POC Conf. Call 1-3-12

POC meeting, Webex Conference Call; Date: Tuesday Jan 3rd, 2012 10am (PST)

In attendance:

POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_12-20-11?

Back to POC Meetings Minutes

Mistake in the CL/PO coordination

CM raised the issue below: spot the inconsistency:

/ PO:0025131 ! plant anatomical entity 
 is_a PO:0009011 ! plant structure 
  is_a PO:0000004 ! in vitro plant structure 
   is_a PO:0000005 ! cultured plant cell ***  
  is_a PO:0009002 ! plant cell [xref: GO:0005623] 
   is_a PO:0000005 ! cultured plant cell ***  

/ CL:0000000 ! cell [xref: FMA:68646] [xref: GO:0005623 "cell"] [xref: KUPO:0000002] [xref: WBbt:0004017] [xref: XAO:0003012]

 is_a CL:0000003 ! cell in vivo
  is_a CL:0000004 ! cell by organism
   is_a CL:0000255 ! eukaryotic cell
    is_a CL:0000610 ! plant cell ***  [xref: PO:0009002]

if the xrefs are equivalent and in vivo is (presumably) disjoint from in vitro, then plant cell is unsatisfiable.

Link to CL:0000610 plant cell on CL.

They should be using our definition of plant cell as well: "A cell which is a plant structure. [source: GO:0005623, POC:Curators]"

• SOLUTION 1:

With it's current placement, CL:0000610 must really be equivalent to a PO:0009002 that is in-vivo - this doesn't correspond to a named class in PO. We could rename CL:0000610 to "in vivo plant cell" and have a bridging axioms that says this is a subclass of PO:0009002

• SOLUTION 2:

obsolete CL:0000610, with a consider link (not replaced by) to PO:0009002

add an xref to PO:0009002 to CL:0000000 (just as we have for the other taxon-centric AOs).

Remove: 'treat-xrefs-as-equivalent: PO'

Add: 'treat-xref-as-genus-differentia: PO part_of NCBITaxon:nnnnn ! viridiplantae'

• SOLUTION 3:

move CL:0000610 ! plant cell to be a direct child of CL:0000000 ! cell

we would probably want to move CL:0000255 ! eukaryotic cell at the same time

From CM:

"I don't like solution 1. Neutral w.r.t. 2 and 3."

"Note that whatever the solution, we need a consistent cross-ontology naming strategy. I don't think it's necessary to prefix every in-vivo class with "in-vivo". But we need to be consistent. At the moment "eukaryotic cell" means "eukaryotic in vivo cell", whereas "plant cell" (in PO) means "plant cell, in vivo or in-vitro".

"How about this: if we have a taxonomic qualification, it doesn't imply in-vivo. If we have a named cell type (e.g. "neuron") or some other qualification, it implies in-vivo?"

CL should us the PO definition of plant cell. We should put it on the CL plant tracker.

The problem is if someone tries to import PO into CL, because of the conflict with in vivo cell. This should be address in the document from MH proposing changes to CL.

PJ raised an issue with experimentally modified cell -- you can experimentally modify a cell then stick it back in an organism, so it is in vivo.

Not everyone received Melissa's document. RW will circulate to PO internal, and we will review it before we discuss this more.

Wood Anatomy Ontology Meeting

Please see the Wood_Anatomy and the Wood anatomy ontology meeting, 2012 at NYBG, agenda wiki pages for more information.

Tentative dates are Feb. 5th-7th, 2012 (Sun-Tues)

Update and status:

Invitation letter went out 12/15/11 from DWS, to experts (below) signed by all three Co-PIs, along with Jill Wegrzyn of the TreeGenes Database at UCDavis (Bioinformatics) and Andrew Groover Geneticist, USDA Forest Service, Institute of Forest Genetics, Davis CA. Deadline for their response was Dec 31st 2011.

• Frederic Lens: Netherlands Centre for Biodiversity Naturalis
• Barb Lachenbruch link
• Elisabeth Wheeler (paleobotanist and wood anatomist at NC State
• Rachel Spicer Connecticut College
• John Carlson (jec16@psu.edu) link
• Meg (Margeret) Staton (mestato@yahoo.com) Clemson University (the lead on both the hardwoods website and the Fagaceae Genomics Web

So far, Fredich Lens, Meg Staton, Barb Lachenbruch and Rachel Spicer have responded positively, and RW has followed up with them. John Carlson has declined to attend as he is having surgery at the end of January.

Still waiting to hear from Elisabeth Wheeler, who has been out of town. Maybe Ale could follow up with her?

Travel forms have been sent to all to confirmed domestic invitees and LC is collecting them. So far we have received them from Jill and Andrew.

The paperwork for FL has been submitted to the dept and is in progress.

BS is available to give his presentation on Sunday morning (see: Wood anatomy ontology meeting, 2012 at NYBG, agenda). He suggested that this presentation may be of interest to others in the NYC area. He will advertise it to a wider audience, and RW will advertise it on the NYBG list. If we need a bigger room, we can get a classroom. DWS (after meeting) said that it would be okay to invite other people.

Upcoming meetings and Presentations 2011/2012:

PAG 2012

January 14-18, 2012, San Diego, California

PO will be represented at the following events:

• Ontology workshop, Saturday January 14th from 10:20am-12:30pm: Use of Ontologies for Organizing Plant and Animal Genomics Data. We have 5 speakers and time at the end for a panel discussion.

PJ will give the introductory remarks at the Ontology workshop, and hopefully take part in the Panel Discussion.

For more info, see the PAG 2012 Ontology workshop wiki page.

• LC is also presenting in the Non-Seed Plant Workshop on Saturday, Jan 14th, (3:50pm-6pm) and in the Plant Phenotypes workshop on Sunday, Jan. 15th, (8:00am - 10:10am).

• We will also do a computer demo Monday 12:50 pm for the PO.

• The PO will also take part in an Outreach booth organized by MaizeGDB- schedule TBA

-Do we want to host the wiki page for the booth again?

Phenotype RCN meeting, 23-25 February 2012

The dates: February 23-25, 2012 (Thursday, Friday, 1/2 Saturday) have been confirmed for the next annual Phenotype RCN meeting.

It will be held again at NESCent (Durham, NC).

RW has a friend there she can stay with and is interested in going.

Any news??

Maize Genetics Meeting, March 15-18, 2012

The maize meetings are being held in Portland, OR this year.

For more info see: Maize Genetics Meeting 2012

Registration Link: 2012 Maize Genetics Conference Registration Page will open on December 30, 2011.

Deadlines: Advance meeting registration is due by January 31, 2012.

5th International Biocuration Conference

April 2-4, 2012, Washington DC

• Abstract was submitted December 9, 2011 for consideration for a talk (or else a poster). MS was co-author.

See link: File:Abs Biocuration 2012 (LC 12-9-11).pdf

• Notification date: February 3, 2012

From 9-27-11: PJ is planning to attend and will be running a biocuration workshop- is this happening?

SPNHC 2012

Annual meeting of the Society for the Preservation of Natural History Collections

Yale University, New Haven Connecticut June 11-16, 2012

Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).

The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).

From PJ: If we can show progress in the FNA work or Morphobank yes we should

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

Call for Symposia, Colloquia and Workshops:

RW, DWS and MAG put together a proposal for a half day hands-on workshop. The goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.

Proposal was submitted, waiting for news.

PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrixes.

exhibitor's booth

We should also consider 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. (plus all the extras!)

• 2 months of Rotating Banner Ads in the online American Journal of Botany

• A Rotating Banner Ad in one edition of the online Plant Science Bulletin

• A Rotating Banner Ad on the Botany 2012 abstract submission site

• A Rotating Banner Ad on the 2012 Conference Registration site.

PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.

Annotation wiki

JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.

ASPB Plant Biology 2012

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

Registration scheduled to open first week in January.

Early Bird Registration: by May 11

Advance Discounted: May 12-June 15

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)

Relevant dates

• Jan. 31st, 2012: Paper submission deadline
• Feb. 28th, 2012: Notification of paper acceptance
• March 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
• April 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance
• June 30th 2012: Deadline for all camera-ready copies for the proceedings

We have until Jan. 31 to submit a paper. Do we want to try to prepare a manuscript for this?

Possible topics: finding commonality in development stages across the plant kingdom (revisions of PGDSO), plant phenotypes in ontologies, community driven annotation efforts (new application from JP and others), others?

BS would like to collaborate on a preliminary paper on Plant Disease Ontology. RW will review IDO and summarize what is there already for plants, what is needed, how it will link to PO. LC will also collaborate.

BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts