POC Conf. Call 8-2-11
POC meeting, Webex Conference Call; Date: Tuesday Aug 2nd, 2011 10am (PDT)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC_Conf._Call_7-19-11?
Conference/Meetings updates:
IBC 2011, Melbourne, Australia
The POC hosted the IBC_2011_Bio-Ontologies_Symposium on Thursday, July 28th.
The PO and our symposium (and the MaizeCyc database) were publicized in the conference newspaper.
Both PJ and MAG had their research mentioned during the plenary lectures!
Throughout the meeting, RW and DWS spoke to a number of people from the plant systematics community who are interested in potential uses of the PO.
PO will also look into collaboration with/tagging terms in JStor Plant Science.
Talked to Rudi Appels about using PO terms for wheat gene expression data.
See additional info under collaborators link from wiki home page.
ICBO, 2011, Buffalo, NY
ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York ICBO
-LC presented the Plant Ontology on Thursday, July 28th, 3:40pm in the session: "Introduction to The OBO Foundry Initiative"
Link: ICBO Program
July 27 8.30am-4pm: LC co-organized the workshop "From Fins to Limbs to Leaves: Facilitating Anatomy Ontology Interoperability and the OBO to OWL workshop, along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.
LC had many discussions with various groups about ontology interoperability,
- ICBO proceedings. This includes all papers from the main conference, conference workshops, and other associated events.
Link to the slides: ICBO slides
MaizeGDB mappings for Annotations
Mary Schaeffer of MaizeGDB is preparing a large number of annotations to our terms from a large microarray data set. As part of that, she has prepared a mapping between the samples in the studies and our terms. We need to look these over and make sure they make sense.
We should deal with these SF requests from them as well:
PAO terms for MaizeGDB
transition leaf - definition
From Mary at MaizeGDB: It would be helpful to add some insights on the transition leaf.
For example - Leaves that have mosaics of juvenile and adult tissues. In maize, the juvenile will be at the tip, which differentiates first, with adult at the base. Other grasses may have other arrangements, eg Brachypodium, which may have both juvenile and adult across the breadth of a leaf.
Provided by Erin Irish, who references this paper: Irish, E. E. and Karlen, S. (1998) Restoration of juvenility in maize shoots by meristem culture. International Journal of Plant Science 159, 695-701. The Brachy. information is more recent.
Suggest adding to the comment of juvenile leaf, transition leaf and adult leaf: Many species have juvenile leaves are at the base of the stem, adult leaves at the apex, and transition leaves in between. In maize, juvenile leaves will be at the tip of the stem, which differentiates first, with adult at the base, while other grasses may have other arrangements. Transition leaves may have mosaics of juvenile and adult tissues, as in Brachypodium.
Can add Irish and Karlen reference to definition dbxrefs if it is appropriate.
leaf base
See tracker item for details.
I think Mary's questions have been answered, and this item can be closed. We can add a comment to it once we resolve the issue of transferring annotations for parts of leaf.
style, silk, Poaceae style
From Mary at MaizeGDB: Suggest that you merge these, keeping style, obsoleting silk and Poaceae style. Do the same for other floral parts that have a species spin on them, but are really the same as other more generic names for flower parts.
From PJ: Poaceae / Zea was necessary in some terms because often detail structures referred to parts of tassel/ear floret and it has conflict with floret compositeae besides the spatial aspects.
Rather than working on this piecemeal, we need to have an organized approach to eliminating the Poacaeae/Zea terms. Need to look at the structure from the top down and ensure part_of relations remain correct. Do we want to allocate time to this now or wait for next release?
See page for Eliminating Zea/Poaceae terms from PO
42 terms in PAO with Poaceae in the name.
28 terms in PAO with Zea in the name.
Only one Poaceae term in PGDSO (PO:0007012 Poaceae inflorescence visible), and there is a Source Forge item requesting that we merge it with another term.
PGDSO terms for MaizeGDB
We can discuss these items, if time allows.
See: Items_for_future_meetings#Maize_GDB
Upcoming meetings 2011:
- 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 and we are invited to take part. We are hosting the website.
- 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.
We agreed that the PO meeting will be all day Saturday Sep. 10 and morning of Sunday Sep. 11. DWS, PJ, BS, LC, and RW can make it. Need to find out if MAG can attend.
RW has reserved the NYBG apartment for the nights of Sep. 9 and 10.
