Integrating plant phenotypic and genotypic data in the AGENT project: a BrAPI service implementation.

Abstract

Motivation The AGENT project established a network of actively cooperating European genebanks, integrating genomic and phenotypic data from accessions of wheat and barley. Due to specific storage demands for phenotypic and genotypic data, the project used separate database instances and backend technologies to manage integrated phenotypic and genotypic data. Results We discuss the challenges encountered when integrating dispersed data to serve through a single interface such as the Plant Breeding Application Programming Interface, BrAPI. We examine how the consistent mappability of genebank data to the BrAPI model can enable the implementation of effective services. The advantages of BrAPI in transparently linking distributed data entities through embedded, unique identifiers are highlighted. We present a technical solution involving a BrAPI proxy, which combines and merges separate BrAPI endpoints. Finally, we demonstrate the AGENT BrAPI implementation with an illustrative example that validates a suggested SNP for a trait from the literature by linking phenotypic, genotypic and passport data. Availability and implementation The BrAPI proxy implementation and documentation is available at the Python Package Index (https://pypi.org/project/brapi-proxy) and archived in Zenodo (doi: 10.5281/zenodo.19436445). Supplementary information A Jupyter Notebook file for the validation example using a marker-trait relationship found in the literature.

Plant phenotyping relevance

植物の表現型データを含む分散データを統合・提供するBrAPIプロキシの技術実装が中心であり、表現型データ基盤・再利用可能なソフトウェアとして対象に含める。

Code and data availability

The paper's authors publicly released the BrAPI proxy software used to merge the AGENT project's phenotypic/genotypic BrAPI endpoints, available on PyPI and archived in Zenodo. The supplementary Jupyter Notebook for the marker-trait validation example is mentioned but no public URL is provided, so it is not listed as a