| --- |
| language: |
| - en |
| license: other |
| tags: |
| - biology |
| - genomics |
| - medical |
| - bioinformatics |
| - variant-annotation |
| - clinical |
| - wgs |
| - wes |
| pretty_name: SchemaBio Bundle |
| --- |
| |
| # 🧬 SchemaBio Bundle |
|
|
| ## 📖 Overview |
| This dataset is a comprehensive, meticulously curated, one-stop annotation library designed for bioinformatics and genomic variant analysis (e.g., WES/WGS pipelines). It aggregates essential variant effect predictors, clinical databases, and genomic reference files into a unified repository, significantly reducing the time spent on data collection, format alignment, and preprocessing. |
|
|
|
|
|
|
| ## 🗂️ Included Data & Sources |
|
|
| This repository includes data from the following categories: |
| 1. **Variant Effect Predictors & Scores:** AlphaMissense, EVOScore2, Pangolin. |
| 2. **Clinical & Population Frequencies:** gnomAD, CIViC, mskcc_hotspot. |
| 3. **Genomic References & Regions:** UCSC annotations (`cytoband`, `ncbiRefSeq.gtf`), Ensembl references (`GRCh38/37 FASTA`, `vep_cache`), ManeSelectBed. |
|
|
|
|
|
|
| ## ⚖️ Licensing & Commercial Use |
|
|
| **Great news: All underlying datasets included in this repository currently permit commercial use**, provided that users strictly adhere to their respective attribution and share-alike requirements. |
|
|
| Because this repository acts as an aggregator, **it does not fall under a single license**. You must comply with the individual licenses of the respective underlying data sources. The table below outlines the specific license for each component: |
|
|
| ### 📊 Database Licenses Summary |
|
|
| | Database / Source | Version | Official License | Commercial Use | Redistribution | Key Requirements & Notes | |
| | :--- | :--- | :--- | :--- | :--- | :--- | |
| | [**AlphaMissense**](https://zenodo.org/records/10813168) | v3 | **CC BY 4.0** | ✅ Allowed | ✅ Allowed | Must attribute to DeepMind Technologies Limited. | |
| | [**EVOScore2**](https://huggingface.co/datasets/pzweuj/EVOScore-2) | 20260128 | **MIT** | ✅ Allowed | ✅ Allowed | Must include the original copyright notice. | |
| | [**Pangolin**](https://zenodo.org/records/15649338) | v1 | **CC BY 4.0** | ✅ Allowed | ✅ Allowed | Must provide proper attribution. | |
| | [**ManeSelectBed**](https://github.com/pzweuj/ManeSelectBed) | v49 | **MIT** | ✅ Allowed | ✅ Allowed | Must include the original copyright notice. | |
| | [**mskcc_hotspot**](https://www.cancerhotspots.org/) | v2 | **ODbL** | ✅ Allowed | ✅ Allowed | **Share-Alike:** If you modify/adapt this database, the derivative must also be ODbL. | |
| | [**CIViC**](https://civicdb.org/welcome) | 20260301 | **CC0 1.0** | ✅ Allowed | ✅ Allowed | Public Domain. No restrictions. | |
| | [**gnomAD**](https://gnomad.broadinstitute.org/) | v4.1 | **Unrestricted** | ✅ Allowed | ✅ Allowed | Broad Institute claims no restrictions on use. | |
| | [**UCSC Data**](https://hgdownload.soe.ucsc.edu/goldenPath) | / | **Public Domain** | ✅ Allowed | ✅ Allowed | Publicly funded data, free for all uses. | |
| | [**Ensembl Data**](https://ftp.ensembl.org/pub/release-115/) | release 115 | **Unrestricted** | ✅ Allowed | ✅ Allowed | EMBL-EBI places no restrictions on use or redistribution. | |
|
|
| *Disclaimer: The creator of this combined dataset claims no ownership over the original source data. Users are solely responsible for ensuring their downstream use complies with the original data providers' terms.* |
|
|
|
|
