Thursday Aug 20th, 2015

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Agenda

Topic: Planteome Project All Hands Meeting Time: Aug 20, 2015 8:00 AM (GMT-7:00) Pacific Time (US and Canada) Join from PC, Mac, iOS or Android: https://zoom.us/j/431144926

  • Who: LC, PJ, AM, JE, JP, MAL, GG, JD, CM, EZ
  • Regrets: BS, EA, DWS
  • Link to recording- Video: TBA
  • Link to recording- Audio: TBA

A. General Comments and Updates:

Introductions:

  • Any new faces- Updates on new hires:
    • Georgios moving to Birmingham, has not hired a postdoc, will re-advertise, joint position with John Doonan
    • No Updates from NYBG
  • New Postdoc Curator has joined the team since late June: Austin Meier
  • Austin's Background: Born: Omaha, NE
    • Undergraduate: BS biology (genetics): University of Iowa, Iowa City
    • Internship: Monsanto, Huxley IA
    • Graduate: PhD Plant Breeding, Plant Genetics: University of Wisconsin, Madison.

News and Announcements:

NSF PI meeting Sept 9th to 11th, Washington DC

  • Need 2 pager report- PJ and LC are working on, will circulate
  • Poster for presenting- needs photos of all participants
  • End of Year One coming up- will need to prepare annual report soon

Ontology Development Workshop planned for this fall:

  • Dates: Possibly Nov-Dec, in Corvallis
  • Goal: not just ontology training (OWL/Protege)
  • See wiki page for more details:
  • Stay for a couple days (1 week total) for actual hands on, get people actually comfortable in the system.
  • Bring in OSU Conferences coordinators to help manage logistics

Birmingham/Aberystwyth/Montpellier Meeting ~May 2016

  • Goal of the meeting is to ...??

ICBO Meeting Aug 1-4th, 2016

Location- to be held in Corvallis

  • May include an Annotation Jamboree??

Other items:

  • Chris could demo update of new AmiGO curation pathway for the data viz meeting next 11am next wed?
  • GG and JD show their data structure- When?
  • Next all hands: planned for Sept 24th- LC will send out a doodle poll

B. Update from Ontologies Working Group:

From OSU: Lol update:

  • All the ontology development work and files have been moved from SVN to the new Planteome Site on Github (https://github.com/Planteome)
  • Reference Ontologies: PO, TO, PSO, EO
  • Ontology files and issue trackers, Association files are still on the SVN as they are too large for GH
  • Some Crop Ontology (IBP-maize wheat, rice, cassava)
  • Everyone needs github IDs for access to our project- JD and GG still need GH ids

'GG has a GH id, will send, JD will get one

Updates from Bioversity:Marie-Angelique

  • Crop Ontology webpage: http://www.cropontology.org/
    • Twelve of the CO vocabs have been updated to the new Trait Template Ver. 5- uploading the 12 ontologies to the CO site
    • MAL continues to work on the Mapping between crop ontologies, and ref. ontologies
    • Need to check on which of the files have been updated not sure what this is referring to
  • Roots Tubers, Banana Development meeting in Montpellier:
    • 3 days week of Aug 20th
    • discussing NGS
    • RTB with BTI will split the work
  • Converting spreadsheets to ontology, but they lack complex mapping
    • Priority is mapping, using an automated tool
    • working with chris to develop a workflow
    • MAL has tried tools, chris has tools, need to find out what tool works best.
    • prospective mapping is better than reterospective mapping
  • Pankaj: ideal goal is to have a tool available for the workflow
    • Goal is to map back to reference ontology
    • Power comes from the cross products

C. Update from IT group- Data Store, AmiGO2- Justin Elser

Migration to github

  • Seems to be mostly complete. Let me know if there are any more files to transfer with history.

AmiGO 2

Fixed annotation loading issue (well, a workaround)

  • Working on bisecting issue so we can stay current with Owltools and AmiGO 2 development.

- Justin Elser

 - all files (minus SVN) are over on github
 - AmiGO2.0
   - Far FAR faster
   - won't load any annotations
     - found a workaround with an old version of OWLtools
       "not ideal"
     - GO doesn't have this issue
   - Can ChrisS help?
     - can't help until the beginning of Sept.
     - if JE can't figure it out by sept, ChrisS can help
   - Post issues to Github's issues tracker on the Planteome-amigo2 repository
   - JE will have it up and down frequently, so be wary when you're 'testing' it.
   - iPlant won't get looked at until it is working on the live version
 - iPlant
   - where are we going to put the association files?
   - the association files are too big for Github
   - they are cluttered within the SVN
     - keep association files on SVN, but keep them alone, not mixed with things that have migrated to Github.
   - irods: iPlant's 'big iron' is a possibility
   - In the long run, it makes more sense to keep annotation/association files on iPlant
     - mirror the latest version from version control(SVN) over on iPlant for 'bulk download' options for end users.

D. Update from AISO/BisQue group- Justin Preece

- Main goal: getting a web module for people to segment images, and link those segments to ontology terms/metadata

   - There are desktop programs/algorithms that work, they are moving them to the web as 'modules'
     - TL;DR-Newer/better/shinier graph cuts
   - putting a module on iPlant BisQue that allows you to segment an image, and annotate it with ontologies.
     - Doing a test environment locally, will expand to testing groups that are larger
   - working with two students from CompSci 
     - 1. C++ and Matlab under the hood
     - 2. Matlab and python on the surface for UI

E. Other Comments:

Next meeting TBA