POC Conf. Call 4-10-12
POC meeting, Webex Conference Call; Date: Tuesday Apr 10th, 2012 10am PDT/1pm EDT
POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Preece (OSU), Pankaj Jaiswal (OSU), Justin Elser (OSU), Barry Smith (University at Buffalo, NY), Justin Elser (OSU).
Absent: Marie Alejandra Gandolfo (Cornell), Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab)
Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_3-27-12? no changes, additions, or deletions
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Demo - Integrating Annotated Images with PO terms
JP gave a short demo with "mock-ups" to display one approach to integrating annotated images with PO terms on the PO web site (screenshots below). This one envisions pop-ups driven from links on PO term information pages -- perhaps in the External References section, or somewhere else on the page -- we have options and flexibility in this regard.
The long-term goal: A database on a PO server that stores images annotated with PO terms (internally and externally-generated), and a corresponding web interface to display them online in conjunction with other PO data. Database currently being designed by JP and BA.
The desktop image annotation tool that allows curators to generate annotated images for future integration with web sites and other applications will be available for testing within a few weeks, but any db storage and web-based display of annotated images in conjunction with the PO site is not currently scheduled for active development and is a few months away, at a minimum.
Screenshots (click to see full resolution)
- Give the "secondary" annotation terms a more prominent location, perhaps on the left or right instead of the bottom.
- field for annotators on the desktop app, also can zoom on the segmentation tool.
- Keeping things up to date- will not be an issue, as they will go through the webservices. All the parts will draw from from the database.
Pop-up (eg. shown above) would pull out any annotations to all images with that key words.
Discussions about the options for linking to keywords and the level of curation needed: One approach is to link to keywords, but their def'n may or may not match our def'n, or the curate the images themselves. May also mirror ale's images at OSU and those would be curated. Could apply for curating other images such as the foxtail images. Would be attributed back to source site.
Desktop application could most likely be ready to demo for the workshop at the BSA meeting. Will pull taxonomy terms from UBio and could in the future pull terms from TO or GO. Database should be developed for fall. Will plan to do another demo when Ale and KS can take part. RW will coordinate it.
Other notes about Images
- Journal Bioinformatics- new section called "Bioimage informatics
Might be able to put together a publication about this new tool? LC 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.
Should see if we can get permission to Link to or mirror their images on PO and add annotations. See if they can list PO ids as a source on their web page, like they do for GO and NCBI.
- 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
SOP needs updating- also need to know what needs to be done on the database side -JE should prepare a SOP from his side.
- 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.
This is a good idea, although at this point, the creation of the asserted file cannot be done automatically and will have to be hand tweaked by the editors each time.
We should follow up on running Oort to create the asserted version in the dev loading script- LC sent the link to JE to run Oort on the command line
Discussion of the PO Filenames
Reason for having separate versions- we keep the editors version unasserted. Relationships as that are asserted are based on what axioms are put in the file and those can change.
editors version:- has inferred relations, then when we post it on AmiGO browser, we assert all the relations that have been inferred and call it po-asserted.
BS suggested that using "plant_ontology_assert" was misleading, and because this is the inferred file. RW pointed out that it was called "assert" based on the OboEdit function "assert implied links".
BS: Users should see the file with inferred relations asserted: They do, since that is what is on the AmiGO browser on the PO site.
Comments from BS about the file names: this way of naming the files is backwards, this is the wrong way to call the files. The "Law" says that the asserted file should be the one that has no inferred relations, so we should be calling the editors version PO_inferred and then the file with the relations asserted would be just plantontology.obo
BS: the asserted version should be the one that is edited. The editors file should be po-edit or po-asserted: without the inferences- (does this mean before thet are put in or before they are asserted?)
"asserted" vs "implied or inferred" relations
We will look at the naming scheme that CM suggested (what GO uses) and see if that makes sense for PO. Could change names if we do it carefully and document it
Goals and Timeline for the next Release #18
Timeline: End of june to Mid- July- before BSA and ASPB meetings?
- finish whole plant stages, prioritize by ones with most annotations
- PJ: reproductive stage, seed germination
Continue major revision of PSDS
Focus on the revisions on:
PO:0007033 : whole plant development stage
> PO:0028002 : sporophyte development stage
>> PO:0007130 : sporophyte reproductive stage : (Some still have the numbers preceding them, others don't)
>>> PO:0007047 : 3 inflorescence detectable stage 
>>>PO:0007016 : 4 flowering 
>>>PO:0007042 : 5 fruit formation 
>>>PO:0007010 : 6 ripening 
>> PO:0007134 : sporophyte vegetative stage : (Some still have the numbers preceding them, others don't)
>>>PO:0007057 : 0 seed germination stage 
>>>PO:0007112 : 1 main shoot growth stage 
>>>PO:0007131 : seedling development stage 
PO:0009012 : plant structure development stage:
> PO:0007615 : flower development stage 
>PO:0001083 : inflorescence development stage 
PO:0025339 : plant organ development stage 
>PO:0001050 : leaf development stage 
>PO:0007520 : root development stage 
PO:0025338 : collective plant structure development stage 
>PO:0007615 : flower development stage 
Continue revisions and adding new terms for wood ontology
Most terms are in the PAE branch or for GO.
Can continue to add annotations as we go along, as well.
New or expanded association files:
- cotton- AgBase
- soybean- SoyBase
RW will email Stefan and Daniel to find out if either of them are planning to attend the moss meeting at NYBG this summer.
Plant Ontology Web Site and Browser Update:
Please see Plant_Ontology_Web_Site_Update:_2012 for more details
- Items on the tracker:
PO:IDs in definitions working as links, fixes to web page headers
- Browser update- what is the status of this?
Complete old user requests/SF tracker items
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
- Community annotation
- Functional annotation and pathways
- Databases & Journals – How to have a sustainable long term plan for journals and databases?
- Careers in biocuration
- Curation workflows and tools
- Integrating text mining into biocuration workflows
- Ontologies and standards
Interactive Text Mining in the Biocuration Workflow
Upcoming meetings and Presentations 2012:
May 16 - 18, 2012
University of Kansas Biodiversity Institute, Lawrence, Kansas
The goals of this workshop (still being refined): 1) Clarification of terms used in the biodiversity, genomics, and ecological communities, and 2) Steps to take in building a Biocollections Ontology.
BS, MAG, and RW are attending.
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.
Can we consider September? RB is available 12th -25th September
July 7 - 11, 2012 - Columbus, Ohio
- PO workshop on Sunday, July 8th, 9:00AM - 12:00PM
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.
A desktop version of the image annotation software should be ready to demo at this meeting.
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.
We should do the booth. PJ will attend to host the booth for both Gramene and PO.
Bio-Ontologies SIG 2012
Where: July 13 - 14, 2012, Long Beach, CA. Co-located with ISMB 2012
When: Submissions Due: April 13th, 2012 (Fri)
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
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.
- 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 sent around a draft of an abstract for a poster summarizing the PO-FNA collaboration, with the folks from FNA.
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: 
Application deadline is April 4th, 2012 (extended through mid-April)
LC will forward email to PO announce list and post on PO Facebook page.