Update README.md

README.md

@@ -1,3 +1,130 @@
----
-license: pddl
----
+---
+license: pddl
+task_categories:
+- text-classification
+- question-answering
+- clinical-variant-annotation
+- text2text-generation
+---
+
+language:
+  - en
+
+---
+
+# stxbp1_clinvar_curated
+
+_Curated STXBP1 and related variant records from ClinVar, ready for LLM and biomedical NLP applications._
+
+**License:**  
+This dataset is licensed under the ODC Public Domain Dedication and License (PDDL).  
+To the extent possible under law, the author(s) have dedicated this data to the public domain worldwide by waiving all rights to the work under copyright law, including all related and neighboring rights, to the extent allowed by law.  
+NO WARRANTY is provided.  
+See [ODC-PDDL](https://opendatacommons.org/licenses/pddl/1-0/) for full legal text.
+
+---
+
+## Dataset Overview
+
+A curated, LLM-friendly dataset of **STXBP1 and related variant records from ClinVar**, converted from ClinVar VCF and annotated for clinical, research, rare disease, and advanced AI applications.  
+This resource is suitable for medical language modeling, rare disease NLP, variant curation, and biomedical Q&A.  
+
+**Formats included:**  
+- Structured JSONL (main split)
+- Q/A pairs (txt, 7,013,256 examples, 1.66 GB)
+- Curated summaries (txt, 24,548,655 examples, 1.51 GB)
+- Parquet conversion is recommended for large-scale use
+
+---
+
+## Curation Criteria
+
+Variants were selected from ClinVar using the following inclusion keywords (case-insensitive):
+
+- STXBP1
+- MUNC18
+- STXBP2
+- STXBP3
+- STXBP4
+- STXBP5
+- STXBP6
+- syntaxin.binding
+- CRISPR Cas9
+- CRISPR Cas12
+- encephalopathy
+- SNARE
+
+Any variant record containing one or more of these keywords (in gene symbols, molecular consequence, disease name, or database annotations) was included. This ensures comprehensive coverage of the STXBP gene family, SNARE-complex biology, CRISPR-mediated editing, and associated neurological disorders (notably epileptic encephalopathies).
+
+---
+
+## Features
+
+- **Natural language clinical summaries for each variant**
+- **Structured JSONL** (parquet-compatible) for easy data science/NLP use
+- **Ready-to-use Q/A pairs** for instruction and LLM fine-tuning
+- Full field coverage: variant position, gene, disease, clinical significance, HGVS description, database cross-links, review status, and more
+
+---
+
+## Dataset Statistics
+
+| Format            | Size (bytes)   | Number of Examples/Lines |
+|-------------------|---------------:|-------------------------:|
+| QA (.txt)         | 1,664,122,880  | 7,013,256                |
+| Curated summaries | 1,511,260,160  | 24,548,655               |
+| JSONL             | 1,935,069,184  | 3,506,628                |
+
+_Main split for Hugging Face: JSONL format (see above for statistics)._
+
+---
+
+## Schema
+
+| Field                  | Description                                                    |
+|------------------------|----------------------------------------------------------------|
+| ID                     | ClinVar Variation ID                                           |
+| chrom                  | Chromosome                                                    |
+| pos                    | Genomic position (GRCh38)                                     |
+| ref                    | Reference allele                                              |
+| alt                    | Alternate allele                                              |
+| gene                   | Gene symbol                                                   |
+| disease                | Disease/phenotype name                                        |
+| significance           | Clinical significance (e.g., Pathogenic, Benign, Uncertain)   |
+| hgvs                   | HGVS variant description                                      |
+| review                 | ClinVar review status                                         |
+| molecular_consequence  | Sequence Ontology + effect                                    |
+| variant_type           | SNV, Insertion, Deletion, etc.                                |
+| clndisdb               | Disease database links (OMIM, MedGen, etc.)                   |
+| clndnincl              | Included variant disease name                                 |
+| clndisdbincl           | Included variant disease database links                       |
+| onc_fields             | Dict of oncogenicity fields                                   |
+| sci_fields             | Dict of somatic clinical impact fields                        |
+| incl_fields            | Dict of included fields (INCL)                                |
+
+---
+
+## Data Examples
+
+**JSON record:**
+```json
+{
+  "ID": "3385321",
+  "chrom": "1",
+  "pos": "66926",
+  "ref": "AG",
+  "alt": "A",
+  "gene": "OR4F5",
+  "disease": "Retinitis_pigmentosa",
+  "significance": "Uncertain_significance",
+  "hgvs": "NC_000001.11:g.66927del",
+  "review": "criteria_provided, single_submitter",
+  "molecular_consequence": "SO:0001627: intron_variant",
+  "variant_type": "Deletion",
+  "clndisdb": "Human_Phenotype_Ontology:HP:0000547,MONDO:MONDO:0019200,MeSH:D012174,MedGen:C0035334,OMIM:268000,OMIM:PS268000,Orphanet:791",
+  "clndnincl": null,
+  "clndisdbincl": null,
+  "onc_fields": {},
+  "sci_fields": {},
+  "incl_fields": {}
+}