Harmonisation Pilot


The harmonisation pilot service will evaluate how to establish EMPHASIS as a central point of information on Good Phenotyping Practices developed in close collaboration with the phenotyping community and based on state-of-the-art procedures.

The aim is to develop and communicate with the plant phenotyping community best practices (Good Phenotyping Practice). This will be a prerequisite to allow experimental reproducibility between infrastructures and reusability of the obtained data (e.g., by defining standards).  This will include collecting/ defining standards, minimum requirements and guidelines on experimental procedures and the use of equipment.

The aim is to collect minimum requirements for plant phenotyping experiments under controlled and field conditions and guidelines on use and calibration of sensors.

Two tasks have been formulated in this pilot service in the Implementation phase.

 

1. Outreach

Community exchange on harmonisation

We actively interact with the community via targeted e-mailing of experts, general online outings (social media), workshops and via mailings and webinar announcements.

We are organising workshops and round-table discussions with operators of plant phenotyping facilities and users on Good Phenotyping Practice in all infrastructure categories:

                 i) controlled conditions,

                 ii) intensive field,

                 iii) lean field,

                 iv) data and computational services,

                 v) modelling

 

2. Collect information

Requirements for Good Phenotyping Practice are:
  • Evaluate and define experimental procedures required to enable comparability of experiments with focus on experimental design and analysis for single and multiple installation experiments, environmental monitoring, sensor calibration and application etc. (including work from EPPN/EPPN2020 and enable access for EMPHASIS members)
  • Map, evaluate and offer access to existing repositories hosting plant phenotyping protocols and their accessibility for the user community;
  • Develop an EMPHASIS repository integrating information from existing repositories as well as new protocols and quality measures required for Good Phenotyping practice in plant phenotyping.
  • Establishment of a processes continuing quality assurance for the Operational Phase of EMPHASIS.

 

Examples of collected information


Existing protocols/standards

EPPN standards

Prometheus WIKI

Bio-protocol

Springer Nature Experiments

F1000Research potocol collections

FAIRsharing

 

Publications on harmonisation

Arend D et al (2020) The on-premise data sharing infrastructure e!DAL: Foster FAIR data for faster data acquisition. GigaScience, Volume 9, Issue 10, giaa107, doi.org:10.1093/gigascience/giaa107

Watt M et al (2020) Phenotyping: New Windows into the Plant for Breeders. Annual Review of Plant Biology, Vol. 71:689-712, https://doi.org/10.1146/annurev-arplant-042916-041124

Eliana Papoutsoglou on behalf of The MIAPPE Team (2020) Agricultural Ontologies in Use: The MIAPPE Standard, CGIAR Platform for Big Data in Agriculture (blog post)

Papoutsoglou et al (2020) Enabling reusability of plant phenomic datasets with MIAPPE 1.1. New Phytologist 227: 260–273, doi:10.1111/nph.16544

Hendrik Poorter et al (2019) A meta‐analysis of plant responses to light intensity for 70 traits ranging from molecules to whole plant performance. New Phytologist, Volume 223, Issue 3, Pages 1073-1105, https://doi.org/10.1111/nph.15754

Halbritter A et al (2018) The handbook for standardised field measurements in terrestrial global change experiments

Coppens F (2017) Unlocking the potential of plant phenotyping data through integration and data-driven approaches. Current Opinion in Systems Biology, Volume 4, Pages 58-63, https://doi.org/10.1016/j.coisb.2017.07.002

Tardieu et al (2017) Plant Phenomics, From Sensors to Knowledge, Volume 27, Issue 15, PR770-R783, https://doi.org/10.1016/j.cub.2017.05.055

Ćwiek‑Kupczyńska et al (2016) Measures for interoperability of phenotypic data: minimum information requirements and formatting Plant Methods (2016) 12:44

Krajewski et al (2015) Towards recommendations for metadata and data handling in plant phenotyping. Journal of Experimental Botany, 66, 5417–5427

Lobet G et al (2015) Root System Markup Language: Toward a Unified Root Architecture Description Language. Plant Physiology, Vol. 167, pp. 617–627, DOI: https://doi.org/10.1104/pp.114.253625

Pérez-Harguindeguy et al (2013) New handbook for standardised measurement of plant functional traits worldwide. Australian Journal of Botany

Poorter et at (2012) The art of growing plants for experimental purposes: a practical guide for the plant biologist. Functional Plant Biology, 2012, 39, 821–838

Poorter et al (2012) Pot size matters: a meta-analysis of the effects of rooting volume on plant growth. Functional Plant Biology, 2012, 39, 839–850    also discussed in this webinar

Reynolds et al (2012) Physiological Breeding I: Interdisciplinary Approaches to Improve Crop Adaptation. CIMMYT

Pask et al (2012) Physiological Breeding II: A field Guide to Wheat Phenotyping. CIMMYT

Massonnet C et al (2010) Probing the Reproducibility of Leaf Growth and Molecular Phenotypes: A Comparison of Three Arabidopsis Accessions Cultivated in Ten Laboratories. Plant Physiology, Vol. 152, pp. 2142–2157

Volk G M (2010) Advantages for the Use of Standardized Phenotyping in Databases. HortScience, Volume 45: Issue 9, https://doi.org/10.21273/HORTSCI.45.9.1310

 

Videos and video articles

Dalal A et al (2020) A Telemetric, Gravimetric Platform for Real-Time Physiological Phenotyping of Plant–Environment Interactions, JoVE Journal, Environment, doi: 10.3791/61280

Hanna Ćwiek Kupczyńska (2019) The Minimum Information About Plant Phenotyping Experiment MIAPPE , YouTube (recorded presentation)

Gernot Bodner et al (2017) RGB and Spectral Root Imaging for Plant Phenotyping and Physiological Research: Experimental Setup and Imaging Protocols, JoVE Journal, Environment, doi: 10.3791/56251

  

Webinars

Hendrik Poorter (2020) Phenomics, MetaPhenomics, and the many ways plants acclimate growth to light intensity

Daniel Arend (2018) The de.NBI/ELIXIR Service "PGP" for Phenomics Data Publication (webinar on data sharing) 

Hendrik Poorter (2017) Pampered inside, pestered outside? Ways to bridge the gap between lab and field experiments

 

Initiatives towards harmonisation

MIAPPE

ELIXIR

BrAPI

 transPLANT

ISA-TAB for Phenotyping

Data repositories

e!DAL-PGP

ZENODO

DRYAD

 


You can contribute by recommending resources


If you would like to add your recommendations, papers, existing repositories or links to this list, please use this form and we will add them:
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If you have yet unpublished protocols that you would like to share with the phenotyping community, please forward this via email.