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
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.
Will fill in more details.
Preparations for Botany meeting workshop
Website refresh
There was discussion of a refresh to the PO website (see Plant Ontology Web Site Update: Winter 2012). RW: I need to know if this will happen before the BSA meeting (July 8), so I can make slides that will match the live browser.
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.
Presentations/tutorials that need to be updated:
- Introduction to the project - Slide show. There are links to this from both the web page and the wiki. Much of it is still valid, so it could be updated, rater than replaced.
- http://wiki.plantontology.org/index.php/Plant_Ontology_Tutorials and http://plantontology.org/docs/otherdocs/tutorials.html
Problem opening quicktime movies. ppt files are probably out of date. RW will check them. Includes the following links:
Introduction to ontologies: http://plantontology.org/docs/presentations/tutorials/poc_intro.mov, http://plantontology.org/docs/presentations/tutorials/poc_intro.ppt Powerpoint slides
Development of ontologies: http://plantontology.org/docs/presentations/tutorials/ontology.mov, http://plantontology.org/docs/presentations/tutorials/ontology.ppt
Annotations: http://plantontology.org/docs/presentations/tutorials/annotation.mov, http://plantontology.org/docs/presentations/tutorials/annotation.ppt
Plant ontology browser and POC web site: http://plantontology.org/docs/presentations/tutorials/website.mov, http://plantontology.org/docs/presentations/tutorials/website.ppt
From the wiki:
Principles, Rationales and Key Organizing Rules of the PO:
- Plant Structure Ontology Rationale for high nodes in the ontology, examples and explanation of three "patterns" of the ontology structure.
- Growth Stages Ontology and frequently asked questions
- Developmental Stages Ontology
- These correspond to the out of date web pages mentioned below.
- Wiki page with instructions on How to use the Source Forge tracker. Need to add details and images.
- wiki home page: under Formats of the Ontology Files, needs info on OWL (provide link).
Mistakes on website
Pages that should be fixed before the workshop:
- http://plantontology.org/amigo_user_guide/index.html#intro - "Plant Ontology Browser Users Guide" - No images show up. Text not displaying correctly (missing spaces).
- http://plantontology.org/docs/otherdocs/principles_rationales.html - Out of date.
- http://plantontology.org/docs/growth/growth_stages.html - Out of date. Should merge with page for developmental stages.
- http://plantontology.org/docs/faq/growth_faq.html - Out of date.
- http://plantontology.org/docs/development/developmental_stages.html - Out of date. Should merge with page for growth stages.
Less important fixes:
- http://plantontology.org/docs/otherdocs/poc_project.html - Was updated in the past year, but needs new updates. Still refers to "Plant Growth and Developmental Stages". Could use more detail on the project.
- http://plantontology.org/docs/otherdocs/charter.html POC charter is out of date.
- http://plantontology.org/docs/otherdocs/ontology_doc.html not too bad. Could use updating
- http://plantontology.org/docs/otherdocs/resources.html out of date
- http://plantontology.org/docs/references/pub.html out of date
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.
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)
