using ovuliferous scale ovule instead of non-ovarian ovule. See Items_for_future_meetings#ovuliferous_scale.


Antiraphe, chalaza, integument, nucellus, and raphe are part_of ovule. Will need to add comment to each of these saying: "If you are annotating to this structure for an angiosperm, please add an additional annotation to ovarian ovule (PO:id). If you are annotating to this structure for an gymnosperm, please add an additional annotation to ovuliferous scale ovule (PO:id)."

PO-CARO

The Common Anatomy Reference Ontology (CARO) is undergoing a major revision as CARO 2.

Since all of the PAE root terms are defined based on CARO, it would be good to review their proposed definitions and provide them with feedback before their release.

This will be especially important if we want to include structures that were part of a plant, as this may not be covered by their definition.

Also, it is not clear how or if in vitro plant structures would fit into CARO.

Upcoming meetings and Presentations 2012:

Semantics of Biodiversity Workshop

May 16 - 18, 2012

University of Kansas Biodiversity Institute, Lawrence, Kansas

The goals of this workshop (still being refined): 1) Clarification of terms used in the biodiversity, genomics, and ecological communities, and 2) Steps to take in building a Biocollections Ontology.

BS, MAG, and RW are attending.

MOSS 2012 and The 3rd International Symposium on Molecular Systematics of Bryophytes

Sunday, May 6, 2012, 11:59 PM - The submission period for oral presentation and poster abstracts closes in order to allow for printing of conference materials.

Attendees have the option of registering for MOSS 2102 ($225), the Symposium on Molecular Systematics of Bryophytes ($225) or both ($400).

RW submitteed an abstract for a poster.

Crop Ontology Workshop

For more information see the wiki page: Crop_Ontology_Workshop_at_OSU,_2012

Dates TBA: probably Sept. 13-15th

The focus of the workshop will be on mostly development stages and traits for the crop plants

Ruth Bastow is contacting some of the interested people to see which of these dates work best.

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

see: Botany 2012 workshops

The meeting web site has been fixed so this is now listed as a half-day (morning) workshop. The schedule now links to the correct abstract.

RW will prepare an announcement for the PO home page and FB page.

Workshop goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.

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

A desktop version of the image annotation software should be ready to demo at this meeting.

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.

We should do the booth. PJ will attend to host the booth for both Gramene and PO.

Bio-Ontologies SIG 2012

Where: July 13 - 14, 2012, Long Beach, CA. Co-located with ISMB 2012

When: Submissions Due: April 13th, 2012 (Fri)

See: Bio-Ontologies SIG 2012

Three types of submissions.

- Short papers, up to 4 pages. - Poster abstracts, up to 1 page. - Flash updates, up to 1 page

Successful papers will be presented at the Bio-Ontologies SIG.

Poster abstracts: time will be allocated during the 2 days for at least one poster session.

Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.

ASPB Plant Biology 2012

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

Link to meeting page: ASPB2012

Abstract was submitted for submission for minisymposia consideration.

Joint workshop is planned with PO, Gramene and TAIR

Registration is open, 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)

RW and BS (with JE, AG, DWS and PJ) submitted a short paper describing a plant disease extension of the Infectious Disease Ontology. This paper was accepted and is being revised. Wiki page for notes on Plant Disease Ontology.

Relevant dates

  • Feb. 28th, 2012: Notification of paper acceptance
  • April 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
  • May 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

RW sent around a draft of an abstract for a poster summarizing the PO-FNA collaboration, with the folks from FNA.

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

Anatomy Ontology Course at NESCent, July 30th- Aug 3rd, 2012

Link to: Anatomy Ontology course

from Paula Mabee: Opening are available the Anatomy Ontology course.

Link to Course materials

This course aims to teach proper ontology design principles and practices such that anatomical interoperability across evolutionarily disparate taxa is achieved. It further seeks to promote community growth and adoption of ontology-based methods and tools. The subsequent benefit is in the form of shared access to the unique data store of each community (e.g. genetic, genomic, developmental, and evolutionary data).

Apply here: [1]

Application deadline is April 4th, 2012 (extended through mid-April)

Next meeting scheduled for Tuesday, May 15th, 2012 at 10am PDT/1pm EDT

See: POC_Conf._Call_5-15-12: MAG, RW and BS will be away

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