Oct 5th, 2017 Ontology Working Group Meeting

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Planteome Ontology WG Zoom Meeting

  • Date: Thursday Oct 5th, 2017
  • Time: 8:15am PDT (GMT-7)


  • Meeting Recordings:

Agenda and Notes

PJ

  • Applying for no cost extension, should be planning to start applying for renewal by spring
  • Ideally should include people who may have their own sources of funding
  • Planning for a database release by Dec 15th, in advance of PAG 2018
  • Metadata annotations automated,
  • Neural network approach
  • Using the images- recognition of leaf, flower, stem- ~ 60% accuracy
  • Need to bring in engineering/computing folks, people doing high throughput phenotyping

GG

  • Working to develop Plant PhenomeNet further, but need a good source of annotated data
  • Qualities vs values in the data annotations
  • New person hired…
  • Luke Slater working on AberOwl
  • Also focusing on updating PATO
  • How to convert quantitative data to qualitative data??

EA

  • phenotyping platforms, automating annotations
  • MIAPPE meeting, concern about having ontology terms for the environment and experimental conditions
  • Setting up collaboration with groups doing High Throughput Phenotyping
    • French group at Agropolis in Montpellier
    • John Doonan
    • PODD- Australian group
  • Invite them to one of our calls

GG: - most of the data is proprietary

  • Can we partner with them? Use the data/images with the sources removed, feed back to them?
  • Find phenotypic features
  • Machine learning as an approach

PJ: Set up separate call with George and John to see what we can get working on

  • Need the data
  • Also would like to have Bjorn Usadel come to one of our meetings

EA:

  • HTP work going on at IRRI and other sites, that data may be more available
  • Will work on setting up a conf call with the folks French group at Agropolis in Montpellier

MAL:

  • Breeding API
  • Mapping CO to TO will facilitate finding the data
  • Next two CO vocabs are groundnut and Musa
  • Working with Ethy Cannon on traits from PeanutBase, follow up with Steve Cannnon as well
  • Do we have any peanut data?- Not at this time

PJ: demo of the Ontology Enrichment Tool http://planteome.org/oat/

  • Demo of the tool,
  • test with the input gene example sets available from the bottom right hand side of the gene list box. Or add your own gene IDs from another species to test.
  • Similar to AgriGO, but revised the methods
  • Collaboration with software development company Sanmita
  • Developing the ability to edit genes, add info etc
  • May be able to merge with Noctua at some point in the future
  • Community engagement portal

AM: Update on OoPS

  • Samara scrape for APS and germplasm
  • GRIN descriptors converted to gaf files
  • Mapping files,
  • Using INCA tool -https://planteome.github.io/planteome-inca-form
  • Some steps need to be done manually- like pushing to GH
  • Plant disease patterns, issues with names that are obtained from script
  • Probably need to have meeting with Dan Keith and CM to see what needs to be done on the INCA tool to get it configured
  • Scrape of diseases had about 11,000 lines, narrowed down to about 7000 as there are redundancies
  • GG interested in doing text mining on the data set, or maybe a test set
  • MAL- Crop dictionaries may also be helpful

LC:

  • NAR paper in review
  • Collaboration with Hong Cui and James Macklin- they have digitized the flora of North America descriptions
  • Working on TO and PECO revisions
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