Thursday Aug 20th, 2015: Difference between revisions
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==Pankaj Announcements:== | ==Pankaj Announcements:== | ||
==Ontology Development Workshop== | === Ontology Development Workshop === | ||
* Planning for this fall - possibly Nov-Dec, in Corvallis | * Planning for this fall - possibly Nov-Dec, in Corvallis | ||
* Goal: not just ontology training (OWL/Protege) | * Goal: not just ontology training (OWL/Protege) | ||
Line 45: | Line 45: | ||
* GG and JD show their data structure- When? | * GG and JD show their data structure- When? | ||
* Next all hands: planned for Sept 24th- LC will send out a doodle poll | * Next all hands: planned for Sept 24th- LC will send out a doodle poll | ||
== B. Update from Ontologies Working Group:== | == B. Update from Ontologies Working Group:== |
Revision as of 10:27, 25 August 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.
Pankaj Announcements:
Ontology Development Workshop
- Planning for this fall - 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
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
ICBO Meeting Aug 1-4th, 2016
- Location- to be held in Corvallis
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