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 University of Birmingham, UK
- 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/Montpellier Meeting ~May 2016
- Will be in conjunction with another meeting, working with Ruth Bastow to organize
- 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- See above
- Almost complete. Let me know if there are any more files to transfer with history
- All files (minus SVN) are over on github (almost, still moving a few extras)
- Association files: moving to iPlant eventually?
- Where are we going to put the association files?- the association files are too big for Github
- They are cluttered within the SVN- JE will move them all to a new SVN repository
- 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, but lacks any version control system
- 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.
AmiGO 2
Fixed annotation loading issue (well, a workaround)
- Working on bisecting issue so we can stay current with Owltools and AmiGO 2 development
Not sure what this is referring to
- Loading is far far faster, but issue is that it won't load any annotations
- JE found a workaround with an old version of OWLtools, but its "not ideal"
- GO doesn't have this issue- Can Chris or Seth help?
- CM can't help until the beginning of Sept.
- If JE can't figure it out by sept, Chris 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.
- Migrating live version to iPLant- need to check on virtual machines
- Need to work on customization and tools
- iPlant won't get looked at until it is working on the live version (????)
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 Comp Sci- Sinisa's Lab
- 1. C++ and Matlab under the hood
- 2. Matlab and python on the surface for UI
E. Other Comments:
Next meeting TBA
Planned for Sept 24th- LC will send out a doodle poll as GG has a conflict