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 or maybe another central location
• See wiki page for more details:
• Goal: Focus on ontology training (OWL/Protege), but stay for a several days to a week total for actual hands on, get people actually comfortable in the system.
• Bring in OSU Conferences coordinators to help manage logistics
• may be able to utilize OSU Conference people to help organize.

Birmingham/Montpellier Meeting ~May 2016

• Will be in conjunction with another meeting, GG and JD are working with Ruth Bastow to organize
• 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:

• GG and JD could show their data structure at a future meeting- When, next all hands meeeting

• Chris could demo update of new AmiGO curation NGS Annotation for the GO annotation with pathway curation, possibly in the next week
• Next Data viz meeting next 11am next Wed

• Next All Hands: planned for Sept 24th- LC will send out a doodle poll, GG has a conflict on the 24th

B. Update from Ontologies Working Group:

Updates from OSU: Laurel

• 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 GitHub id, will send, JD will get one

Updates from Bioversity: Marie-Angelique

• Crop Ontology webpage: http://www.cropontology.org/
  • Curation efforts have been going on during the summer to update them to the new Trait Template Ver. 5
  • Twelve of the CO vocabs are done- will be uploaded - Where, to the CO site or to GH??

Mapping between Crop Ontologies and the Ref Ontologies:

• MAL continues to work on the mapping between crop ontologies and ref. ontologies
• Priority is mapping, using an automated tool: Agreement Maker Light (AML) (http://agreementmaker.org/) tool

For details of the mapping algorithm- see the Ontology working group meeting June 21st

• Need to check on which of the files have been updated... not sure what this is referring to

• The CO vocabs are being revised to include fields in TT spreadsheet for the enttiy and attribute
• Mappings will be added as they are developed, based on the E + A

• MAL has tried tools, CM has tools, need to find out what tool works best
• New version of the TT has more information

• From CM: Prospective mapping is better than retrospective mapping- by creating logical definitions
• It would be good to work with CM to develop a workflow, power comes from the cross products
• Will review the workflow at the next ontology call

Ask CM to show us the mapping tool and if he has a more up to date version of the XP file, the one on the SVN is quite old

• Pankaj: Ideal goal is to have a tool available for the workflow by the curators
  • Suggestion to each run a common panel of files through and compare the results- e.g. rice and maize

Need to get the most recent version of the CO file- Updated TT version 5. Are these on the GH repository?

• Goal is to map back to reference ontologies through the XPs. If the terms are composed in the XPs then we are
• Suggestion: A Term Genie instance for the generation of the terms for the CO vocabs.

• MAL will share her slides to illustrate, that were presented for the RTB meeting.

Roots, Tubers, Banana Development (TRB) meeting in Montpellier:

• Funded by Bill Gates Foundation, three days week of Aug 20th
  • Discussing NGS and ontologies
  • Development and curation for the RTB crops with Boyce Thompson Institute will split the work
• Cassava has been uploaded, but it is not the up to date version, still needs to be finalized and now has a Read-Me file

Question: which of the CO species does this include? cassava, potato, banana, others?

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

Next meeting TBA

Planned for Sept 24th- LC will send out a doodle poll as GG has a conflict