From 6c4ce3dbe098e7202e4f44ed82cd85bbf0f2b3d4 Mon Sep 17 00:00:00 2001 From: Valentin Guignon Date: Wed, 17 Apr 2024 16:57:22 +0200 Subject: [PATCH] Added BrAPI Mapper part Added BrAPI Mapper part. A figure will come later. --- content/03.03.federation-infrastructure.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/content/03.03.federation-infrastructure.md b/content/03.03.federation-infrastructure.md index 2cc9544..9f60591 100644 --- a/content/03.03.federation-infrastructure.md +++ b/content/03.03.federation-infrastructure.md @@ -37,3 +37,8 @@ MIRA is a tool that enables the automatic deployment of a BrAPI server on a MIAP #### MIAPPE "BrAPI to ISA" service Since the release of BrAPI 1.3, efforts have been made to incorporate support for the Minimum Information About Plant Phenotyping Experiments (MIAPPE) standard into the specification [@doi:10.1111/nph.16544]. This integration was finalized in BrAPI 2.0, resulting in full compatibility between the two standards. Consequently, BrAPI now encompasses all attributes necessary for MIAPPE compliance, adhering to standardized descriptions in accordance with MIAPPE guidelines. Leveraging BrAPI as a standardized RESTful web service API specification, we employ the ISA standard for storing metadata and phenotyping data in a standardized manner. This data is structured in the ISA-TAB file format and subjected to validation using the [MIAPPE ISA configuration](https://github.com/ELIXIR-Belgium/isatab-validation). The "BrAPI to ISA" service functions as a converter between BrAPI RESTful endpoints and ISA-TAB, facilitating the archiving of metadata and data and thereby enhancing data preservation and accessibility. The [BrAPI2ISA](https://github.com/elixir-europe/plant-brapi-to-isa) tool is designed to be compatible with BrAPI 1.3, and we invite contributions from the community to extend support for the latest versions of BrAPI. + +#### BrAPIMapper + + +BrAPIMapper is a full BrAPI implementation of all calls for any data source missing BrAPI implementation or compliance with some BrAPI versions. BrAPIMapper is provided as a docker application that can get its external data sources from mySQL or PostgreSQL databases (with a dedicated interface for Chado database schema), generic REST services (with a dedicated interface for BrAPI endpoints), flat files (XML, JSON, CSV/TSV/GFF3/VCF, YAML) or any combination of any of those. It provides an administration interface to map BrAPI data models to external data sources. The interface allows administrators to select the BrAPI specification versions to use and the calls to enable. Data mapping configuration export and import features simplify upgrades to future BrAPI specifications changes as administrators would only have to map missing fields or make minor adjustments. Amongst others, it supports paging, search calls, either by providing direct results or using deferred results with a search identifier, lists, authentication and manages access restrictions to calls that can be setup through the administration interface as well. This tool aims to accelerate BrAPI services deployment while ensuring specification compliance.