POC Conf. Call 4-24-12

POC meeting, Webex Conference Call; Date: Tuesday Apr 24th, 2012 10am PDT/1pm EDT

In attendance:

POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_4-17-12?

Back to POC Meetings Minutes

Items from old agendas and open SF trackers

root tuber

Propose adding a new term for root tuber. This is the structure found in cassava and Ipomoea (sweet potato).

proposed def., root tuber: An enlarged storage root (PO:0009005).

Comment: Root tubers often develop from shoot-borne roots (PO:0000042). Root tubers may be distinguished from shoot tubers (PO:0004543) by the presences of a root cap (PO:0020123) when very young or the presence of lateral roots (PO:0020121) or their remnants. Sometime root tubers bear vegetative buds (PO:0000058) like shoot tubers, but these arise from adventitious buds or are derived from the stem (PO:0009047) to which the shoot-borne root is attached.

Refs.: Bell and Bryan, ISBN:978088192850. See also: Cassava of Tropical Africa, ISBN:9781310413

This would be is_a root and would be separate from the existing term tuber (PO:0004543).

Suggest renaming PO:0004543 (and its subtypes) shoot tuber. Its definition is okay. Add comment that shoot tubers can be distinguished from root tubers by the presence of scale-like leaves and/or axillary buds.

Primordium

primordium (PO:0025127), current def.: A portion of plant tissue that differentiates and develops from meristem tissue into a new plant structure. [source: POC:Curators]

Comment: The primordium is the first distinct form in the development of a plant structure.

At previous meetings, there was a discussion of making this a subtype of plant organ, but we decided it was better as portion of meristem tissue (can have as parts different types of meristem tissue).

proposed def.: A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and ground meristem (PO:id) and is committed to the development of a particular plant structure (PO:0009011).

Comment: A primordium appears as a protrusion and is the first distinct form of a plant organ (PO:0009008), cardinal organ part (PO:0025001), or collective plant structure (PO:0025007). The transition from a primordium to the plant structure it develops into is marked by the development of non-meristematic cells, although meristematic cells may be present after the transition.

ground meristem

We don't actually have a term for ground meristem. Propose that we add one.

Esau says "A primary meristem or meristematic tissue, derived from the apical meristem and giving rise to ground tissues." Raven't definition is similar. However, the ground meristem can also give rise to other types of meristematic tissue.

ground meristem (new term), proposed def.: A portion of meristem tissue (PO:0009013) that develops from an apical meristem (PO:0020144) and develops primarily into ground tissue.

comment: May also develop into other types of meristematic tissue.

Should rib zone (PO:0000226) (aka rib meristem) be is_a ground meristem?

and "periblem(PO:0008036): A portion of meristem tissue that forms the cortex"?

subtypes of primordium

CPS: anther, gynoecium (seems like if we are going to have gynoecium, we should have androecium), flower (will obsolete)

COP: lodicule (should also add leaflet)

Organ: root, including later root and adventitious root; phyllome, including carpel, cotyledon, leaf, petal, sepal, stamen

Other: abaxial side of leaf primodordium, adaxial side of leaf primordium

Currentlly, each type of primordium is defined as "as primordium will develop into an xxxx". However, it might be better to say "is committed to the development of xxx", or something like that.

floral organ primordium (new term): A phyllome primordium (PO:0025128) that is committed to the development of a floral organ (PO:0025395).

comment: A floral organ primordium may develop into a carpel, petal, sepal, or stamen.

Add carpel, petal, sepal, and stamen primordium as subtypes. Will have dual parentage.

If we want to include anther primordium and gynoecium primordium here, then we need to call it "floral structure primordium".

floral structure primordium (alternative term and definitions): A primordium (PO:0025127) that is committed to the development of a floral organ (PO:0025395) or other floral structure such as a gynoecium (PO:0009062) or anther (PO:0009066).

Other types of primordia, proposed definition: A primordium (PO:0025127) that is committed to the development of a anther/gynoecium/lodicule/phyllome/etc.

Proposed definitions and comments for specific types of primordia:

root primordium (PO:0005029: A primordium (PO:0025127) that 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:id) and shoot-borne root primordia (PO:id). 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).

adventitious root primordium (PO:0008038):

We don't actually have a term for adventitious root, so it would be better to obsolete this term and add new terms for basal root primordium and shoot-borne root primordium. There are no annotations on adventitious root primordium. Same goes for adventitious root apical meristem (PO:0006021) and adventitious root epidermis (PO:0006039).

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

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

(add appropriate develops_from relations to roots)

lateral root primordium (PO:0000016): A root primordium (PO:0005029) that is committed to the development of a lateral root (O:0009005).

comment: A lateral root primordium generally develop 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.

ovule primordium (PO:0000018): A primordium (PO:0025127) that is committed to the development of an ovule (PO:0020003).

Comment: The transition from ovule primordium to ovule occurs when an integument (PO:0020021) begins to develop from the protoderm (PO:0006210).

(ref.: Esau p. 564)

phyllome primordium (PO:0025128): A primordium (PO:0025127) that is committed to the development of a phyllome (PO:0006001).

comment: The transition from phyllome primordium to phyllome occurs when the ???

leaf primordium, current def.: A phyllome primordium that will develop into a leaf. [source: POC:Curators]

Comment: Emerges as an outgrowth in the shoot apex (flanking the meristem).

I think we should modify this to say that it develops from the peripheral zone (PO:0000225) and is part of the shoot apex.

"The SAM consists of two zones. The cells of the central zone (CZ), which occupy the center of the SAM, are undifferentiated and divide to produce cells in the peripheral zone (PZ), a ring of cells below the CZ (21). Cells in the CZ are unable to form primordia. LPs (leaf primordia) only occur in the PZ."

leaf: when ab/adaxial meristems start to form - works for other phyllomes too.

Even though we don't have a PO term for it, people also use the term "leaflet primordium", which is also a cardinal organ part. (We have a term for formation of leaflet primordium).

anlagen

We have terms for root anlagen, phyllome anlagen, carpel anlagen, leaf anlagen, and cotyledon anlagen. We have develops_from relations between leaf, carpel, and cotyledon primordia and their respective anlagen. Suggest adding similar relations for phyllome and root.

misc. notes

Note: leaf marginal meristem is part_of leaf primordium and part_of vascular leaf. Can't be both, unless leaf primordium is a leaf, which it isn't. Same for phyllome marginal meristem.

Note: promeristem should be a synonym of AM, not RAM.

ovule

current def. of ovule (PO:0020003): A stalked or sessile structure in a seed plant within which one or more megaspores are formed and later the female gametophyte or embryo sac develops.

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.

From Fahn: A structure (in a seed plant) consisting of the nucellus which contains the female gametophyte, one or two integuments, and the funiculus.

proposed def.: 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), but does not have as part an ovary (PO:0009072).

comment: A seed develops from an ovule. In angiosperms, an ovule is located in an ovary.

RW: I don't really like the wording of the last part, but I put it in there to distinguish it from carpel, which is also a plant organ that has as parts a nucellus containing a female gametophyte , one or two integuments, and a funicle.

PJ requested separate subtypes for ovarian ovule and non-ovarian ovule, to make annotation easier.

There is nothing special to distinguish a non-ovarian ovule, so we could do like we did for sporangium, and have a specific subtypes for ovarian ovule, but classify other types of ovules as simply ovule.

If we add a term for ovarian ovule, then we also need subtypes for the parts of the ovule in an ovary (antiraphe, chalaza, integument, nucellus, raphe).

Alternatively, we could add ovary has_part ovule, then put a comment on ovule, antiraphe, chalaza, integument, nucellus, and raphe to add an additional annotation to ovary, as we did for leaf.

pericarp and seed coat

Changes to recently completed emergence terms:

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.

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

Crop Ontology Workshop

For more information see the wiki page: Crop_Ontology_Workshop_at_OSU,_2012

Dates TBA: probably Aug 6th to 8th or in Sept.

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.

Can we consider September? RB is available 12th -25th September

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

• PO workshop on Sunday, July 8th, 9:00AM - 12:00PM

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)

LC will forward email to PO announce list and post on PO Facebook page.