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--- |
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license: mit |
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tags: |
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- biology |
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- protien-sequences |
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- dna-database |
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- raw-fasta |
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- dna |
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size_categories: |
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- 10M<n<100M |
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--- |
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## DNA Sequence Database from NCBI |
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Welcome to the curated DNA sequence dataset, automatically gathered from NCBI using the Enigma2 pipeline. This repository provides ready-to-use CSV and Parquet files for downstream machine-learning and bioinformatics tasks. |
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## 📋 Dataset Overview |
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* **Scope** |
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* A collection of topic-specific DNA sequence sets (e.g., BRCA1, TP53, CFTR) sourced directly from NCBI’s Nucleotide database. |
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* **Curation Process** |
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1. **Query Design** |
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* Predefined Entrez queries (gene names, organism filters) identify relevant GenBank records. |
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2. **Batch Retrieval** |
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* Sequences fetched in controlled batches to respect rate limits and ensure reliability. |
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3. **Quality Control & Filtering** |
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* Records shorter than 100 bp or exhibiting parsing errors were omitted. |
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4. **Metadata Extraction** |
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* For each sequence, we record: |
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* **ID** (accession number) |
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* **Name** (full FASTA description) |
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* **Length** (base-pair count) |
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5. **Export** |
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* Data saved in both CSV and Parquet formats for seamless integration with Python, R, and big-data frameworks. |
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## 📂 Dataset Structure |
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Each topic is stored in its own file under the `datasets/` directory: |
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``` |
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datasets/ |
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├── BRCA1_Gene_AND_Homo_sapiens_Organism.csv |
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├── BRCA1_Gene_AND_Homo_sapiens_Organism.parquet |
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├── TP53_Gene_AND_Homo_sapiens_Organism.csv |
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├── TP53_Gene_AND_Homo_sapiens_Organism.parquet |
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… |
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``` |
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**File contents** (4 columns): |
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| Column | Description | |
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| ---------- | ---------------------------------------------- | |
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| `id` | NCBI accession ID | |
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| `name` | Full FASTA-style description | |
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| `length` | Original sequence length (in base pairs) | |
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| `sequence` | Raw DNA string (A/C/G/T; no alignment padding) | |
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## 🚀 How to Use |
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```python |
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from enigma2 import Database, EntrezQueries, convert_fasta |
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queries = EntrezQueries() # contains about 20 queries |
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db = Database(topics=queries(), out_dir="./data/", mode='csv', email="your@mail.com", retmax=500, max_rate=10, raw=True) |
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db.build_raw() |
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# inspect first record |
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print(ds[0]) |
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# → {'id': 'NM_007294.3', 'name': 'Homo sapiens BRCA1 transcript …', 'length': 1863, 'sequence': 'ATGGATT…'} |
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``` |
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Or, in a Unix shell: |
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```bash |
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pip install datasets |
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datasets-cli download -d shivendrra/dna-ncbi -s BRCA1_Gene_AND_Homo_sapiens_Organism.csv |
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``` |
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## 🔍 Recommended Workflows |
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* **Feature Engineering**: k-mer counting, GC content analysis |
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* **Sequence Modeling**: RNNs, Transformers on raw DNA |
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* **Phylogenetic Studies**: distance matrices from sequence distances |
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## 🔗 Source Code |
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The full data-gathering and processing pipeline is open-source: |
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[Enigma2](https://github.com/shivendrra/enigma2) |
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## 📖 Citation |
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If you use this dataset in your work, please cite: |
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``` |
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@misc{shivendrra_enigma2_2025, |
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author = {Shivendrra, Harsh and contributors}, |
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title = {Enigma2 NCBI DNA Dataset}, |
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year = {2025}, |
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howpublished = {\\url{https://huggingface.co/datasets/shivendrra/EnigmaDataset}} |
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} |
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``` |
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## 📝 License |
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This dataset is released under the [MIT License](LICENSE). |
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Feel free to reuse and adapt—with attribution. |
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