POC Conf. Call 5-17-11
POC meeting, Webex Conference Call; Date: Tuesday May 17th, 2011 10am (PDT)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC_Conf._Call_5-03-11?
Tech Issues from POC_Conf._Call_5-10-11:
Also added to the POC Technical Issues Page
* New images needed for browser
JE: I noticed in the server logs that errors are being created because we are missing images for participates_in and adjacent_to. Can someone create these for me to add to the browser?
We have an image for participates_in, need one for adjacent_to. Will send to JE.
* Problem on the dev browser- can't filter by the new 'plant anatomy' name
Looked at filtering problem on dev browser. It does not seem to be related to differences in capitalization or word form, as these also exist on the live browser, with no problem. JE is looking into it.
* Problems displaying AmiGO Browser in Internet Explorer
PJ sent a note out by email that some users are having problems displaying AmiGO Browser in Internet Explorer: IE views are not similar to the ones in Firefox.
-See the comment at:link "On my computer, this displays correctly in FireFox 3.6.13, but not Internet Explorer 8.0.6' on this page."
- RW confirmed it: "The Amigo browser tree view does not display correctly in Internet Explorer on my PC either. All of the terms at one level of the tree are displayed on one line, instead of in a hierarchy. I'm sure I've griped about this before, but don't know if I have a written record. It works fine on Safari and Firefox on my Mac."
* Need script for inserting the translations as synonyms into the obo file
Status Report for Upcoming Release:
=*Highlights and Major Accomplishments in this Release:
-Addition of 41 new terms requested by the Physcomitrella group, 44 associated new terms that can be used for pteridophytes, and the addition of synonyms or minor modifications to 21 existing terms to make them applicable to a broader range of plants.
-Renamed Plant Structure Ontology to Plant Anatomy Ontology- note this is just the branch of the Plant Ontology, all terms still have the PO:xxxxxxx identifier
See note above about filtering issue on 'plant anatomy'
-Revised the in vitro plant structures branch and the embryonic plant structures branch
-many other minor changes and fixes- see below for more details
-See the List of changes on our wiki which is available from the May_2011_Release_Page. In progress...
-List of terms that have been obsoleted or merged: New_terms_and_obsolete_terms_for_May2011_release. In progress...
Timeline for release:
-Complete required edits and changes (by the end of this week)
This should be possible.
Week of May 16th to 20th:
-Reassign annotations from terms that been obsoleted (about 10), along with database groups TAIR, Gramene, SGN, MaizeGDB, etc
-Load new file onto Beta browser to check for any issues with loading, annotations
- send link to reviewers- Physcomitrella group, po-internal, others??
-prepare release notices, update on PO page
PJ suggested that we schedule a webex session to give reviewers a brief tutorial on how to use PO. This should make it easier for them to do a more useful review.
The idea would be to demonstrate the new plant anatomy terms that have been added to accommodate mosses
People to invite: Physco group (Stefan Rensing, Daniel Lang, others), Scott Schuette (Southern Illinois University -- will present talk on Physco bioinformatics at our symposium at the IBC), Brent Mischler, Bill Buck (NYBG), M.L. Christianson (University of Kansas), B. Crandall-Stotler (Southern Illinois University), B. Goffinet (University of Connecticut), others.
Week of May 23-27th:
-fix any final issues that have come up
-Release on live browser
-Send out announcements
Items arising from previous meetings:
Upcoming meetings 2011:
Phenotype RCN Meeting: June 1-3rd, Boulder CO
Goals of the Plant Working Group at this meeting (from the Phenotype RCN webpage):
"Plants – Go through relevant parts of Plant Ontology in order to develop proofs of concept; explore how to make links to homology. Examine existing annotations and determine kinds of info can be extracted. Analyze quantitative data and look for ways to annotate them."
PJ will attend
More details TBA
2011 Semantic Web Workshop June 6th and 7th, Santa Fe, NM.
Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.
-JE and JP will be attending
-JE has already worked with Damian to implement a SSWAP web service for PO terms, so further collaboration with him and iPlant will benefit the POC going forward.
For more Workshop details: Semantic web.
* ICBO 2011 Second International Conference on Biomedical Ontology
July 26-30, 2011
Buffalo, New York
LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.
Full-Day Workshops Schedule:
July 26 9am-6pm The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies
July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability
July 26 6.30pm-9pm Evening Workshop: Common Logic
July 27 4pm-8pm Evening Workshop: Doctoral and Post-Doctoral Consortium
- LC will attend and represent the PO. Invite other plant people?
*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn
Early-bird registration ends May 13.
Gramene will be putting together a workshop again, focusing on pathways. PJ will present a PO poster.
TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.
For inclusion on the program memory stick and in the program book, abstracts must be submitted by May 27.
* International Botanical Congress (IBC2011)
July 23rd-30th 2011, Melbourne, Australia
Registration is open Important dates
Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30.
Dennis, Alejandra, Pankaj and Ramona are planning to attend.
Scott Schuette from the Department of Plant Biology at Southern Illinois University has been added as the sixth speaker in our symposium. He will speak on "Predicted Protein-Protein Interactions in the Moss Physcomitrella patens: A New Bioinformatic Resource".
See IBC 2011 Bio-Ontologies Symposium wiki page for more details
