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
- 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
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 (GO term?).
comment: Functions in storage. 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)
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?
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).
is_a tuberous root and is_a shoot-borne root
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:
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
need to revise the definition of lateral root- can arise from other roots, not just the primary root.
revised name + def'n:
- 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)
Added new comment to both tuber and subterranean tuber (PO:0004547): Functions in storage. This term should be used for tubers derived from branches, as found in potatoes, yams, and other species, not for tubers derived from roots. Use the term tuber root (PO:0025476) for tubers derived from roots, as in Cassava.
this will need to be updated now
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).
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).
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
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).
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 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).
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).
added basal root develops_from basal root primordium
synonym: adventitious root primordium (broad)
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).
added shoot-borne root develops_from shoot-borne root primordium
synonym: adventitious root primordium (broad)
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: 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.
synonym: adventitious root primordium (broad)
Removed the relation lateral root primordium develops_from pericycle (PO:0006203), because it is not always true.
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 bract/scale ovule instead of non-ovarian ovule.
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 bract ovule (PO:id)."
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.
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
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)
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.
