Documentation: https://b2ri-documentation.readthedocs.io/

Docker Hub Image: https://hub.docker.com/r/manuelrueda/beacon2-ri-tools/tags

Actively maintained by the original author

• Description
  • B2RI Diagram
  • Roadmap
• Installation
  • Containerized
  • Non-Containerized
• Citation
  • Author
• License

beacon2-ri-tools is part of the ELIXIR-Beacon v2 Reference Implementation (B2RI). It provides essential tools for ingesting, validating, and visualizing genomic and phenotypic data.

• Beacon Script (bin/beacon): A command-line tool for converting VCF data into BFF format. The tool also enables loading BFF (metadata + genomicVariations] into a MongoDB instance.
• Utility Suite: A collection of tools to aid in data ingestion. Key among them:
  • BFF Validator: This tool includes an Excel template for converting your metadata (including phenotypic and clinical data) into Beacon v2 models, along with a validator for verifying and serializing the data into BFF format.
• CINECA Synthetic Cohort - EUROPE_UK1: A synthetic dataset for testing and demonstration purposes.

            * Beacon v2 Reference Implementation *

                ___________
          XLSX  |          |
           or   | Metadata | (incl. Phenotypic data)
          JSON  |__________|
                     |
                     |
                     | Validation (bff-validator)
                     |
 _________       ____v____        __________         ______
 |       |       |       |       |          |        |     | <---- Request
 |  VCF  | ----> |  BFF  | ----> | Database | <----> | API |
 |_______|       |_ _____|       |__________|        |_____| ----> Response
                     |             MongoDB
          beacon     |    beacon
                     |
                     |
                  Optional
                     |
               ______v_______
               |            |
               | BFF        |
               | Genomic    | Visualization
               | Variations |
               | Browser    |
               |____________|

------------------------------------------------|||------------------------
beacon2-ri-tools                                             beacon2-ri-api

Latest Update: Nov-2024

We know that this repository has been downloaded and used in many Beacon v2 implementations, so our plan is to keep supporting it and improving it. These are our plans:

• Implement Beacon 2.1 changes

  For VCF, this will imply adopting VRS nomenclature and maybe moving away from LegacyVariation. Adding support for Structural variants if present.

  For other entities, make sure that we follow the latest schema in bff-validator, and the Excel file.

  Update CINECA synthetic dataset.

• Improve Genomic Variations Browser

  So that it works as a web-server instead of a static web-page.

You can install beacon2-ri-tools using one of two methods:

Follow the guide here to use Docker for a streamlined setup.

See here for manual installation instructions.

The author requests that any published work that utilizes B2RI includes a cite to the the following reference:

Rueda, M, Ariosa R. "Beacon v2 Reference Implementation: a toolkit to enable federated sharing of genomic and phenotypic data". Bioinformatics, btac568, https://doi.org/10.1093/bioinformatics/btac568

Written by Manuel Rueda, PhD. Info about CNAG can be found at https://www.cnag.eu

This repository is copyrighted, (C) 2021-2024 Manuel Rueda. See the LICENSE file included in this distribution.