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?
Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=64281402&rKey=aee3768e22f1e4c0
Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=64281402&rKey=d755be76d6ec0bba
Back to POC Meetings Minutes
User question
"We have two types of flowers, those that "open" and those that don't. Sometimes they occur on the same plant, sometimes a plant "tends" to produce one type or the other and there is a strong environmental influence. There are two terms for these, cleistogamous (closed) and chasmogamous (open). Should these be developmental stages of "Flower" or are they "types" of flowers? "
I think these are clearly types of flowers, but do we need to have this in the PO, seems like it should be a trait term.
RW will add cleistogamous and chasmogamous to list of adjectives to request in PATO.
These could go in TO as flower traits too (cleistogamy and chasmogamy), if there is a need, or we could add them as synonyms of flower ("cleistogamous flower" and "chasmogamous flower"), or even subtypes of flower in the PO, if there is data associated with them.
LC will respond to user and find out if he has specific need for the terms for data annotation.
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 new term: 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.
LC: I agree that it is a good idea to create a new term to describe the storage root tubers in plants like Cassava, but I think naming it root tuber will be confusing as we have the shoot axis aerial and subterranean tubers already.
LC suggested the following:
storage root (PO:xxxxxxx): A root (PO:0009005) that is enlarged and specialized for storage. (or something to that effect)
This would also make it (more or less) consistent with the Cassava ontology at GCP (http://www.cropontology.org/ontology/CO_334/Cassava)
Comment by RW is ok, except for minor change suggested (in italics) :
Comment: A storage root may be distinguished from a shoot axis tuber (PO:0004543) by the presence of a root cap (PO:0020123) when very young, or the presence of lateral roots (PO:0020121) or their remnants. Sometimes a storage root bears vegetative buds (PO:0000058) like a tuber of the shoot axis (PO:0025029), but these arise from adventitious buds or are derived from the stem (PO:0009047) to which the shoot-borne root is attached. A storage root often develops from a shoot-borne root (PO:0000042).
We could add 'root tuber' as a synonym
This will prevent having to rename the 48 subtypes of tuber (PO:0004543), as suggested 'shoot tuber' (should probably be shoot axis for clarity. Many of the these already have very long names For example: subterranean tuber axillary vegetative bud (PO:0025042) would become: subterranean shoot (axis) tuber axillary vegetative bud.
We agreed that re-naming all of the existing tuber terms would be problematic, but were not comfortable with naming root tuber "storage root". A storage root could really be any root that participates in storage, and many root serve some storage function.
Discussion of using "enlarged". This is the PATO term, and is important to distinguish it from "swollen", which means a temporary enlargement. We thought it would be better to say "radially enlarged" for clarity.
After meeting: RW discussed this DWS and he felt that "root tuber" was the most appropriate name, because other names are not widely used. Even though Bell and Bryan say that any kind of root, including a tap root, can be a root tuber, he felt that it was more appropriate to use root tuber for lateral and shoot-borne roots.
Perhaps the best solution would be to keep the other term names as they are and name this one root tuber. There is no easy way to make help users pick from list of terms unless they read the definitions. We can add comments to make it clear which one is which.
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.
Discussed whether or not to say "is committed to" or "develops into". Problem with "develops into" is that a primordium may not develop into the structure it is committed to.
We do not have a term for inflorescence primordium. Should use inflorescence apical meristem (PO:0009108).
Revised proposed def.: A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011).
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"?
After some discussion, we decided it would be better not to make a term for ground meristem, because it is too difficult to define and is questionable as an entity.
subtypes of primordium
CPS: anther, gynoecium (seems like if we are going to have gynoecium, we should have androecium), flower (will obsolete)
COP: should add leaflet
Organ: root, including later root and adventitious root; phyllome, including carpel, cotyledon, leaf, petal, sepal, stamen, lodicule
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.
Okay to add androecium primordium. Should also add term for bract primordium.
General definition of primordia, proposed: A primordium (PO:0025127) that is committed to the development of a anther/gynoecium/lodicule/phyllome/etc.
flowers
floral organ (or floral phyllome) 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.
See below for definition of phyllome primordium.
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).
A possible exception to this is for Asteraceae, in which each floret arises as a buldge which might technically be an apical meristem, but is often called a primordium. We may want to add a term for disk flower primordium.
roots
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)
phyllomes
phyllome primordium (PO:0025128): A primordium (PO:0025127) that develops from a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148) and is committed to the development of a phyllome (PO:0006001).
comment: A phyllome primordium may contain a phyllome abaxial meristem(PO:0025402), phyllome adaxial meristem (PO:0025400), a phyllome marginal meristem (PO:0025404), or a phyllome plate meristem (PO:0025428), each of which may persist after the transition to a phyllome. The transition from phyllome primordium to phyllome occurs when the first non-meristematic tissue develops (epidermis or primary vascular tissue?) begins to develop , or with expansion and secondary morphogenisis?
Add part_of shoot apex. This relation is currently there for leaf primordium, but should apply to all phyllome primordia.
Add develops_from peripheral zone (PO:0000225), if this is appropriate for all plant. For angiosperms: "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 primordium (PO:0000017): A phyllome primordium (PO:0025128) that is committed to the development of a vascular leaf (PO:0009025).
Suggest changing from leaf to vascular leaf, because people don't use the term primordium for non-vascular leaves, which develop via an apical cell.
Other types of phyllome primordia would be defined similarly, e.g.:
lodicule primordium (PO:0008040): A primordium (PO:0025127) that is committed to the development of a lodicule (PO:0009036)
other
leaflet primordium (new term): A primordium (PO:0025127) that develops as part of a leaf primordium (PO:0000017) of a compound leaf (PO:0020043) and is committed to the development of a leaflet (PO:0020049).
Comment: Leaflets of palms does not develop from leaflet primordia but by separation of segments of the lamina.
We have a term for formation of leaflet primordium, which is a development stage of leaf.
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.
Moved to POC_Conf._Call_5-1-12
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
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.
