POC Conf. Call 4-10-12

POC meeting, Webex Conference Call; Date: Tuesday Apr 10th, 2012 10am PDT/1pm EDT

In attendance:

POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_3-27-12?

Back to POC Meetings Minutes

Demo of Integrating Annotated Images with PO terms

JP will give a short demo with "mock-ups" to display one approach to integrating annotated images with PO terms on the PO web site.

This one involves pop-ups from the External References section on PO term detail pages.

Other notes about Images

• Journal Bioinformatics- new section called "Bioimage informatics

Might be able to put together a publication about this new tool? I would be interested in taking part.

• From the BioCuration meeting: David Orloff, Senior Manager, Image Library, The American Society for Cell Biology.

"I would welcome a conversation to discuss presenting your images, videos, or animations in The Cell: An Image Library www.cellimagelibrary.org, and then linking back to your websites so that researchers can easily interact with the data. "

See link to image of Hibiscus Pollen grain on their site.

• Ale got the ok to use the Setaria germination images: we need to give credit to Drs. John Dekker and Mitt Haar.

Update on the Release #17, April 2012

• Review and Assessments:

• Issue of files on Bioportal all "PO"- are we going to keep posting the separate aspect files?

• Updates to the SOP page: PO_Release_SOP_Page

Need to clarify where the various files go

• What do we need to do better next time?

Now that we can use Oort, we can easily generate the asserted file earlier in the process and test load it onto Dev or beta. That way if we run into problems, it will not hold up the database loading. I suggest adding this conversion step to the dev loading script. That will make it easier to diagnose any issues early.

Goals and Timeline for the next Release #18

Timeline:

End of june to Mid- July- before BSA and ASPB meetings?

Continue major revision of PSDS

Focus on the revsions on:

PO:0007033 : whole plant development stage

> PO:0028002 : sporophyte development stage

>> PO:0007130 : sporophyte reproductive stage [46604]: (Some still have the numbers preceding them, others don't)

>>> PO:0007047 : 3 inflorescence detectable stage [29131]

>>>PO:0007016 : 4 flowering [28057]

>>>PO:0007042 : 5 fruit formation [31009]

>>>PO:0007010 : 6 ripening [37642]

>> PO:0007134 : sporophyte vegetative stage [60370]: (Some still have the numbers preceding them, others don't)

>>>PO:0007057 : 0 seed germination stage [29568]

>>>PO:0007112 : 1 main shoot growth stage [47411]

>>>PO:0007131 : seedling development stage [26673]

PO:0009012 : plant structure development stage:

> PO:0007615 : flower development stage [48067]

>PO:0001083 : inflorescence development stage [48067]

PO:0025339 : plant organ development stage [46618]

>PO:0001050 : leaf development stage [45968]

>PO:0007520 : root development stage [25208]

PO:0025338 : collective plant structure development stage [49645]

>PO:0007615 : flower development stage [48067]

Continue revisions and adding new terms for wood ontology

More details TBA....

New or expanded association files:

• wood genes TreeGenes and Fagaceae Genomics Web

• cotton- AgBase

• soybean- SoyBase

• potato

• rice

• grape

Plant Ontology Web Site and Browser Update:

Please see Plant_Ontology_Web_Site_Update:_Winter_2012 for more details

PO:IDs in definitions working as links?

Complete old user requests/SF tracker items

Ongoing process....

priorities

Report from the 5th International Biocuration Conference

April 2-4, 2012, Washington DC

Link to poster Abstract: File:Abs Biocuration 2012 (LC 12-9-11).pdf

• LC attended and took part in the BioCreative workshop

More details TBA....

Upcoming meetings and Presentations 2012:

Semantics of Biodiversity Workshop

From Barry:

May 16 - 18, 2012

University of Kansas Biodiversity Institute, Lawrence, Kansas

BS, MAG, and RW are attending.

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

Crop Ontology Workshop

For more information see the wiki page: Crop_Ontology_Workshop_at_OSU,_2012

We are looking at the tentative dates of either: June 11-13th or Aug 6th to 8th

The focus of the workshop will be on mostly development stages and traits for the crop plants

Ruth Bastow is contacting some of the interested people to see which of these dates work best.

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

• PO workshop on Sunday, July 8th, 9:00AM - 12:00PM

see: Botany 2012 workshops

The meeting web site has been fixed so this is now listed as a half-day (morning) workshop. The schedule now links to the correct abstract.

RW will prepare an announcement for the PO home page and FB page.

Workshop goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.

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

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.

Bio-Ontologies SIG 2012

Where: July 13 - 14, 2012, Long Beach, CA. Co-located with ISMB 2012

When: Submissions Due: April 13th, 2012 (Fri)

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.

ASPB Plant Biology 2012

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

Link to meeting page: ASPB2012

Abstract was submitted for submission for minisymposia consideration.

Joint workshop is planned with PO, Gramene and TAIR

Registration is open, 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)

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 and is being revised. Wiki page for notes on Plant Disease Ontology.

Relevant dates

• Feb. 28th, 2012: Notification of paper acceptance
• April 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
• May 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

RW is working on an abstract summarizing the PO-FNA collaboration, with the folks from FNA. Will circulate soon. This will be either for a poster or a short talk in the Early Career Researcher session.

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]

Application deadline is April 4th, 2012 (extended through mid-April)

Next meeting scheduled for Tuesday, April. 17th, 2012 at 10am PDT/1pm EDT

POC_Conf._Call_4-17-12