Duplicate from GustavoHCruz/DNA_coding_regions

Co-authored-by: Gustavo Henrique Ferreira Cruz <GustavoHCruz@users.noreply.huggingface.co>

.gitattributes

@@ -0,0 +1,59 @@
+*.7z filter=lfs diff=lfs merge=lfs -text
+*.arrow filter=lfs diff=lfs merge=lfs -text
+*.bin filter=lfs diff=lfs merge=lfs -text
+*.bz2 filter=lfs diff=lfs merge=lfs -text
+*.ckpt filter=lfs diff=lfs merge=lfs -text
+*.ftz filter=lfs diff=lfs merge=lfs -text
+*.gz filter=lfs diff=lfs merge=lfs -text
+*.h5 filter=lfs diff=lfs merge=lfs -text
+*.joblib filter=lfs diff=lfs merge=lfs -text
+*.lfs.* filter=lfs diff=lfs merge=lfs -text
+*.lz4 filter=lfs diff=lfs merge=lfs -text
+*.mds filter=lfs diff=lfs merge=lfs -text
+*.mlmodel filter=lfs diff=lfs merge=lfs -text
+*.model filter=lfs diff=lfs merge=lfs -text
+*.msgpack filter=lfs diff=lfs merge=lfs -text
+*.npy filter=lfs diff=lfs merge=lfs -text
+*.npz filter=lfs diff=lfs merge=lfs -text
+*.onnx filter=lfs diff=lfs merge=lfs -text
+*.ot filter=lfs diff=lfs merge=lfs -text
+*.parquet filter=lfs diff=lfs merge=lfs -text
+*.pb filter=lfs diff=lfs merge=lfs -text
+*.pickle filter=lfs diff=lfs merge=lfs -text
+*.pkl filter=lfs diff=lfs merge=lfs -text
+*.pt filter=lfs diff=lfs merge=lfs -text
+*.pth filter=lfs diff=lfs merge=lfs -text
+*.rar filter=lfs diff=lfs merge=lfs -text
+*.safetensors filter=lfs diff=lfs merge=lfs -text
+saved_model/**/* filter=lfs diff=lfs merge=lfs -text
+*.tar.* filter=lfs diff=lfs merge=lfs -text
+*.tar filter=lfs diff=lfs merge=lfs -text
+*.tflite filter=lfs diff=lfs merge=lfs -text
+*.tgz filter=lfs diff=lfs merge=lfs -text
+*.wasm filter=lfs diff=lfs merge=lfs -text
+*.xz filter=lfs diff=lfs merge=lfs -text
+*.zip filter=lfs diff=lfs merge=lfs -text
+*.zst filter=lfs diff=lfs merge=lfs -text
+*tfevents* filter=lfs diff=lfs merge=lfs -text
+# Audio files - uncompressed
+*.pcm filter=lfs diff=lfs merge=lfs -text
+*.sam filter=lfs diff=lfs merge=lfs -text
+*.raw filter=lfs diff=lfs merge=lfs -text
+# Audio files - compressed
+*.aac filter=lfs diff=lfs merge=lfs -text
+*.flac filter=lfs diff=lfs merge=lfs -text
+*.mp3 filter=lfs diff=lfs merge=lfs -text
+*.ogg filter=lfs diff=lfs merge=lfs -text
+*.wav filter=lfs diff=lfs merge=lfs -text
+# Image files - uncompressed
+*.bmp filter=lfs diff=lfs merge=lfs -text
+*.gif filter=lfs diff=lfs merge=lfs -text
+*.png filter=lfs diff=lfs merge=lfs -text
+*.tiff filter=lfs diff=lfs merge=lfs -text
+# Image files - compressed
+*.jpg filter=lfs diff=lfs merge=lfs -text
+*.jpeg filter=lfs diff=lfs merge=lfs -text
+*.webp filter=lfs diff=lfs merge=lfs -text
+# Video files - compressed
+*.mp4 filter=lfs diff=lfs merge=lfs -text
+*.webm filter=lfs diff=lfs merge=lfs -text

README.md

@@ -0,0 +1,243 @@
+---
+license: cc-by-4.0
+configs:
+- config_name: default
+  data_files:
+  - split: train
+    path: data/train-*
+dataset_info:
+  features:
+  - name: accession
+    dtype: string
+  - name: organism
+    dtype: string
+  - name: sequence
+    dtype: string
+  - name: introns
+    list:
+    - name: after
+      dtype: string
+    - name: before
+      dtype: string
+    - name: end
+      dtype: int64
+    - name: gene
+      dtype: string
+    - name: sequence
+      dtype: string
+    - name: start
+      dtype: int64
+  - name: exons
+    list:
+    - name: after
+      dtype: string
+    - name: before
+      dtype: string
+    - name: end
+      dtype: int64
+    - name: gene
+      dtype: string
+    - name: sequence
+      dtype: string
+    - name: start
+      dtype: int64
+  - name: proteins
+    list:
+    - name: end
+      dtype: int64
+    - name: gene
+      dtype: string
+    - name: sequence
+      dtype: string
+    - name: start
+      dtype: int64
+  splits:
+  - name: train
+    num_bytes: 11536678696
+    num_examples: 1677609
+  download_size: 5448417115
+  dataset_size: 11536678696
+task_categories:
+- text-classification
+- token-classification
+- translation
+tags:
+- Exons
+- Introns
+- Proteins
+- DNA
+pretty_name: DNA Coding Regions
+size_categories:
+- 1M<n<10M
+---
+
+# DNA Coding Regions Dataset
+
+This is a curated collection of genomic sequences extracted directly from **NCBI GenBank**, designed to support research in **introns and exons classification**, **DNA-to-protein translation**, **gene structure analysis**, and **biological sequence modeling** with deep learning architectures.
+
+---
+
+## Source and Extraction Pipeline
+
+All records were extracted from **GenBank** using [Biopython](https://biopython.org/).  
+The dataset construction followed a reproducible data processing pipeline written in Python, which:
+
+- Downloads and parses GenBank records.
+- Extracts **genomic DNA sequences**, their associated **exons**, **introns**, and **coding sequences (CDS)**.
+- Processes the `strand` orientation to produce normalized sequences.
+- Removes duplicate entries based on `(sequence, organism)` pairs.
+- Assembles each record into a structured JSONL format suitable for machine learning models.
+
+The GenBank **search query** used for data collection was:
+
+```
+"genomic DNA"[Filter]
+AND ("exon"[Feature Key] OR "intron"[Feature Key])
+AND "CDS"[Feature Key]
+AND ("3"[SLEN] : "16384"[SLEN])
+````
+
+You can find more information about the pipeline in the GitHub from the [DNA Coding Regions](https://github.com/GustavoHCruz/CodingDNATransformers) repository.
+
+---
+
+## Dataset Structure
+
+Each entry in the dataset corresponds to a **unique DNA sequence**, identified by its **GenBank accession**.  
+The dataset is serialized in JSON Lines (`.jsonl`) format and can be loaded with the Hugging Face `datasets` library.
+
+### Example record
+
+```json
+{
+  "accession": "NC_045512.2",
+  "organism": "Homo sapiens",
+  "sequence": "ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGAT...",
+  "introns": [
+    {
+      "sequence": "TTGTAGACCAGTGCAGTA...",
+      "start": 1450,
+      "end": 1783,
+      "gene": "ORF1ab",
+      "before": "ATGCCDG",
+      "after": "TAACAFG"
+    }
+  ],
+  "exons": [
+    {
+      "sequence": "ATGGACACAAGTCAGG...",
+      "start": 1,
+      "end": 1449,
+      "gene": "ORF1ab",
+      "before": null,
+      "after": "GT"
+    }
+  ],
+  "proteins": [
+    {
+      "sequence": "MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVL...",
+      "start": 1,
+      "end": 4405,
+      "gene": "ORF1ab"
+    }
+  ]
+}
+````
+
+---
+
+## Field Descriptions
+
+| Field         | Type   | Description                                                                                                                                                                                                                                                                                                            |
+| ------------- | ------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **accession** | `str`  | GenBank accession number for the DNA sequence.                                                                                                                                                                                                                                                                         |
+| **organism**  | `str`  | Name of the organism from which the sequence was derived.                                                                                                                                                                                                                                                              |
+| **sequence**  | `str`  | The full genomic DNA sequence (processed strand).                                                                                                                                                                                                                                                                      |
+| **introns**   | `list` | List of intronic regions associated with this DNA sequence. Each item contains: <ul><li>`sequence`: only the nucleotide sequence of the intron</li><li>`start`, `end`: coordinates relative to the DNA sequence</li><li>`gene`: gene name when annotated</li><li>`before`, `after`: short flanking sequences</li></ul> |
+| **exons**     | `list` | List of exonic regions associated with this DNA sequence. Same structure as `introns`.                                                                                                                                                                                                                                 |
+| **proteins**  | `list` | List of coding sequences (CDS) translated to amino acid sequences, with: <ul><li>`sequence`: protein sequence</li><li>`start`, `end`: coordinates in the DNA sequence</li><li>`gene`: gene name</li></ul>                                                                                                              |
+
+---
+
+## Applications
+
+This dataset can be directly used for:
+
+* **DNA to protein translation modeling**
+* **Exon and Introns classification**
+* **Splicing prediction**
+* **Genomic representation learning**
+* **Bioinformatics-focused LLM pretraining (DAPT)**
+
+---
+
+## Loading Example
+
+```python
+from datasets import load_dataset
+
+dataset = load_dataset("gu-dudi/DNA_coding_regions")
+
+print(dataset)
+print(dataset["train"][0])
+```
+
+---
+
+## Dataset Metadata
+
+* **Source:** NCBI GenBank
+* **Processed with:** Biopython, Pandas, tqdm
+* **Maintainer:** [Gustavo Henrique Ferreira Cruz](https://huggingface.co/GustavoHCruz)
+* **License:** Open for research and educational use
+* **Format:** JSON Lines (UTF-8)
+
+---
+
+## Disclaimer on data completeness
+
+Not all genomic entries in this dataset contain every type of annotation (exons, introns, and proteins).
+
+While the GenBank records were filtered to include sequences annotated with "exon", "intron", and "CDS" feature keys, the underlying annotations in GenBank are not always deterministic or complete.
+
+Some sequences may include only exons or introns without corresponding protein-coding regions, or vice versa.
+
+This reflects the inherent variability and curation differences across submissions in the GenBank database.
+
+---
+
+
+### Citation
+
+If you use this dataset in your research, please cite:
+
+```bibtex
+@misc{gustavo_henrique_ferreira_cruz_2025,
+  author       = {Gustavo Henrique Ferreira Cruz},
+  title        = {DNA\_coding\_regions (Revision 16f4e3a)},
+  year         = 2025,
+  url          = {https://huggingface.co/datasets/GustavoHCruz/DNA_coding_regions},
+  doi          = {10.57967/hf/7238},
+  publisher    = {Hugging Face}
+}
+```
+---
+
+### Version and Integrity
+
+* **Version:** 1.0
+* **Total entries:** 1,677,609
+* **Deduplication:** duplicates removed based on `(sequence, organism)` pair
+* **Strand normalization:** handled during extraction
+
+---
+
+### Notes
+
+* Coordinates (`start`, `end`) are **relative to the parent DNA sequence**.
+* `sequence` inside each **intron/exon** corresponds *only to that region* (not the full DNA).
+* Protein sequences are already **translated amino acid chains**, not nucleotide fragments.
+
+---
+
+*Developed as part of the Master’s research project on DNA sequence understanding and translation using deep learning models.*

data/train-00000-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:11cacae79c5bbae61bf00833708cbf3dde452cd125a8bd496459552abbe9d548
+size 229516829

data/train-00001-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:24281e82377a4f61f4a21ee0fef376bfb4dfa44e4c11f3778edda306f9d98c84
+size 224549655

data/train-00002-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:aef2b9c0cc597ab552207ece9cd084b35030e9d834adc8f2ae287bd4de0d0005
+size 273285759

data/train-00003-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:94499b2f3f29110db67e2536369797c63fc1694d4dffe0269d717f0f99dd16e4
+size 242182335

data/train-00004-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:95d81ea7516ab94f2c6b379cf4c944bf9f6a7f37c4882cb87566f610c3655378
+size 190356063

data/train-00005-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e0a2dd2150820550736a4d13f3db337a94fe985c5b30d0232e2c7c75062de959
+size 160302165

data/train-00006-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b03b643b3638fc4ffbf63355074b19081cd1811af7fddf93205a0e91b5dd3c63
+size 324318851

data/train-00007-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:6b9b136d6ddaf559f487ad8f850642d2c568daa04dfc3f1a88c3dcc33b7f2b4c
+size 156308224

data/train-00008-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a52bed61cacc04fb9824f158108dbf378f957ec345d285003efcb74e709169b6
+size 241711076

data/train-00009-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1f1b73bdd297b89a755c2897dddbb2569018611615ced2b286186ec58b621906
+size 211334850

data/train-00010-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:04bc35a9d66e3f1d890b2bdc1854fa9b82874a9ff4c5faec110b9b6e7893b1a7
+size 185469218

data/train-00011-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:40d2794eca3bc989ac4aadf389641cf56f25ad07f36d8a6bc189d1b14c01d978
+size 361463288

data/train-00012-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:03cae8f472acdd68f10219ce7194b1fa7407299f5cfde2a105a2bd5407aec53f
+size 257230587

data/train-00013-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:5df8d6b81bfa5559a0c3c27ad4cc08188bc297e2a0f3c0cebdb57fcc5388b76d
+size 249164427

data/train-00014-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:bfe39c3243b347676b1f5a2929d0f751d446b0264082b7bff4063c35e2ca141d
+size 280897420

data/train-00015-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0012978d7c9276bb4a7d143c82cf21989f82c20d2b48bc372947bb74dcfc499a
+size 219872017

data/train-00016-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2c656a588f5e45a963dc2524cb53bb26d107960acc3ba65b56a2bbfaea16d523
+size 333023542

data/train-00017-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9f39fc708f78f05a249ab7e3250797e9573a71e9aa045adab48dfcfb60c55934
+size 252520239

data/train-00018-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:85c38c6e09e0ae1469892037f4e994b331d2ec7987eda11f2cf642fe7448e737
+size 192974465

data/train-00019-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c2fd8bd37abf4af88862908944c375bd9e4ca24c55ae69a2ed22fd0a556a3705
+size 253985313

data/train-00020-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4cc856235febf23ad98683100b212ae857f212b7058e67d291f53e47490a2fec
+size 211995243

data/train-00021-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d452cbd60da4b3d34a034d1826025e27f1a7a04e6f59c575725241067a4b37ea
+size 185830126

data/train-00022-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:048e9802796c3d248948794077775fc1f8d02d93ff42ea8ac4836922337ab47d
+size 130692559

data/train-00023-of-00024.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7d8311ddd88dce9cd008eccef23a3f3154889463b076881d7d05ddda1b2c2864
+size 79432864