POC Conf. Call 6-5-12
POC meeting, Webex Conference Call; Date: Tuesday June 6th, 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_5-29-12?
Back to POC Meetings Minutes
Preparations for Botany meeting workshop
Updated tutorials and presentations
We agreed that updating the PO tutorial videos/ppt presentations was a priority for the next release. RW will need these for the Botany workshop.
See Plant_Ontology_Web_Site_Update:_Winter_2012#Tutorials_and_Demos_out-of-date
Mistakes on website and wiki
See Plant_Ontology_Web_Site_Update:_Winter_2012#High_priority_fixes
Booklet
MAG suggested that we create a booklet for participants to take with them. Some people prefer to have printed guidelines, rather than relying on the website. Maybe two double sided pages, folded in half and stapled in the middle. Just enough to explain the basics of the PO and the website.
Might be good to make it as a PDF, so it can include web links if people open it online.
New upper level terms for PO
This came up as the need to describe things that are part of a seed, along with some other problems.
New and revised collective terms
Background
At the POC Conf. Call 5-8-12 we discussed the need for a general term for collective plant structures that are collections of things other than organs. This general term would be parent of collective plant organ structure, collective organ part structure and other types of collective structures.
If we want this term to be parent to seed, we need to define it broadly. What is a seed? It has as parts a mature ovule, some accessory structures like an aril, and parts derived from the ovule like the seed funicle. It also contains endosperm and an embryo. (See below about located in relation.) Is this a collective plant structure? What does it collect? Maybe seed coat, endosperm, and embryo.
We also need a term to cover structures that are part of a seed (like arilloid and seed funicle) and terms like ovary that are parts of a plant, but do not fit any of the other categories. These are not necessarily collections. Could use something like CARO term multi-tissue structure. This would be parent to CPS, but also plant organ, cardinal organ part, and things like arilloid.
Note from earlier meeting: If we include seed under the new CPS, we should mention that some of the parts of this new CPS are part of the mother plant and some are new organism. Some of the cells may be from the mother plant, but they take on a new developmental pathways, function, etc.
structures that are located other organisms
The located_in relation has been to the PO file. Right now it is only used for embryo sac located in plant ovary ovule, but should be applied whenever there are two plant structures that are parts of different organisms.
Located_in replaces contained_in. Located_in can be used for both part_of and contained_in.
Could also add the "inverse located in" relation. For example, we now have seed has_part plant embryo, but this should really be inverse_located_in. This is a terrible name for the relation.
mulit-tissue plant structure
CARO:multi-tissue structure: Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. -- Examples are simple organ and compound organ component. This is basically the same as PO plant organ.
We probably do not want to constrain our term to have bona-fide boundaries (otherwise, we can't include most cardinal organ parts or things like ovaries). RW has written to CARO to ask if they can modify this, but no specific response.
Also, we don't just want to include "distinct structural units" here, as that more or less confines it to plant organs or discrete organ parts. This terms should also be able to cove "regional parts" or organs or other structures.
proposed definition, multi-tissue plant structure: A plant structure that has as parts two or more portions of plant tissue of at least two different types.
Comment: Includes plant structures that form distinct structural units, such as plant organs like leaves or roots, as well as regional parts of plants such as an ovary or leaf lamina base.
Alternatively, we could define this term similar to CARO, which is similar to our definition of plant organ, but not call it a plant organ and thereby lose all the baggage associated with the term "plant organ". That way, we could classify a seed as a multi-tissue structure.
We would then have to figure out some other way of dealing with the parts of a seed (maybe "cardinal part of a multi-tissue structure" instead of "cardinal part of plant organ"?).
collective plant structure (new)
needs work
A multi-tissue plant structure that has as parts two or more other multi-tissue plant structures.
collective plant organ structure
Changed name, and slight change to clarify that the two organs must be adjacent, not one part of the other. Otherwise, a sporophyll would be a collective plant organ structure.
New proposed def.: A collective plant structure (PO:id) that is a proper part of a whole plant (PO:0000003) and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007).
comment: A collective plant structure must have as parts at least two organs that do not have a part of relation between them, that is, one must be adjacent to the other, rather than one part of the other. The organs in a collective plant structure can be of the same type, such as a corolla (PO:0009059) composed of multiple petals (PO:0009032), or of different types, such as a shoot system (PO:0009006) composed of shoot axes (PO:0025029) and phyllomes (PO:0006001). Other examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for collective plant structures composed of parts of multiple organs, but no complete organs.
Modified comment for plant organ:
new proposed def. for plant organ (PO:0009008): A plant structure (PO:0009011) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path.
comment: Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual cell types that are not part of tissues (e.g., idioblasts). A plant organ may have one or more different plant organs as parts, such as sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel that may have as part an ovule.
Slight modification to cardinal organ part (add comment to see also COPS, add ids):
cardinal organ part (PO:0025001), proposed def.: A plant structure (PO:0009011) that is a proper part of a plant organ (PO:0009008) and includes portions of plant tissue (PO:0009007) of at least two different types.
comment: Cardinal refers to the fact that these are biologically meaningful parts, not arbitrary. Examples include petiole (PO:0020038), lamina (PO:0025060), and leaflet (PO:0020049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs.
From discussion on 5-8-12:
Maybe it would be better to say "cardinal part of collective plant structure" and "cardinal part of plant organ.
FMA has "regional parts". It is like a "zone", which PO uses in a few terms. We also have terms like leaf tip or leaf lobe that are regional parts.
This is what we call a cardinal part. BS: Biological significance is not all of the story for cardinal parts. They should also have their own boudaries on all sides (??), as opposed to regional parts, which just have a boundary on one side.
collective organ part structure
Current def.: A plant structure composed of two or more cardinal organ parts from adjacent organs and any associated portions of plant tissue.
comment: A collective organ part structure is composed of parts of multiple organs, but no complete organs. The organ parts are often of the same type (e.g., petioles, carpel walls), but may be of different types. Includes plant structures like a septum that consists of the walls of two fused carpels or a pseudostem that consist of multiple, overlapping leaf sheaths. Unlike a collective plant structure, a collective organ part structure does not contain any complete organs.
Add PO ids. Say "plant organs" instead of "organs".
cardinal part of collective plant structure
This is really just to cover the parts of a seed plus a few fruit parts, because most other structures are a cardinal part of an organ or a collective organ part structure.
Upcoming meetings and Presentations 2012:
MOSS 2012 and The 3rd International Symposium on Molecular Systematics of Bryophytes
Thursday, June 14, 2012 - Friday, June 22, 2012
The New York Botanical Garden
Attendees have the option of registering for MOSS 2102 ($225), the Symposium on Molecular Systematics of Bryophytes ($225) or both ($400).
RW submitted an abstract for a poster File:PO poster Moss 2012.pdf.
Crop Ontology Workshop
For more information see the wiki page: Crop_Ontology_Workshop_at_OSU,_2012
Dates TBA: probably Sept. 13-15th
The focus of the workshop will be on mostly development stages and traits for the crop plants
Botany 2012
July 7 - 11, 2012 - Columbus, Ohio
- PO workshop on Sunday, July 8th, 9:00AM - 12:00PM
This is a half-day (morning) workshop. The schedule now links to the correct abstract.
An announcement has been posted on the PO home page and FB page.
Goal of workshop: 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, 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. 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 will present the IDO-Plant paper and a poster on the PO-FNA collaboration.
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)
