View source for 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:

==Pankaj Announcements==
==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
* End of Year One coming up- will need to prepare annual report soon   
  
==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 Github
* Reference Ontology 4 of ours
* Some Crop ontology (maize wheat, rice, casava)
* Everyone needs github IDs for access to our project
      "john and george still need"

== Updates from Bioversity:bMaria 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.

- 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==