This use case deals with the integration of an open, standardized interface (Breeding API) to make the proprietary data management systems available in the PhenoSphere system FAIR.

Background

Currently, proprietary data management systems are used in the PhenoSphere system to store, access and analyze image data. These vendor-specific solutions make it difficult to reuse the data and prevent compliance with the FAIR principles (Findable, Accessible, Interoperable, Reusable). To change this, the integration of an open, standardized access such as BrAPI (Breeding API, brapi.org) is required. BrAPI provides an open interface that enables phenotyping data to be collected and shared in accordance with the MIAPPE (Minimum Information About a Plant Phenotyping Experiment) standards.

As part of this use case pilot, we are developing a BrAPI-compliant interface for processing phenotyping images in collaboration with PSI. These images are captured using PSI phenotyping systems, which are used in numerous European high-throughput phenotyping facilities. Specifically, the development will initially be carried out on the PhenoSphere PhenoCrane system at IPK Gatersleben, which was built by PSI.

The BrAPI integration developed here is being implemented as an example at IPK Gatersleben. In total, up to 50 other European research institutions that also use PSI infrastructures could benefit from this development. These include, among others:

• NPEC Wageningen: PSI Systems here use the “Fytotron” environmental control software vis adapted APIs
• Vienna BioCenter Core
• PhenomUK

The BrAPI integration makes it possible to create phenotyping images from systems such as the PhenoCrane “FAIR”. This means that the data can be reused and combined more easily with other data sources. An important advantage is that environmental data (e.g. temperature or light intensity) can also be incorporated into the integration in the future.

Technical implementation

The use case includes the integration of the BrAPI core and BrAPI phenotyping modules into the PSI databases. We are developing a user interface that guides users step-by-step through filling in the metadata so that the MIAPPE standards are adhered to. This ensures that the data is available in a structured and standardized form for BrAPI pull requests and can be reused by other research institutions.

Long-term added value

The interface developed not only supports the IPK Gatersleben and NPEC Wageningen, but can also be passed on to other European partners. The project thus contributes significantly to the FAIRification of phenotyping data and supports the entire FAIRagro community in the implementation of open data standards.

Progress & next steps

UC Update: BrAPI4PSI – BrAPI Integration on PSI Hardware

The UC11 team led by Marc C. Heuermann  presents  the development of BrAPI4PSI, a Breeding API (BrAPI) integration for PSI hardware to manage and store phenotyping images in European high-throughput phenotyping facilities. Its goal is to replace proprietary data management with open standards such as BrAPI and ISA-JSON, adhering to FAIR and MIAPPE guidelines. The ISA Wizard supports users in creating standardized study and investigation metadata, which can be transferred to the PSI software. Overall, the system enables experiment registration, automated assay file generation from imaging events, and extraction of metadata and image URLs.

At the ELIXIR Plant Community Call on November 14, Marc Heuermann and Manuel Feser presented the current status of Use Case 11. We have compiled the charts of this exciting report here.

ISA* Wizard: Simplifying FAIR Metadata Annotation for Life Sciences

Managing and analyzing large-scale life science data is becoming increasingly complex due to rapid growth and the need for high-quality, well-annotated datasets. Manual metadata annotation is often time-consuming and error-prone, making robust tools essential for data quality, interoperability, and reusability.

The ISA Wizard is a configurable, browser-based tool that facilitates intuitive metadata annotation for life science experiments based on the ISA data model. It supports metadata standards such as MIAPPE, integrates ontology services (e.g., TIB Terminology Service) and identifier resolution (e.g., ORCID), significantly reducing user workload and minimizing the need for prior ISA expertise.

Within FAIRagro Use Case 11 (BrAPI4PSI), the ISA Wizard has been integrated into the PSI software environment to streamline the registration of experimental setups with enriched metadata following open standards. This enables agricultural researchers—especially those preparing data submissions or capturing data in ISA-compatible formats from the outset—to efficiently register investigations and studies in the Phenosphere platform. The collected metadata supports downstream usage in BrAPI server endpoints, facilitating data sharing and interoperability.

The ISA Wizard is domain-agnostic and configurable for various data types, originally developed for plant phenotyping (MIAPPE compliance), with expanding applications including ongoing development for animal phenomics.

You want to know more? Check the publication: Improving Metadata Collection and Aggregation in Plant Phenotyping Experiments with MIAPPE Wizard and DataPLANT

* The ISA framework is an established metadata standard format for the structured description of life science experiments that supports compliance with the FAIR principles . It organizes experimental data into three hierarchical levels: Investigation, Study, and Assay, enabling comprehensive and standardized annotation of experimental outcomes.