Jan 23rd, 2018 Ontology Working Group Meeting

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  • Date: Tuesday Jan 23rd, 2018
  • Time: 8:15am PST (GMT-8)
  • Connection details:

Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/831712725

Meeting recordings:

Agenda and Notes

Special presentation on PhenoArch Data Management at INRA by Pascal Neveu, INRA SupAgro- (data & databases) and François Tardieu (platform leader).

  • PhenoArch is a phenotyping platform aimed at analysing the genetic determinisms of plant responses to environmental conditions in particular drought, temperature and light. It is hosted in the LEPSE group (INRA), with users belonging to several groups in INRA and CIRAD.

Characterization of genotypes

  • Ecophysiology

Phenotyping platforms: --> Omics

  • roots for 200 plants
  • stomatal conductance- from transpiration and environmental conditions
  • Penman Monteith Equation- reversed
  • Field platforms- large mobile, rainout shelters
  • large scale offsite platforms- evaluate...
  • Network of field experiments- 16 fields X 2 years x 2 w. treatments -- QTL analyses
  • Three National, methodological ??
  • Images to traits- e.g. light interception
  • Phenomobiles, drones, RGB camera, field...?

Information systems:

  • Organize and share data
  • Cyril Pommier- ontologies
  • Pascal- different scales, levels, interactions

PHIS- Big data Management System

  • Different instances
  • FAIR data management, sparql queries based on:
    • object class- instances identified by URI
    • events- semantics relate object classes and events

Platform Ontology

  • links to reference ontologies- SKOS
  • measurements associated
  • QR codes
  • Structuring the data- metadata, ontologies

PHIS Architecture

  • based on web services
  • R Interfaces
  • galaxy, Cline ??

Phenoharmonis - from Images to traits

  • EA: linking data back to germplasm
  • PHIS- links to other info systems
  • GWAS analysis done outside PHIS
  • network or pipeline

Needs for ontology development:

  • Need transversal links - e.g. links between plants and plots
  • Ontology of events...?
  • Environmental ontology
  • definition of objects-
  • description in MIAPPE - EMPHASIS project
  • Sensor data
  • core metadata of MIAPPE
  • Comment: Ann Sylvester NSF - familiar with EMPHASIS project
  • US Network on phenotyping interaction- new project in USA

Notes from AM:

  • Some traits measured:
    • TO:0000522 - stomatal conductance
    • TO:0012001 - leaf area index
    • TO:0000207 - plant height
    • root traits: branching angle, depth, amount of branching/hairs
  • all software is in-house??
  • KOS ontology? says reference ontology
  • raw data to clean data -- this is your most difficult challenge. They are responsible for doing some of this, and providing an overview for what was done.
  • Don't actually do experiments, they just maintain the facilities - and the DATA
  • knime - some sort of workflow software.
  • linking to the source germplasm = QR code
  • no standards. They deliver data, and the users decide how to interpret it. This is frustrating, because it does the opposite of standardizing. However, the metadata is standardized. What cameras, what environmental conditions.
  • They would like to have some terms for groupings of plants (plot) because they measure data on plots, or stands, not always individual plants.
  • they would also like standardizing of the "elements" plot, field, plant, etc

Upcoming Events

  • Phenome 2018, Tucson, AZ, Feb 14th-17th, 2018
  • Phenoharmonis May 14th-18th, 2018
  • ICBO 2018- Corvallis, OR, August 6-10th

Next meeting: TBA