POC Conf. Call 5-1-12

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

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Marie Alejandra Gandolfo (Cornell), Pankaj Jaiswal (OSU), Justin Elser (OSU)

Absent: Dennis Stevenson (NYBG), Justin Preece (OSU), 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_4-24-12?

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=64468552&rKey=8194ed9e79a15ff8

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=64468552&rKey=0ecd56f981624935

Back to POC Meetings Minutes

Update and Progress report from Cornell (MAG)

Comments from MAG:

• Number of slides/photos

• Back up systems,

• New website at Cornell for the PO project CUPAC

• Expenses

MAG has been invited to give a talk at the next Southern Connection Congress on fossils, suggest to prepare one on the PO project as well.

21 - 25 January 2013

University of Otago, Dunedin, New Zealand

Prioritize model species

PJ will set up separate meeting with MAG, Kevin, and informatics staff at OSU.

Auricle

This feedback came in from the live site:

"comments: When searching for 'ear' synonyms, PO returns 'auricle', which is an animal definition (i.e. your ear not the ear of corn)- but gives the correct defenition for auricle! Hysterical!"

"ear" is listed as a synonym of auricle (PO:0020106), as part of the PO-FNA mapping.

Many plant structures could be ear shaped, so maybe this term name and synonym are too general.

We will change the name to "vascular leaf auricle" and the synonym to "vascular leaf ear", to make it clearer.

The current def. says: "Outgrowth at the base of a leaf blade that may wrap around the stem."

From PJ via email: an ear-shaped appendage that occurs at the upper part of the sheath. Size and prominence varies greatly among species.

New proposed def. of vascular leaf auricle: A cardinal organ part (PO:0025001) that is an ear-shaped outgrowth of the distal part of a leaf sheath (PO:0020104).

Comment: May wrap around the stem (PO:0009047) or branch (PO:0025073) to which the vascular leaf (PO:0009025) it is part of is attached. Found in some Poaceae.

part_of leaf sheath (which is already part_of vascular leaf).

RW: A better name would be leaf sheath auricle.

Open items

tuberous root

We discussed this at last week's meeting. There is concern about users choosing "root tuber" when they should use "subterranean tuber, but it is hard to get around.

Propose new name: "tuberous root" to make it more clear that it is a root.

tuberous root (PO:0025476), new proposed def.: A root (PO:0009005) that is radially enlarged through primary growth.

comment: Functions in storage of photosynthate metabolites. May be either a shoot-borne root (PO:0000042) or a lateral root (PO:0020121). This term should be used for tubers derived from roots, as found in Cassava, Ipomoea, or Hemerocallis, not for tubers derived from branches (PO:0025073), as found in Solanum tuberosum (potatoes) or Dioscorea (yams).

Use one of these terms: tuber (PO:0004543), aerial tuber (PO:0004548), or subterranean tuber (PO:0004547) for tubers derived from branches.

A tuberous root may be distinguished from a tuber that is derived from a branch by the presence of a root cap (PO:0020123) early in development, or the presence of lateral roots (PO:0020121) or their remnants.

Sometimes tuberous roots bear vegetative buds (PO:0000058) like a tuber derived from a branch, but these arise from adventitious buds (synonym of bud PO:0000055) or are derived from the stem (PO:0009047) to which the tuberous root is attached.

synonyms: root tuber (exact), storage root (broad)

Revised comment: Functions in storage of photosynthate metabolites. May develop from either a shoot-borne root (PO:0000042) or a lateral root (PO:0020121). This term, or its subclasses, should be used for tubers that develop from roots, as found in Cassava, Ipomoea, or Hemerocallis, not for tubers that develop from branches (PO:0025073), as found in Solanum tuberosum (potatoes) or Dioscorea (yams). Use tuber (PO:0004543), aerial tuber (PO:0004548), or subterranean tuber (PO:0004547) for tubers derived from branches. A tuberous root may be distinguished from a tuber that develops from a branch by the presence of a root cap (PO:0020123) early in development, or the presence of lateral roots (PO:0020121) or their remnants. Sometimes tuberous roots bear vegetative buds (PO:0000058) like a tuber derived from a branch, but these arise from adventitious buds (synonym of bud PO:0000055) or are derived from the stem (PO:0009047) to which the tuberous root is attached.

On further investigation, it seems that not only primary growth is involved in the formation of root tubers. There is secondary thickening, and may even some growth from the vascular or cork cambium. Need to look into it more.

Also, it seems there are both tuberous roots (enlarged roots that form tubers along part of their length), and tubers, that form within those roots (see http://aob.oxfordjournals.org/content/38/2/307.full.pdf+html and hortsci.ashspublications.org/content/44/3/651.full.pdf).

http://www.springerlink.com/content/16l02n16131l284j/fulltext.html

Will post more on SourceForge.

• Note: A primary root (PO:0020127) may also function in storage and enlarge radially, as in Daucus carota. Should these structures be included in the class of tuberous roots? How do we distinguish them?

We will not add term for "tuberous tap root" yet. Can add it if someone needs it.

Need to change definition of lateral root (PO:0020121): should be a root that develops from another root (not just form a primary root). Also, doesn't always develop from pericycle.

Should involve the root nomenclature group in reviewing these definitions.

New subtypes of tuberous root:

shoot-borne tuberous root (PO:xxxxxxx), proposed def.: A tuberous root (PO:0025476) that is a radially enlarged shoot-borne root (PO:0000042).

synonym: shoot-borne root tuber

revised name + def'n: tuberous shoot-borne root (PO:xxxxxxx): A tuberous root (PO:0025476) that develops from a shoot-borne root (PO:0000042).

Add comment: Functions in storage of photosynthate metabolites. This term should be used for a tuber that develop from a shoot-borne root, as found in Cassava, not for tubers (PO:0004543) that develop from branches (PO:0025073), as found in Solanum tuberosum (potatoes) or Dioscorea (yams). Use tuber (PO:0004543), aerial tuber (PO:0004548), or subterranean tuber (PO:0004547) for tubers derived from branches. A tuberous root may be distinguished from a tuber that develops from a branch by the presence of a root cap (PO:0020123) early in development, or the presence of lateral roots (PO:0020121) or their remnants. Sometimes tuberous shoot-borne roots bear vegetative buds (PO:0000058) like a tuber derived from a branch, but these arise from adventitious buds (synonym of bud PO:0000055) or are derived from the stem (PO:0009047) to which the shoot-borne tuberous root is attached.

lateral tuberous root (PO:xxxxxxx), proposed def.: A tuberous root (PO:0025476) that is a radially enlarged lateral root (PO:0020121).

is_a tuberous root and is_a lateral root

synonym: lateral root tuber

revised name + def'n: A tuberous root (PO:0025476) that develops from a lateral root (PO:0020121).

Add comment: Functions in storage of photosynthate metabolites. This term should be used for a tuber that develop from a lateral root, as found in xxxx, not for tubers (PO:0004543) that develop from branches (PO:0025073), as found in Solanum tuberosum (potatoes) or Dioscorea (yams). Use tuber (PO:0004543), aerial tuber (PO:0004548), or subterranean tuber (PO:0004547) for tubers derived from branches. A tuberous root may be distinguished from a tuber that develops from a branch by the presence of a root cap (PO:0020123) early in development, or the presence of lateral roots (PO:0020121) or their remnants. Sometimes tuberous lateral roots bear vegetative buds (PO:0000058) like a tuber derived from a branch, but these arise from adventitious buds (synonym of bud PO:0000055).

• There can also be tubers of the hypocotyl-root junction (PO:0004724), like Beta vulgaris, Raphanus sativus, or Cyclamen. These are sometimes called "stem tubers", but it is actually hard to distinguish between stem and primary root in these structures.

Also suggest minor change to definition of tuber (PO:0004543):

tuber (PO:0004543), new proposed def.: A branch (PO:ID) that is radially enlarged through primary growth.

look up if we should say something about which tissue enlarge

new synonym: tuber branch (exact)

tuber (PO:0004543): revised def'n: A shoot axis (PO:00025029) that is radially enlarged and develops from a branch (PO:00025073).

new synonyms: tuber branch (exact), shoot axis branch tuber (exact)

done, ok

revised comment for both tuber (PO:0004543) and subterranean tuber (PO:0004547): Functions in storage of photosynthate metabolites. This term should be used for tubers derived from branches, as found in Solanum spp. (e.g. potato) or Dioscorea spp. (e.g. yam) and other species. Use the term tuberous root (PO:0025476) for tubers derived from roots, such as those found in Cassava, Ipomoea, or Hemerocallis.

added exact synonym to branch (PO:00025073): shoot axis branch

done, ok

Primordium

general definition

General definition was agreed upon at last week's meeting (see SF tracker).

The subtypes of primordium will be defined as "A primordium (PO:0025127) that is committed to the development of a anther/gynoecium/lodicule/phyllome/etc. (PO:id)," with comments as needed.

floral structure primordium

Created new term: floral structure primordium (PO:0025477)

Androecium primordium, anther primordium, gynoecium primordium, ovule primordium are subtypes of floral structure primordium. Others (carpel, etc.) are subtypes of both phyllome primordium and floral structure primordium.

For CM: It would be great if we could set up logical definitions to the effect "floral structure primordium is any plant structure that has a develops_from child that is part of a flower."

androecium primordium (PO:0025478): A floral structure primordium (PO:0025477) that is committed to the development of an androecium (PO:0009061).

comment: Use stamen primordium (PO:0004705) for the primordium (PO:0025127) of an individual stamen (PO:0009029).

gynoecium primordium (PO:0000019): A floral structure primordium (PO:0025477) that is committed to the development of a gynoecium (PO:0009062).

comment: Use carpel primordium (PO:0004703) for the primordium (PO:0025127) of an individual carpel (PO:0009030).

Add pistil primordium as an exact synonym of gynoecium primordium, and change "pistil" as synonym of gynoecium to exact. Add pistil as broad synonym to carpel. Add comments to gynoecium and carpel.

anther primordium (PO:0006089): A floral structure primordium (PO:0025477) that is committed to the development of an anther (PO:0009066).

ovule primordium (PO:0000018): A floral structure primordium (PO:0025477) 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).

related item: phyllome and leaf meristems

Right now, phyllome marginal meristem (PO:0025404) is part_of phyllome and part_of phyllome primordium and leaf marginal meristem (PO:0025405) is part_of both leaf and leaf primordium. Suggest making these just part of phyllome or leaf. Although there can be marginal growth in a phyllome primordium or leaf primordium, it does not necessarily come from a marginal meristem as we have defined it. If need be, we could make specific terms for phyllome primordium marginal meristem and leaf primordium marginal meristem.

phyllome primordium

phyllome primordium (PO:0025128): A primordium (PO:0025127) that develops from a phyllome anlagen (PO:0025430) that is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148) and is committed to the development of a phyllome (PO:0006001).

comment: The transition from phyllome primordium to phyllome occurs when the first non-meristematic tissue develops begins to develop.

POC:curators and PMID:11572953

Added phyllome anlagen part_of peripheral zone (PO:0000225) and removed leaf anlagen and carpel anlagen part_of peripheral zone.

Added phyllome primordium part of shoot apex.

leaf primordium (PO:0000017) -- changed to vascular leaf primordium

vascular leaf primordium (PO:0000017): A phyllome primordium (PO:0025128) that develops from a leaf anlagen (PO:0025430) and is committed to the development of a vascular leaf (PO:0009025).

Removed vascular leaf primordium part_of shoot apex and added vascular leaf primordium part_of vegetative shoot apex (PO:0025223).

Leaf anlagen is already defined as part of peripheral zone of a vegetative shoot apical meristem.

See leaf morphogenesis ppt by MAG: Media:MAG_Leaf-morph_B.pdf

carpel primordium (PO:0004703): A phyllome primordium (PO:0025128) that develops from a carpel anlagen (PO:0006005) and is committed to the development of a carpel (PO:0009030).

Carpel anlagen is already defined as part of peripheral zone of a flower meristem.

Added carpel primordium part_of reproductive shoot apex (PO:0025222). is_a phyllome primordium and is_a floral structure primordium.

cotyledon primordium (PO:0000015): A phyllome primordium (PO:0025128) that develops from a cotyledon anlagen (PO:0025432) and is committed to the development of a cotyledon (PO:0020030).

Cotyledon anlagen is defined as a part of embryo (unlike other anlagen). Changed it to part of peripheral zone of an embryo shoot apical meristem (PO:0006362) to parallel other types of phyllome anlagen.

Added cotyledon primordium part_of vegetative shoot apex (PO:0025223).

bract primordium (new term): A phyllome primordium (PO:0025128) that develops from a bract anlagen (PO:id) and is committed to the development of a bract (PO:0009055).

Suggest we go ahead and add terms for bract, lodicule, petal, sepal, and stamen anlagen.

lodicule primordium (PO:0008040): A phyllome primordium (PO:0025128) that develops from a lodicule anlagen (PO:id) and is committed to the development of a lodicule (PO:0009036).

is_a phyllome primordium, is_a floral structure primordium

Added lodicule primordium part_of reproductive shoot apex (PO:0025222).

petal primordium (PO:0000021): A phyllome primordium (PO:0025128) that develops from a petal anlagen (PO:id) and is committed to the development of a petal (PO:0009032).

is_a phyllome primordium, is_a floral structure primordium

Added petal primordium part_of reproductive shoot apex (PO:0025222).

sepal primordium (PO:0004704): A phyllome primordium (PO:0025128) that develops from a sepal anlagen (PO:id) and is committed to the development of a petal (PO:0009032).

is_a phyllome primordium, is_a floral structure primordium

Added sepal primordium part_of reproductive shoot apex (PO:0025222).

stamen primordium (PO:0004705): A phyllome primordium (PO:0025128) that develops from a stamen anlagen (PO:id) and is committed to the development of a stamen (PO:0009029).

is_a phyllome primordium, is_a floral structure primordium

Added stamen primordium part_of reproductive shoot apex (PO:0025222).

root primordia

Moved to POC Conf. Call 5-8-12

ovule

Moved to POC Conf. Call 5-8-12

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 could present a poster, based on the talk we gave at least year's meeting. Will need to register and prepare the abstract this week.

RW will prepare abstract for poster. Can add something vague about analysis with Physco data.

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 forwarded email to PO announce list and posted on PO Facebook page to help them increase awareness.

Next meeting scheduled for Tuesday, May 8th, 2012 at 10am PDT/1pm EDT

POC_Conf._Call_5-8-12