Kidney-Genetics - Designing a reproducible and curated database of kidney-related genes

Welcome to the GitHub repository "Kidney-Genetics", a systematically curated, reproducible list of all relevant kidney-related genes known to date. This project aims to provide a unified and standardized database of kidney disease-associated genes, contributing to improved diagnosis, treatment selection, and monitoring of kidney diseases. The database is designed to be automatically updated on a regular basis, ensuring the incorporation of the most up-to-date genetic findings in kidney research.

Table of contents

• Overview and Methods
• Usage
• Documentation
• File structure
• License
• Creators
• Contact

Overview and Methods

The Kidney-Genetics Atlas contains information for about 3.000 kidney-associated genes. This information was gathered from various reliable sources, such as Genomics England PanelApp, PanelApp Australia, PubTator, OMIM, Orphanet, clinical diagnostic panels, and comprehensive literature review.

Usage

The Kidney-Genetics Atlas is publicly available and accessible through GitHub. Furthermore, the database is automatically and regularly updated to ensure its currency and relevance. The documentation also shows the current result from each analysis and the merged list of genes as filterable data tables.

Documentation

Please explore The Kidney-Genetics Documentation hosted on GitHub pages and build with bookdown.

File Structure

The repository has the following structure:

.
├── analyses/
│   ├── 01_PanelApp/
│   │   ├── data/
│   │   ├── results/
│   │   └── 01_PanelApp.R
│   ├── 02_Literature/
│   │   ├── data/
│   │   ├── results/
│   │   └── 02_Literature.R
│   ├── 03_DiagnosticPanels/
│   │   ├── data/
│   │   ├── results/
│   │   └── 03_DiagnosticPanels.R
│   ├── 04_HPO/
│   │   ├── data/
│   │   ├── results/
│   │   └── 04_HPO.R
│   ├── 05_PubTator/
│   │   ├── data/
│   │   ├── results/
│   │   └── 05_PubTator.R
│   ├── A_MergeAnalysesSources/
│   │   ├── data/
│   │   ├── results/
│   │   └── A_MergeAnalysesSources.R
│   ├── B_AnnotationHGNC/
│   │   ├── data/
│   │   ├── results/
│   │   └── B_AnnotationHGNC.R
│   └── AnnotateMergedTable.R
└── functions/
    ├── blueprintgenetics-functions.R
    ├── hgnc-functions.R
    ├── hpo-functions.R
    ├── natera-functions.R
    ├── NCBI-datasets-v2-API-functions.R
    ├── phantomjs-functions.R
    └── PubTator-functions.R

• The analyses/ directory contains the R scripts for different analyses.
• The functions/ directory contains the necessary functions for HGNC processing.
• The data/ sub-directory in each analysis folder stores the input data files, including the publication-specific files and the curated overview Excel table.
• The results/ sub-directory in each analysis folder stores the generated results.

License

This project is licensed under the terms of the MIT license. For more information, please refer to the License file.

Creators and contributors

Bernt Popp

• https://twitter.com/berntpopp
• https://github.com/berntpopp
• https://orcid.org/0000-0002-3679-1081
• https://scholar.google.com/citations?user=Uvhu3t0AAAAJ

Constantin Aaron Wolff

• https://github.com/ConstantinWolff
• https://orcid.org/0000-0002-3277-4559

Nina Rank

• https://github.com/ninarank
• https://orcid.org/0000-0002-5984-4836

Jan Halbritter

• https://orcid.org/0000-0002-1377-9880
• https://scholar.google.com/citations?user=Jt1S5fkAAAAJ

Contact

If you have any questions, suggestions, or feedback, please feel free to contact us.