PhenoHarmonIS 2018

The PhenoHarmonIs Workshop was held 14-18 May at CIRAD & Agropolis Scientific Park, Montpellier, France

The workshop focused on tools and practices for harmonization of phenotyping and agronomic data from capture to publishing. Scientific domains tackled included conservation, breeding including the needs for Participatory Varietal Selection, quality traits, agronomy and agro-ecology with its specific needs for surveys.

As per the recommendation made by participants in 2016, PhenoHarmonIS 2018 workshop assessed progress made since 2016 by the community in adopting, further developing and connecting the largely accepted standards and tools into a functional workflow.

Demonstrations, hands-on and training sessions were included for both users and developers on:

• Crop Trait Dictionaries development and curation on the use of agriculture relevant ontologies: GO, CO, AgrO, ENVO, Planteome ontologies, Plant Phenotype Experiment Ontology and more

• Use of metadata standards: MIAPPE, ISA-TAB

• Look up services: EBI-OLS, etc

• Annotation tools: COPO

• Data interoperability tools: Breeding API (BrAPI)

• Applications in breeding and agronomy field books: AgroFIMS, BMS, HIDAP, FieldTask, etc

• Use in agro-ecological surveys

• Use in repositories/databases : Dataverse, Planteome, BMS, NextGen Databases, Gardian, etc

Group discussions were conducted around the priorities identified by the consultation of the Ontology CoP of the CGIAR Big Data Platform, which are :

1. Reaching a community agreement on what are the criteria for selecting ontologies to use in agricultural information systems and repositories? What makes an ontology a reference?

2. Defining features of a model ontology-driven annotation tool

3. Defining an adequate term submission and validation workflow

4. Principles for producing a functional ontology mash-up for agricultural data annotation

Improvement of environment variables for standards like MIAPPE and the use of Environmental Ontology, PECO, etc. were discussed as well as the use of ontologies for image tagging, text and data mining.

For more information, visit the PhenoHarmonIs 2018 folder.