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:

Agenda

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