POC Conf. Call 3-27-12
POC meeting, Webex Conference Call; Date: Tuesday Mar 27th, 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_3-20-12?
Back to POC Meetings Minutes
Upcoming PO Release:
Apache update:
JE has transferred all the html content on the web pages to the new Apache version and all seem to go smoothly.
There may be a few remaining link 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.
People will need to update their bookmarks as well, if you have not already done so
Timeline:
- Target date for finishing edits: end of the day Thursday March 22st
Most of the needed edits were completed on schedule.
We will review any additional loose ends and get them completed by hte end of the day today.
- Target date for release: Before March 30th
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
Everyone should review this list and let me know if there are things that need to be added, modified etc.
JE will make a corresponding document to outline the steps that is needed to be done from his end.
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 term 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
- ~125 new terms for this release
- 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) -move out of "test folder"
- Small set of cotton annotations- -move out of "test folder"
- Updated annotations from SGN received
- RW will create an association file for the spruce tree genes that are referenced in the papers. This could be in a non-model plant association file.
RW: Will not be able to finish this by tomorrow. Could have it done by early next week. Takes extra time because they are not standard annotations from an existing database.
Glossary of PO Anatomy terms
- Currently links to the dev version of the ontology database, but on the live site it should read from the live version.
Translations
Status report:
- Ale has completed the new Spanish translations. RW is updating the table file so JE can use it to insert the translations into the obo file.
- Yukiko will try to do the Japanese translations this week, but may not be able to in time. If necessary, we can add them in the next release. She will be at the BioCuration meeting next week.
icons for new relations
- New icon has been added for the has_participant relation so it can be included in the upcoming release.
- icons need to be stored in the folder on the SVN:
Remaining Ontology Things to be fixed
test image links to Plantsystematics.org
Image_at_PlantSystematics:1597 to septum (PO:0000030) and fruit septum (PO:0025268)
See http://www.plantsystematics.org/imagebyid_1597.html
Image_at_PlantSystematics:14891 and Image_at_PlantSystematics:8662 to pappus (PO:0025393) and pappus element (PO:0025394)
See http://www.plantsystematics.org/imagebyid_14891.html and http://www.plantsystematics.org/imagebyid_8662.html
initial cells
RW will fix all names by morning of 3-27, so they say "...cell" as primary name.
May not need this on the agenda.
reaction wood
The following terms have been added to the ontology:
reaction wood (PO:0025472): A portion of secondary xylem (PO:0005848) found on either the upper or lower side of a shoot axis (PO:0025029) that is leaning or crooked, with specific anatomical characteristics that depend on whether it is compression wood (PO:0025473) or tension wood (PO:0025474).
Comment: Functions in restoring a leaning stem (PO:0009047) or branch (PO:0025073) to its original position. May be either compression wood, found on the lower side of a gymnosperm shoot axis or tension wood, found on the upper side of an angiosperm shoot axis.
compression wood (PO:0025473): A portion of reaction wood (PO:0025472) found on the lower side of a shoot axis (PO:0025029) that is leaning or crooked that has as parts heavily lignified tracheids (PO:0000301) that are rounded in transverse section and bear spiral cell wall checks.
Comment: Functions in restoring a leaning stem (PO:0009047) or branch (PO:0025073) to its original position. Found in gymnosperms.
tension wood (PO:0025474): A portion of reaction wood (PO:0025472) found on the upper side of a shoot axis (PO:0025029) that is leaning or crooked that has as parts gelatinous fiber cells (PO:0025422).
Comment: Secondary xylem tracheary elements (PO:0025445) in tension wood are often longer than the tracheary elements in non-tension wood of the same plant. Functions in restoring a leaning stem (PO:0009047) or branch (PO:0025073) to its original position. Found in angiosperms.
References: IAWA Mulitlingual Glossary (PO_REF:00012), Carlquist 2010 (ISBN:3540411739)
Upcoming meetings and Presentations 2012:
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
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
Ruth Bastow is contacting some of the interested people to see which of these dates work best.
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
