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

Publications on harmonisation

Bioinformatics, data management and metadata

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

Papoutsoglou, E. 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

Jonquet, C., et al. (2018) Computers and Electronics in Agriculture, Volume 144, Pages 126-143, https://doi.org/10.1016/j.compag.2017.10.012

Jonquet, C. et al. (2018) Harnessing the power of unified metadata in an ontology repository: the case of AgroPortal, Journal on Data Semantics volume 7, pages191–221, https://doi.org/10.1007/s13740-018-0091-5

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

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

Hollebecq, J.-E. et al. (2019). Identification of objects with Uniform Resource Identifier (URI): recommendations for application in plant phenotyping. 10.5281/zenodo.3560629

(FAIR) data repositories/information system

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:
*required fields