Jan 23rd, 2018 Ontology Working Group Meeting
- 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
- File:Ontology Working Group Meeting-video- 1-23-18.mp4
- File:Ontology Working Group Meeting audio-1-23-18.m4a
- 1 Agenda and Notes
- 1.1 Characterization of genotypes
- 1.2 Phenotyping platforms: --> Omics
- 1.3 Information systems:
- 1.4 PHIS- Big data Management System
- 1.5 Platform Ontology
- 1.6 PHIS Architecture
- 1.7 Phenoharmonis - from Images to traits
- 1.8 Needs for ontology development:
- 1.9 Notes from AM:
- 1.10 Upcoming Events
- 1.11 Next meeting: TBA
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
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...?
- 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
- links to reference ontologies- SKOS
- measurements associated
- QR codes
- Structuring the data- metadata, ontologies
- 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
- Phenome 2018, Tucson, AZ, Feb 14th-17th, 2018
- Phenoharmonis May 14th-18th, 2018
- ICBO 2018- Corvallis, OR, August 6-10th