Oct 5th, 2017 Ontology Working Group Meeting

Planteome Ontology WG Zoom Meeting

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

• Meeting Recordings:
  • File:Ontology WG Meeting 10-5-17 audio only.m4a
  • File:Ontology WG Meeting video 10-5-17.mp4

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