POC Conf. Call 3-20-12
POC meeting, Webex Conference Call; Date: Tuesday Mar 20th, 2012 10am PST/1pm EST
In attendance:
POC members:
Absent:
Collaborators: none
Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_3-13-12?
Back to POC Meetings Minutes
Next PO Release:
Apache update:
JE has managed to port the website code to work with Apache2. Please check http://beta.plantontology.org (no port 8080).
Question: Should we wait until after the release to update? Probably could update with only minor disruption, but there could be unforeseen difficulties. Most of it could be done in parallel to minimize downtime however.
After the switch, all links to :8080 addresses will have to be fixed. There are only about 30, and most of them seem to be links to wiki.plantontology.org.
Timeline:
- Target date for finishing edits: March 21st
- Target date for release: Before March 30th
We should aim to have to release out by the end of this month, so we can then focus on the paper to have manuscripts ready by April 15th.
We probably want to have this release out before we submit, so reviewers and editors can look at the web site. If we get feedback from reviewers on manuscripts, we can work those into the next release in two months.
We can get this week's changes, plus the wood development stages and the coleoptile emergence terms in the file by next week, and review them at next week's meeting.
Goals and Priorities:
For more details see: New terms and obsolete terms-March 2012 Release
PO_Release_SOP_Page
After the release in October 2011, LC put together this page to help facilitate the releases
Revisions of PSDS (formerly PGDSO):
Status to 3-19-12
- ~34 new terms added
- many existing terms have been modified, eg changed all the 'phase' names to 'stage'
- all PSDS terms names are now singular. Some still need to have "stage" appended
- focus has been on the whole plant development stage (PO:0007033) and its children
- Addition of Wood development stages: (See: SF tracker), started at the NYBG Workshop
New and Revised Terms for the PAE
- Addition of new terms and revisions to existing terms to encompass wood- see Goal_1._Anatomical_Entities
- Please see New terms and obsolete terms-March 2012 Release for a complete list
- Complete old user requests/SF tracker items:
- This is an ongoing process
New association files:
- Physcomitrella (released Jan 2012)
- Small set of cotton annotations (TBA Feb 2012)
- Updated annotations from SGN received
Glossary of PO terms
This was discussed at the RCN meetings 2011, plan is to eventually replace APWeb Glossary. This will be useful for users of APWeb Glossary who need a glossary, but don't want to use AmiGO browser. We could eventually incorporate other terms from APweb into PO if needed.
- What is the status of this? PJ will follow up with the developers. It should be updated to the version for the release.
Translations
Will need to update translations for PAE terms before release. Can JE generate a file (after we stop editing) that includes all terms without Spanish or Japanese translations?
icons for new relations
- We need an icon for the has_participant relation so it can be included in the upcoming release.
According to discussion of POC_Conf._Call_1-31-12 we decided:
It would be good to relate the new icon visually to the reciprocal 'participates_in':
has_participant should be "hP" in a circle, (to distinguish it from has_part: Hp) and that a dark background with white letters is more visible
sent reminder after meeting on 3-13-12
- derives by manipulation from icon is present but not showing up in dev browser?
Collaborative projects:
- Mapping of Flora of North America Glossary to PO terms:
For more details see: The FNA collaborators page: Flora_of_North_America-_FNA
Synonyms have been added
Outstanding edits to be finished:
The issues around coleoptile emergence were raised by MaizeGDB and have been open on SF since June 2011.
Discussed on: POC_Conf._Call_3-8-12 and POC_Conf._Call_3-13-12
At the POC meeting on Sunday_Sept_11th,_2011, we agreed to keep the existing terms that reference emergence from the soil, but rename them as stages, and add new terms for emergence from seed coat. Need to copy over list of existing synonyms to new emergence terms.
We had further examination and discussion on POC Conf. Call 3-8-12 and decided we were in favor of eliminating the description of emergence from the ground or growth media, but adding a comment that you might not observe it if the seed is underground.
Additional issue is how to define this as a stage. It is actually a stage of elongation, which starts with emergence from the seed coat (or does it start sooner?)
All of the terms below originally described a single point in time. We need to figure out when the shoot emergence stage should end.
In reviewing these terms, I went back to our discussions of plant embryo, plant zygote and plant embryo stage on POC_Conf._Call_12-13-11. At that time we agreed to rigorously define the plant embryo stage and define the plant embryo as a whole plant that participates in that stage.
But I found a couple of problems:took out comment pteridphytes do not have cotyledons and
plant embryo stage
these changes have been made in the dev file:
plant embryo stage (PO:0007631):
Revised, annotated def'n:
A sporophyte vegetative stage (PO:0007134) that occurs during the interval between the first cell division of the plant zygote (PO:0000423) and beginning of the next stage of growth, which varies among taxa. In seed plants, the plant embryo stage ends with seed germination stage (PO:0007057). In pteridophytes, the plant embryo stage ends with the formation of the first vascular leaf (PO:0009025). In bryophytes, the (plant) embryo stage ends when the seta meristematic apical cell (PO:0030016) stops dividing and the sporangium (PO:0025094) begins to develop. In cultured plant embryos (PO:0000010), the (plant) embryo stage ends when a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or leaf (PO:0025034) begins to form.
Revised, annotated comment:
Succeeds the plant zygote stage (PO:0001097). The plant embryo stage generally starts after the first division of a plant zygote (PO:0000423), but in the case of an adventitious embryo, somatic embryo (PO:0025302), other embryos that arise through apogamy, or microspore-derived cultured plant embryo (PO:0025305), it is formed after the division of a single cell that is not a zygote.
LC: I am not certain about the end in bryophytes- originally it just said apical cell- changed to 'seta meristematic apical cell (PO:0030016)', but I think the plant embryo stage in bryophytes would end when the seta starts to elongate- maybe we need something like a "seta elongation sporophyte vegetative stage". Raven et al calls it the "young sporophyte".
Sporangium formation should mark the beginning of the sporophyte reproductive stage (PO:0007130).
plant embryo
A whole plant (PO:0000003) that participates in the plant embryo stage (PO:0007631).
modified comment:
A plant embryo is generally formed after the first division of a plant zygote (PO:0000423), but in the case of an adventitious embryo (nucellar plant embryo (PO:0004537)), somatic embryo (PO:0025302), other embryos that arise through apogamy, or microspore-derived cultured plant embryo (PO:0025305), it is formed after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa. In seed plants, the plant embryo stage (PO:0007631) ends with germination. In pteridophytes, the plant embryo stage ends with the formation of the first vascular leaf (PO:0009025). In bryophytes, the plant embryo stage ends when the seta meristematic apical cell (PO:0030016) stops dividing and the sporangium (PO:0025094) begins to develop. In cultured plant embryos (PO:0000010), the plant embryo stage ends when a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or leaf (PO:0025034) begins to form.
wood development stages
Will move here from Items for future meetings after Monday.
Upcoming meetings and Presentations 2012:
Katherine Esau Research Symposium
Integrating Plant Structure with Function, Development and Evolution
Hosted by the Katherine Esau Fellowship Program,
Date and location: Thursday, March 29, 2012, 1002 Giedt Hall, UC Davis
Space is limited and registration will close at 5 pm on March 10th.
Organizer; Neelima Sinha (Sinha@ucdavis.edu) The PO will not take part this year, because the timing is too short. We will look at attending next year.
5th International Biocuration Conference
April 2-4, 2012, Washington DC
• Abstract was submitted and has been selected for a poster presentation.
See link: File:Abs Biocuration 2012 (LC 12-9-11).pdf
- LC is attending and is taking part in the BioCreative workshop
The early bird registration is now closed.
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
We are looking at the tentative dates of either: June 11-13th or Aug 6th to 8th
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 for Sunday, July 8th
The organizer have listed it as a whole day workshop, but it is planned for a half day and will be changed on the schedule. Also need to correct link to abstract (currently goes to wrong abstract).
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.
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.
- Annotation wiki: JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.
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 is working on an abstract summarizing the PO-FNA collaboration, with the folks from FNA. Will circulate soon. This will be either for a poster or a short talk in the Early Career Researcher session.
BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts
