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README.md

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-license: mit
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+# CGBench Dataset
+
+This repository contains the CGBench dataset - a comprehensive benchmarking framework for evaluating scientific reasoning in language models using ClinGen (clinicalgenome.org) data. The dataset enables evaluation of language models' ability to extract, interpret, and explain fine-grained results from scientific publications in clinical genetics.
+
+## Dataset Overview
+
+CGBench formulates three separate tasks:
+1. **GCI Evidence Extraction** - Gene-disease association evidence extraction
+2. **VCI Evidence Scoring** - Variant pathogenicity evidence scoring  
+3. **VCI Evidence Sufficiency** - Evidence sufficiency determination
+
+## Directory Structure
+
+### GCI/ - Gene Curation Interface Data
+
+Contains data related to gene-disease association evidence extraction tasks.
+
+#### Core Files
+
+**`Clingen-Gene-Disease-Summary-2025-03-31.csv`**
+- Summary of all ClinGen gene-disease validity classifications
+- **Columns:**
+  - `GENE SYMBOL`: HGNC gene symbol
+  - `GENE ID (HGNC)`: HGNC gene identifier
+  - `DISEASE LABEL`: Human-readable disease name
+  - `DISEASE ID (MONDO)`: MONDO ontology disease identifier
+  - `MOI`: Mode of inheritance (AD=Autosomal Dominant, AR=Autosomal Recessive, XL=X-linked)
+  - `SOP`: Standard Operating Procedure version used for curation
+  - `CLASSIFICATION`: Gene-disease association strength (Definitive, Strong, Moderate, Limited)
+  - `ONLINE REPORT`: URL to full ClinGen report
+  - `CLASSIFICATION DATE`: Date of classification
+  - `GCEP`: Gene Curation Expert Panel responsible for classification
+
+#### SOP/ - Standard Operating Procedures
+
+**`experimental_evidence/`**
+Contains JSON files defining evidence categories and scoring criteria:
+- `SOP5.json` through `SOP11.json`: Different versions of standard operating procedures
+- Each file contains structured evidence categories with titles and descriptions for:
+  - Biochemical Function (A & B)
+  - Protein Interaction
+  - Expression (A & B)
+  - Functional Alteration
+  - Model Systems
+  - Rescue experiments
+
+#### evidence_tables/
+
+**`experimental_evidence/evidence_cleaned_fulltext.csv`**
+- Complete dataset of experimental evidence with full-text paper content
+- **Columns:**
+  - `Label`: Evidence description/title
+  - `Experimental Category`: Type of evidence (e.g., "Model Systems Non-human model organism")
+  - `Reference`: Citation with PMID
+  - `Explanation`: Detailed explanation of the evidence
+  - `Score Status`: Whether evidence was scored
+  - `Points (default points)`: Numerical score assigned
+  - `Reason for Changed Score`: Explanation if score was modified
+  - `url`: Link to ClinGen assertion
+  - `primary_index`: Internal identifier
+  - `pmid`: PubMed identifier
+
+**Train/Test Splits:**
+- `train.csv`, `test.csv`: Standard splits for model training/evaluation
+- `train_datesplit.csv`, `test_datesplit.csv`: Date-based splits to avoid data leakage
+
+#### pubmed/
+
+**`experimental_evidence.csv`**
+- PubMed abstracts associated with evidence entries
+- Links evidence to published literature
+
+### VCI/ - Variant Curation Interface Data
+
+Contains data for variant pathogenicity assessment tasks.
+
+#### Core Files
+
+**`clingen_vci_pubmed_fulltext.csv`**
+- Complete VCI dataset with full-text papers
+- **Columns:**
+  - `entry_index`: Unique identifier
+  - `variant`: HGVS variant notation
+  - `hgnc_gene`: Gene symbol
+  - `disease`: Associated disease
+  - `mondo_id`: MONDO disease identifier
+  - `assertion`: Pathogenicity classification (Pathogenic, Likely Pathogenic, Uncertain Significance, etc.)
+  - `mode_inheritance`: Inheritance pattern
+  - `expert_panel`: Responsible VCEP (Variant Curation Expert Panel)
+  - `pub_date`: Publication date
+  - `evidence_code`: ACMG/AMP evidence code applied
+  - `met_status`: Whether evidence criteria was met
+  - `pmid`: Associated PubMed ID
+  - `comments`: Curator comments
+  - `summary`: Evidence summary
+  - `summary_comments`: Additional summary information
+
+**Data Variants:**
+- `clingen_vci_pubmed_fulltext_dedup_pmid.csv`: Deduplicated by PMID
+- `clingen_vci_pubmed_fulltext_vceps.csv`: VCEP-specific subset
+- `clingen_vci_pubmed_var_na_filtered.csv`: Filtered for missing variants
+
+**`erepo.tabbed_2025-02-25.txt`**
+- Raw ClinGen Evidence Repository export
+- Tab-delimited format with comprehensive variant classification data
+- **Key Columns:**
+  - `#Variation`: Variant identifier
+  - `ClinVar Variation Id`: ClinVar identifier
+  - `HGVS Expressions`: All HGVS representations
+  - `Applied Evidence Codes (Met/Not Met)`: ACMG/AMP criteria
+  - `Summary of interpretation`: Detailed reasoning
+  - `Expert Panel`: Responsible VCEP
+
+**`pubmed_id_to_text.csv`**
+- Maps PubMed IDs to full-text content
+- **Columns:**
+  - `pmid`: PubMed identifier
+  - `abstract`: Paper abstract
+  - `full_text`: Complete paper text when available
+
+#### Task-Specific Splits
+
+**`split_evidence_score/`**
+Evidence scoring task data:
+- `train.csv`, `test.csv`: Basic train/test splits
+- `train_merged.csv`, `test_merged.csv`: Merged with additional metadata
+- Additional `path` column indicates source VCEP specification file
+
+**`split_evidence_sufficiency/`**
+Evidence sufficiency determination task:
+- `train.csv`, `test.csv`: Basic splits
+- `train_dedup.csv`, `test_dedup.csv`: Deduplicated versions
+- `test_dedup_missing.csv`: Test set with missing data scenarios
+
+#### parsing_csr_criteria/
+
+Contains tools and data for parsing Criteria Specification Registry (CSR) documents:
+
+- **`cspec_version_guide.csv`**: Maps VCEP specifications to versions
+- **`cspec_version_guide_processed.csv`**: Processed version mappings
+- **`version_csv_individual/`**: Individual CSV files for each VCEP specification version
+  - Format: `{VCEPName}_version={X.Y.Z}.csv`
+  - Contains parsed criteria specifications for each expert panel
+
+**Python Scripts:**
+- `get_versions.py`: Extract version information
+- `parse_on_date.py`: Parse specifications by date
+- `scrape_criteria.py`: Scrape criteria from registry
+- `scrape_criteria_fn.py`, `scrape_criteria_versions.py`: Helper functions
+
+## Data Usage Notes
+
+### Evidence Codes
+The dataset uses ACMG/AMP variant interpretation guidelines with evidence codes like:
+- **PVS1**: Very strong pathogenic evidence  
+- **PS1-4**: Strong pathogenic evidence
+- **PM1-6**: Moderate pathogenic evidence
+- **PP1-5**: Supporting pathogenic evidence
+- **BA1**: Stand-alone benign
+- **BS1-4**: Strong benign evidence
+- **BP1-7**: Supporting benign evidence
+
+### Expert Panels (VCEPs)
+Various disease-specific Variant Curation Expert Panels contribute data:
+- Phenylketonuria VCEP (PAH gene)
+- Cardiomyopathy VCEP
+- BRCA1/BRCA2 VCEP (ENIGMA)
+- And many others
+
+### Data Splits
+- **Standard splits**: Random train/test division
+- **Date splits**: Temporal division to prevent data leakage
+- **Deduplicated versions**: Remove duplicate entries by PMID or other criteria
+
+## File Formats
+
+- **CSV**: Comma-separated values for tabular data
+- **JSON**: Structured data for evidence category definitions
+- **TXT**: Tab-delimited raw exports from ClinGen systems
+
+## Citation
+
+If you use this dataset, please cite the CGBench paper (publication details forthcoming).
+
+## License
+
+MIT License - see main repository for details.
+