Update README.md

README.md

@@ -1,60 +1,222 @@
----
-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
----
+---
+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 **, **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/gu-dudi)
+* **License:** Open for research and educational use
+* **Format:** JSON Lines (UTF-8)
+
+---
+
+### Citation
+
+If you use this dataset in your research, please cite:
+
+> Cruz, G. H. F. (2025). *DNA Coding Regions Dataset: Genomic Sequences with Introns, Exons, and Protein Mappings Extracted from GenBank.*
+
+---
+
+### 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.*