https://github.com/cnag-biomedical-informatics/omop-cdm-2-beacon-v2
https://github.com/cnag-biomedical-informatics/omop-cdm-2-beacon-v2
Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
-
✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
-
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (7.9%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: CNAG-Biomedical-Informatics
- Language: Jupyter Notebook
- Default Branch: main
- Size: 41 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Enhancing Semantic Interoperability in Precision Medicine: Converting OMOP CDM to Beacon v2 in the Spanish IMPaCT-Data Project
This repository provides resources and a tutorial notebook for converting OMOP CDM data to Beacon v2 format, as described in our study.
Google Colab Tutorial
Access the interactive tutorial on Google Colab via the link below:
Local Copy of the Tutorial
If you prefer running the tutorial locally, the notebook is available here:
Convert-Pheno Tool
The Convert-Pheno tool is a key resource for transforming OMOP CDM datasets into Beacon v2 format. Below are relevant resources for using the tool:
- CLI Source Code: GitHub Repository
- CPAN Distribution: Perl Module Documentation
- Docker Image: Docker Hub Tags
How to Cite
If you use this tutorial or tools in your work, please consider citing our paper:
Rueda et al. Enhancing Semantic Interoperability in Precision Medicine: Converting OMOP CDM to Beacon v2 in the Spanish IMPaCT-Data Project.
DOI (Pre-print; medRxiv): https://doi.org/10.1101/2024.12.25.24319606
Owner
- Name: CNAG Biomedical Informatics
- Login: CNAG-Biomedical-Informatics
- Kind: organization
- Location: Spain
- Repositories: 1
- Profile: https://github.com/CNAG-Biomedical-Informatics
GitHub Events
Total
- Push event: 2
Last Year
- Push event: 2
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0