README.md

# 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.