POC Conf. Call 6-5-12

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POC meeting, Webex Conference Call; Date: Tuesday June 6th, 2012 10am PDT/1pm EDT

In attendance:

POC members:Laurel Cooper (OSU), Ramona Walls (NYBG), Marie Alejandra Gandolfo (Cornell), Pankaj Jaiswal (OSU), Justin Preece (OSU), Justin Elser (OSU), Dennis Stevenson (NYBG)

Absent:Barry Smith (University at Buffalo, NY), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: none

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=65565392&rKey=0c7d839ea1cb7310

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=65565392&rKey=8aee18c021fa41e0

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_5-29-12?

Back to POC Meetings Minutes

Image annotation software demo

Justin Preece will give an updated demo of the ontology-enabled image annotation desktop application and also review these HTML mock-ups (intended for future database and web development) for those who missed the previous demos.

JP demo'd the OEIA desktop application for the group. Thanks to all for their good questions and helpful feedback.

  • Main idea: Markup and annotate images of botanical species w/ ontology terms, and store that data in such a way (structured zip files) that we can transfer it to a database in the future and serve it out to other applications. The application allows you to open an image, highlight individual parts of that image, label those parts with Plant Ontology terms, and save the annotated image accompanied by add'l metadata such as a curator, independent identifier, species, etc.
  • Future use-case example: Build a database to store this annotated image data and write an import utility to pull in .zip files and other annotated images (i.e. from plantsystematics.org). Integrate this database with external web applications, such as the Plant Ontology AmiGO browser.
  • Usage and testing: The Cornell group is invited to begin using the app and providing feedback when it's ready (in a couple of weeks). We will set up a feature request and bug report submission system.
  • Presentation: RW has graciously agreed to demo it at the Botany 2012 conference (July 7-11)
  • Credits: Nikhil Lingutla: software adaptation and development, Justin Preece: software and systems architecture, design, development, and technical oversight. Pankaj: The bright ideas and the funding to make it happen.

There are many UI and usability improvements we would like to make -- we already have a long list of things we look forward to adding or enhancing -- but we've been very focused on getting the fundamental image segmentation functionality, web service integration and data architecture ready. We welcome your feedback and suggestions, and we will prioritize those and implement them in incremental releases. - JP

Updating the pages on the PO website

Some of these changes like the tutorials are nb for the BSA workshop

We will have a separate meeting to go over web site changes. Please fill out Doodle Poll

This poll will be updated- maybe the week of June 18th we should follow-up on the changes

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:_2012#Tutorials_and_Demos_out-of-date

JE fixed the files so that they can be downloaded now.

Mistakes on website and wiki

See Plant_Ontology_Web_Site_Update:_2012#High_priority_fixes

The website refresh (change to Drupal6) will probably take place late summer, early fall 2012, but in the meantime, we will start fixing the out of date pages

RW will work on content of some pages and post to SVN, so we can review them on the beta or dev browser.

PJ will write up something about the PO consortium charter, and how it stands now. This page is a priorty to update. Will also provide feedback on changes to the principles and rationale page.

RW will merge and update the pages for growth stage and development ontologies.

The developers' guide, which is currently on both the web and wiki pages, can move to just the wiki page. Also, we will add link to wiki page from the "Documentation" table. (Note: should also add a link to the curator page, as requested by Barry).

Booklet for the BSA Workshop

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 on screen.

We did not discuss this on today's call.

New upper level terms for PO

This section has moved back to Items_for_future_meetings#background_-_CARO- will go on the next meeting agenda.

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.

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

PO workshop on Sunday, July 8th, 9:00AM - 12:00PM

see: link on Botany 2012 workshops schedule to view the abstract.

Wiki page for workshop: Plant Ontology Workshop, Botany 2012

Goal of workshop: 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.

Announcement has been posted on the PO home page and FB page.

exhibitor's booth

We had considered 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)

We decided that there were not enough people at the conference to man a booth and we could put up a display at the NYBG booth

RW will look into purchasing a TV/monitor (~22") that could display a rotating slideshow. Could also be used for future presentations

Bio-Ontologies SIG 2012

Where: July 13 - 14, 2012, Long Beach, CA. Co-located with ISMB 2012

When: Submissions Due: April 13th, 2012 (Fri)

See: Bio-Ontologies SIG 2012

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)

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

Next meeting scheduled for Tuesday, June 12, 2012 at 10am PDT/1pm EDT

See: POC_Conf._Call_6-12-12