POC Conf. Call 5-1-12
POC meeting, Webex Conference Call; Date: Tuesday May 1th, 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_4-24-12?
Back to POC Meetings Minutes
Open items
root tuber
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. Perhaps calling it "tuber root" will make it more clear that it is a root.
tuber root (PO:0025476), new proposed def.: A radially enlarged root (PO:0009005) that is either a shoot-borne root or a lateral root.
comment: Functions in storage. This term should be used for tubers derived from roots, as found in Cassava, not for tubers derived from branches (PO:0025073), as found in potatoes and yams. Use the term tuber (PO:0004543), aerial tuber (PO:0004548), or subterranean tuber (PO:0004547) for tubers derived from branches. A tuber 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 tuber roots bear vegetative buds (PO:0000058) like a tuber derived from a branch, but these arise from adventitious buds or are derived from the stem (PO:0009047) to which the tuber root is attached. A tuber root usually develops from a shoot-borne root (PO:0000042) or a lateral root (PO:0020121).
synonyms: root tuber (exact), storage root (broad)
Make children shoot-borne tuber root (for cassava) and lateral tuber root.
Also suggest minor change to definition of tuber:
tuber (PO:0004543), new proposed def.: A branch that is radially enlarged through primary growth.
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.
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.
Question: Would it be better to rename meristem (PO:0009013) to "portion of meristem tissue"? As LC pointed out last week, it is confusing when you look at the graph or tree view and see things like "primordium is_a meristem" or "peripheral zone is_a shoot meristem", when what we really mean is "primordium is_a portion of meristem tissue" and "peripheral zone is_a portion of shoot meristem tissue".
flower 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."
Made flower primordium (PO:0004706) obsolete. Added relations "consider flower apical meristem" and "consider floral structure primordium".
Also added comment: This term was made obsolete because it is ambiguous. Use flower meristem (PO:0000229) or floral structure primordium (PO:0025477) instead. If annotating to a primordium of a floral structure, it is better to use the more specific term, such as petal primordium (PO:0000021) or anther primordium (PO:0006089).
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).
phyllome and leaf meristems
Phyllome abaxial meristem (PO:0025402), phyllome adaxial meristem (PO:0025400), phyllome marginal meristem (PO:0025404), and phyllome plate meristem (PO:0025428): Can all of these occur in a phyllome primordium as well as a phyllome, or only marginal meristem?
Right now, phyllome marginal meristem is part_of phyllome and part_of phyllome primordium, but others are only part of phyllome.
Same issue with leaf abaxial meristem (PO:0025403), leaf adaxial meristem (PO:0025401), leaf marginal meristem (PO:0025405), and leaf plate meristem (PO:0025429).
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.
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).
Do we want to go ahead and add lodicule, petal, sepal, and stamen anlagen?
lodicule primordium (PO:0008040): A phyllome primordium (PO:0025128) 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) 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) 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) 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 (see anlagen tracker).
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 on 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, so we agreed 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.
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
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
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.
Removed the relation lateral root primordium develops_from pericycle (PO:0006203), because it is not always true.
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
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.
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 forward email to PO announce list and post on PO Facebook page.
