| # 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. | |