Thursday Aug 20th, 2015

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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:

  • 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:


  • 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

Other items:

  • GG and JD could show their data structure at a future meeting- When? Could be on next all hands meeting
  • 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. EA and MAL have also conflict on the 24th (RDA meeting, Paris)

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 (
  • 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:
    • Curation efforts have been going on during the summer to update them to the new Trait Template Ver. 5
    • Nine of the CO vocabs are done- will be uploaded -
  • Where, to the CO site or to GH?? We are planning to upload the curated ontologies on both Github (probably the rdf version, maybe the Excel Template even if changes cannot be tracked) and CO website.
  • wheat, rice, cassava, soybean, groundnut, chickpea, lentil, cowpea, pigeon pea
  • Wheat TT5 uploaded 8-28. Need to look at a script to convert cleanly to csv or tsv.

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) ( tool

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

  • The CO vocabs are being revised to include fields in TT spreadsheet for the entity 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 than the older version
  • From CM: Prospective mapping is better than retrospective mapping- by creating logical definitions- All agree!
  • 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

LC: 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: Each run a common panel of files through and compare the results- e.g. wheat, rice and maize

LC: Need to get the most recent version of the CO files- Updated TT version 5. Wheat is on the GH repository, MAL and Leo will add rest

  • Goal is to map back to reference ontologies (TO) through the XPs. If the terms are composed in the XPs then we are able to generate the mapping automatically.
  • PJ: Suggestion: A Term Genie instance for the generation of the terms for the CO vocabs.
    • Issue is that the terms must be in the ref ontologies
    • This would be only be helpful if it generates the XP- need to review TG
  • 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?

BTI only works so far on the Cassava ontology. The other RTB crops that will be used by BTI nextgen project, will be the Crop Ontologies (Sweet Potato, Yam, Banana, Potato)

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- Done
    • 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