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

Minutes

A. General Comments and Updates:

Introductions:

• Any new faces- Updates on new hires:
  • Georgios moving to Birmingham, has not hired a postdoc, will readvertise, joint position with John
  • Austin Meier:

Ontology Development Workshop

• Goal is to hold it this fall - possibly Nov-Dec, in Corvallis
• goal: not just ontology training (OWL/Protege)
• stay for a couple days (1 week total) for actual hands on
• get people actually comfortable in the system.
• bring in OSU Conferences cordinators to help manage logistics

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

• Need 2 pager report
• Poster for presenting- needs photos of all participants

 - Chris' update/demo of new AmiGO curation pathway.
   "11am next wed"
 - Next all hands: sept 24th (likely to change)

- 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.

- Justin Preese

 - 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
 

B. Update from Ontologies Working Group:

- LoL update:

 - moved from SVN to Github
   - all 4 of ours
   - some Crop ontology (maize wheat, rice, casava)
   - everyone needs github IDs for access to our project
     "john and george still need"

- Maria Angelique

 - Crop ontologies
   - uploading the 12 ontologies
   - mapping between crop ontologies, and ref. ontologies
 - RTB dev meeting
   - 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.