POC Conf. Call 7-3-12

POC meeting, Webex Conference Call; Date: Tuesday July 3rd, 2012 10am PDT/1pm EDT

In attendance:

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

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

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

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=66342467&rKey=38ece7fe112371b3

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=66342467&rKey=4376f9c0dd8699bf

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

Last minute fixes and final TTD:

• add comment to collective plant structure to clarify that it is a new term:

collective plant structure: A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007). [source: POC:curators]

Add new Comment: This is a parent term to describe both collective organ part structure (PO:0025269) (e.g. septum) as well as collective plant organ structure (PO:0025007), (which was formerly named collective plant structure), for example shoot system (PO:0009006).

Done, updated on svn and directly in database, PO:ids can be added in next week

collective organ part structure (PO:0025269): A collective plant structure (PO:0025497) composed of two or more cardinal organ parts (PO:0025001) that are part of adjacent plant organs (PO:0009008) and any associated portions of plant tissue (PO:0009007). [source: POC:curators]

collective plant organ structure (PO:0025007): collections of plant organs.

Add to the end of existing comment: This was formerly named 'collective plant structure' done

• Need to fix link on "Release Notes Archive" page to Release #17- done

• "Filter annotation objects": is missing 6 species- posted on Jaiswal tracker

Updated webpages

The following pages were updated for the Release:

• PO home page- Pj would prefer to condense the 'Whats New column', move link to News archive, link to glossary under search box, update News archive

• Release notes page: fixed, ok

• Download page (download.html; under /download): Everything is a hyperlink. RW will get it fixed, hopefully JE can update it.

• Developers guide to using PO SVN (svn_doc.html; under /downloads)- We should actually get rid of this page- next release

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

• AmiGO users guide (index.html; under /amigo_users_guide)- include link from Home page ??

• 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), Good, OK

• Page on the plant structure development stage branch (developmental_stages.html; under /docs/development) Good, OK

• Page on the whole plant development stage (growth_stages.html; under /docs/growth) Good, OK

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

• Table under the "Documentation" tab (docs.html; under /docs)- Note for Barry: There is now a link to the curator's page from the [documents] page.

• New slides on the help/intro slide show (Slide1.jpg-Slide21.jpg; under /images/)

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, but they are lower priority. See Plant_Ontology_Web_Site_Update:_2012#Requests_for_Content_Change for documentation and more details.

Located_in icon

Relations wiki page: Relations_in_the_Plant_Ontology

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

PJ created a new icon that will be updated on the browser. Should be stored on the svn

Still need the description

Publications: AJB paper and PAE paper

- RW is ready to resubmit the AJB review paper, needs the letter from DWS as he is corresponding author. Status?

The AJB paper has been accepted. They are preparing page proofs.

- Draft of PAE paper has been circulated to PO-internal. Comments have been received

Key Issues:

- Need to emphasis the focus on the PAE branch, revise the title

- Include near the beginning "this paper is designed to provide to more details on the anatomy portion of the PO to supplement the more general paper which was recently published in AJB- make it clear we are not trying to cover up the fact there are two related papers"

- Need a short write-up on the Inparanoid analysis from JE

- Collaborator groups TAIR, MaizeGDB and SGN are sending in a write up of how they use the PO- still waiting for MaizeGDB and SGN

- Plant Physiology is the target journal

- Revised version will go out later next week for final review, hope to submit by the ASPB meeting

Update from Cornell

From MAG:

We are continuing with the photography. We added 20 more slides and now we have 620.

I am editing some of the images for our BSA presentation.

The web site will be up for everyone to see sometime in the next week before the BSA meeting.

Also added that ...

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.

A desktop version of the image annotation software will be to demo'ed at this meeting.

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

Botany_2012_PO_workshop_planning_page

exhibitor's booth

The PO will 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 31st, 2012 at 10am PDT/1pm EDT

See: POC_Conf._Call_7-31-12