nour0810/mena-microbiome-db

🧬 The first region-scale, harmonized #metagenomic catalog for the Middle East & North Africa — 60,126 runs across 24 countries 🌍, featuring an interactive web platform 🖥️, ecological analytics 📊, and a full reproducible pipeline ⚙️ # 🧬 MENA Microbiome Database > **The first region-scale, harmonized metagenomic catalog for the Middle East and North Africa.** 🌍 --- ## 📋 Overview The **MENA Microbiome Database** consolidates all publicly available metagenomic records from **24 Middle Eastern and North African countries** into a single, harmonized, and fully searchable resource. | Metric | Value | |--------|-------| | 🧪 Metagenomic runs | **60,126** | | 🧬 Unique BioSamples | **51,365** | | 📁 BioProjects | **2,373** | | 🌍 Countries covered | **24** | | 📅 Data span | **2008 – 2026** | | 🧬 Primary sequencing platform | Illumina (87.2%) | Data were retrieved from **ENA**, **NCBI SRA**, and **PubMed**-linked BioProjects, harmonized to a common schema, and enriched with BioSample / experiment / study XML attributes. Community metagenomics runs are algorithmically separated from single-organism genomics using a transparent, rule-based classifier. --- ## 🌐 Interactive Web Platform The platform is deployed via **GitHub Pages** and requires no installation. **→ Open the MENA Microbiome Platform** Features: - 🔍 Full-text & multi-filter search across all 60,126 runs - 🗺️ Per-country, per-category, and per-biome breakdown - 📊 Ecology & diversity analytics (Shannon, Simpson, PCoA, PERMANOVA) - 🗺️ Geospatial sampling map with Moran's I spatial clustering - 🧠 NLP-derived thematic cluster explorer (9 clusters, silhouette = 0.59) - 📤 Export to TSV / CSV / XLSX / JSON > **GitHub Pages setup:** In your repository settings go to **Settings → Pages**, set the source branch to `main` and the folder to `/ (root)`. The `index.html` file is the platform entry point. --- ## 📂 Repository Structure ``` mena-microbiome-db/ ├── index.html # 🌐 Interactive web platform (GitHub Pages entry point) ├── README.md ├── requirements.txt # 📦 Python dependencies for all scripts ├── .gitignore └── scripts/ ├── 01_fetch_mena_v5_patched.py # 📥 Step 1 — Data acquisition from ENA & …