Thursday Aug 20th, 2015

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

• http://icbo.buffalo.edu/index.html

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 5

uploading the 12 ontologies

• 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 - 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 xproducts

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