POC Conf. Call 7-3-12

POC meeting, Webex Conference Call; Date: Tuesday July 3rd, 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_6-26-12?

Back to POC Meetings Minutes

Release #18 is up

• Ontology, annotations and revised webpages are on beta browser

• Details of the Release and the accompanying Announcement are posted on the July_2012_Release page

• For more information about the release, please visit our wikipage with a Summary of Changes to PO July 2012.

• You can also view a list of New terms and obsolete terms July 2012 Release

Updated webpages

The following pages were updated for the Release:

• Download page (download.html; under /download)

• Developers guide to using PO SVN (svn_doc.html; under /downloads)

• Page on the PO Objectives and Principles (principles_rationales.html; under /docs/other_docs)

• AmiGO users guide (index.html; under /amigo_users_guide)

• Figures for the amigo users guide (figures 1, 1A, 2, 2A, 4, 6, 6A, 7, 8, 9, 10, 11, 11A, 12; under /amigo_users_guide)

• growth_faq.html (under /docs/faq) (FAQ for whole plant growth stages)

• developmental_stages.htm (under /docs/development) (Page on the plant structure development stage branch of the PO)

• growth_stages.html (under /docs/growth) (Page on the whole plant development stage branch of the PO)

• docs.html (under /docs) (the table under the "Documentation" tab)

• Slide1.jpg-Slide21.jpg (under /images/) (these are for the help/intro slide show)

More details on exactly what changes were made can be found on the SVN pages, but mostly it consisted of updating the content to reflect the current structure of the PO, replacing out of date links, and fixing grammar.

Many of these pages still need some work, but at least they are no longer grossly inaccurate. There are still more pages to be fixed (http://wiki.plantontology.org/index.php/Plant_Ontology_Web_Site_Update:_2012#Requests_for_Content_Change), but they are lower priority.

See Plant_Ontology_Web_Site_Update:_2012#Requests_for_Content_Change for documentation and more details.

Note for Barry: There is now a link to the curators page from http://beta.plantontology.org/docs/docs.html.

Located_in icon

http://wiki.plantontology.org/index.php/Relations_in_the_Plant_Ontology

We still need an icon for this and the description needs to be added to the relations wiki page

Upcoming meetings and Presentations 2012:

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.

Botany_2012_PO_workshop_planning_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 purchase a monitor (~22") that could display a rotating slideshow. Could also be used for future presentations. This will be on display at the NYBG press booth. We will also have internet access there, so we can demo the PO to interested people.

Bio-Ontologies SIG 2012

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

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.

Currently no one from the PO is planning to attend

ASPB Plant Biology 2012

July 20 - 24, 2012 - Plant Biology 2012, Austin, TX

Link to meeting page: ASPB2012

Abstract was submitted for submission: Poster Number: P28002

Plant Informatics Workshop is planned with TAIR, Gramene and PO : Saturday, July 21, 2012, 7:30 PM - 9:00 PM

LC is attending

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

• 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]

LM will be attending

Online Ontology Workshops at The University at Buffalo

The University at Buffalo is pleased to announce two on-line tutorials in ontology:

1. Introduction to Protégé for absolute beginners:

Saturday and Sunday, August 11-12, 2012.

Faculty: Ron Rudnicki (CUBRC, Buffalo), Alan Ruttenberg (University at Buffalo), Barry Smith (University at Buffalo)

This course will provide an introduction to the Protégé 4.2 ontology editor. It will begin with a brief introduction to ontology building, and to the use and importance of ontologies. This will be followed by an introduction to the Web Ontology Language (OWL). The bulk of the course will consist of an interactive introduction to the use of Protégé in building an ontology. No background in the use of computer languages and programming is presupposed. All sessions will be highly interactive.

2. Basic Formal Ontology 2.0

Saturday and Sunday, August 18-19, 2012

Faculty: Alan Ruttenberg and Barry Smith (University at Buffalo)

Basic Formal Ontology is currently being used by over 100 ontology-based research projects in biomedical informatics and increasingly in other fields. The tutorial will provide an introduction to the content and use of BFO in ontology development. Participants will acquire knowledge of the ontology and of its use as top-level ontology in multiple ontology development projects in a variety of fields. They will learn about the most recent developments in the new version 2.0 of the BFO ontology, including new formalizations of BFO in first-order logic and in OWL.

Both tutorials are also open for face-to-face participation.

PO/TO Crop Annotation Workshop at OSU

For more information see the wiki page: Plant Ontology Crop Annotation Workshop at OSU, 2012

Dates: 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, July 17th, 2012 at 10am PDT/1pm EDT

See: POC_Conf._Call_7-17-12