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adding acronym to tool snippet
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bedroesb committed Oct 9, 2024
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4 changes: 2 additions & 2 deletions _data/tool_and_resource_list.yml
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url: https://retorque.re/zotero-better-bibtex/
- description: Beacon for OMOP (B4OMOP) software allows for the integration of a Beacon onto any OMOP Common Data Model (CDM) database.
id: b4omop
name: Beacon for OMOP
name: Beacon for OMOP (B4OMOP)
url: https://gitlab.bsc.es/impact-data/impd-beacon_omopcdm
- description: Developed through the Global Alliance for Genomics and Health (GA4GH) Discovery workstream with support from ELIXIR, Beacon is a data discovery protocol defining an open standard for discovering genomic and phenoclinic data in research and clinical applications.
id: beacon-v2
name: Beacon v2
url: https://docs.genomebeacons.org/implementations-options/
- description: An open-source out-of-the-box toolkit to initiate a Beacon v2. B2RI includes tools for loading metadata, such as phenotypic data and genomic variants into a MongoDB database, and features a Beacon query engine (REST API).
id: beacon-ri
name: Beacon v2 Reference Implementation
name: Beacon v2 Reference Implementation (B2RI)
url: https://github.com/EGA-archive/beacon2-ri-tools-v2
4 changes: 2 additions & 2 deletions pages/your_tasks/data_discoverability.md
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{% include image.html file="beacon-api.JPG" inline=true caption="Figure 1. Beacon API functionality ([Source](https://docs.genomebeacons.org/implementations-options/))" alt="Beacon API" max-width="30em"%}

* {% tool "beacon-ri" %}: Beacon v2 Reference Implementation, B2RI, is an out-of-the-box example implementation of the Beacon v2 protocol. It is an open-source toolkit based on Python programming language and consists of tools for loading metadata, e.g. phenotypic data, from a CSV file and genomic variants from a VCF file into a MongoDB database. It also features the Beacon query engine (REST API) and comes bundled with an example dataset (CINECA synthetic cohort EUROPE UK1) comprising synthetic data.
* {% tool "beacon-ri" %}: an out-of-the-box example implementation of the Beacon v2 protocol. It is an open-source toolkit based on Python programming language and consists of tools for loading metadata, e.g. phenotypic data, from a CSV file and genomic variants from a VCF file into a MongoDB database. It also features the Beacon query engine (REST API) and comes bundled with an example dataset (CINECA synthetic cohort EUROPE UK1) comprising synthetic data.

{% include image.html file="beacon-ri.JPG" inline=true caption="Figure 2. Beacon RI functionality. ([Source](https://docs.genomebeacons.org/implementations-options/))" alt="Beacon RI" max-width="30em" %}

Documentation for B2RI: https://b2ri-documentation.readthedocs.io/en/latest/
GitHub Repository for Beacon v2: https://github.com/EGA-archive/beacon2-ri-tools-v2

Building on B2RI, the {% tool "b4omop" %} (B4OMOP) software allows for the integration of a Beacon onto any OMOP Common Data Model (CDM) database. This enables organizations using the OMOP CDM to leverage the Beacon framework for querying and sharing genomic and phenotypic data.
Building on B2RI, the {% tool "b4omop" %} software allows for the integration of a Beacon onto any OMOP Common Data Model (CDM) database. This enables organizations using the OMOP CDM to leverage the Beacon framework for querying and sharing genomic and phenotypic data.

Documentation: https://gitlab.bsc.es/impact-data/impd-beacon_omopcdm

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