POC Conf. Call 7-05-11
POC meeting, Webex Conference Call; Date: Tuesday June 14th, 2011 10am (PDT)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC_Conf._Call_6-28-11?
Meeting with Morphobank this afternoon
Time: 2:30pmPT/ 5:30pmET
Not sure where DWS is, or I would list the time (10:30pm England?)
More details TBA...
See meeting page: POC-Morphobank_Webex_meeting_07-05-2011
Publications
- Plant Physiology: RW and LC are working on a manuscript to submit to Plant Physiology. This will be a more detailed description of the changes made to the PO in the past year, focusing on restructuring of PSO . Will focus on how PO is now applicable to a wider range of plant species.
- Short topics paper for American Journal of Botany
The editor of AJBOT asked Dennis to put together a short paper for them- can focus on PO. This would be consistent with the
Compliance with OBO Foundry guidelines
- All but 3 terms now have is_a parents. The last three will be dealt with when we restructure the PGDSO
- Restructuring of PGDSO should make PO compliant with BFO (see item below).
- need to double check that all terms have text definitions
User requests, Plant Anotomy Ontology:
- TraitNet requests:
corm,
- Legume terms submitted by Austin Mast.
Several terms have already been dealt with (Taproot, Stem Hair, Prickles, Anther pore and anther slit).
Remaining: fascicle
bristle (used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
- root terms submitted by Rich Zobel (Nov 2009)
Tech issues
Getting Spanish Synonyms into the Plant Ontology File
-JE has gotten the script to work to integrate the list of Spanish synonyms into the plant_ontology.obo file
Some of these are duplicates, because they represent a live and an obsolete term. These are not a problem.
RW will review these synonyms with MAG to determine if any of them should be changed. See updated list at duplicated Spanish synonyms May2011.
There are a couple of other issues I still need to work out, and haven't tested the Japanese translations, but it should be the same as the Spanish, so I am not too worried about it. (JE)
The Japanese synonyms will stay in the main PO file, then we can strip them out when we go to load it onto AmiGO (rather than maintaining a separate file for Japanese users, as we discussed earlier). JE will try putting them in the file, and see if there are any problems.
- Status update:
Problem with how annotations move through relations
-LC contacted TB at TAIR to let her know we are working on it. They said thought that we had a good plan in mind and appreciated the updates.
TB thought that it would helpful tothem if we just provided the ontology file (without the extra relations) on our SVN for use on their system.
- Status update:
RW added a file to the SVN (tags/live) called "plant_ontology_assert_basic.obo". This is the same as plant_ontology_assert.obo but with only the is_a, part_of and disjoint_from relations. Left in disjoint_from, because it doesn't seem to be causing any problems (Amigo ignores it and TAIR has never reported a problem with it in the past). Should we remove disjoint_from too?
Upcoming meetings 2011:
- Botany 2011 Meeting [Botany 2011] St. Louis, MO at the Chase Park Plaza, July 9-13.
Societies participating: Society for Economic Botany, the American Fern Society (AFS), the American Society of Plant Taxonomists (ASPT), and the Botanical Society of America (BSA).
DWS is attending, but will not present. Many people from the BSA will be at the IBC meeting in Melbourne.
- ICBO 2011 Second International Conference on Biomedical Ontology
July 26-30, 2011 Buffalo, New York ICBO
-LC will present the PO on Friday July 29th, 3:30pm in the session: "Parallel Sessions on Special Topics: The OBO Foundry, featuring discussions of the Infectious Disease Ontology, the Ontology for Biomedical Investigations, the Ontology for General Medical Sciences and the Plant Ontology"
Link to program: [[1]]
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.
Date: July 27 8.30am-4pm 'Facilitating Anatomy Ontology Interoperability
- Plant Biology 2011, Aug 6-10th, Minneapolis, Minn
Gramene and Plant Ontology are hosting a [Data Curation Workshop] again, focusing on pathway curations.
LC and PJ will present a [PO poster.
TAIR (Kate Dreher) is organizing an [Plant_Biology_2011_Outreach_Booth Outreach Booth] and we are invited to take part. We are hosting the website.
- 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.
See IBC 2011 Bio-Ontologies Symposium wiki page for more details
- POC Meeting at New York Botanic Garden Tentative dates, Sept 9th-11th, 2011
DWS will look into booking the apartments at the NYBG for accommodations
More details TBA....
