Datasets:
Formats:
parquet
Languages:
English
Size:
10M - 100M
Tags:
biology
chemistry
drug-discovery
clinical-trials
protein-protein-interaction
gene-essentiality
License:
File size: 6,787 Bytes
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"@context": {
"@vocab": "https://schema.org/",
"sc": "https://schema.org/",
"cr": "http://mlcommons.org/croissant/",
"rai": "http://mlcommons.org/croissant/RAI/"
},
"@type": "sc:Dataset",
"name": "NegBioDB",
"description": "A large-scale database of experimentally confirmed negative results across four biomedical domains (DTI, Clinical Trials, PPI, Gene Essentiality), with dual ML/LLM benchmarks.",
"license": "https://creativecommons.org/licenses/by-sa/4.0/",
"url": "https://github.com/jang1563/NegBioDB",
"version": "1.0.0",
"datePublished": "2026",
"creator": {
"@type": "sc:Person",
"name": "JangKeun Kim",
"affiliation": {
"@type": "sc:Organization",
"name": "Weill Cornell Medicine"
}
},
"keywords": [
"negative results",
"publication bias",
"drug-target interaction",
"clinical trials",
"protein-protein interaction",
"gene essentiality",
"benchmark",
"biomedical AI"
],
"distribution": [
{
"@type": "cr:FileObject",
"name": "dti_pairs",
"contentUrl": "negbiodb_dti_pairs.parquet",
"encodingFormat": "application/x-parquet",
"description": "All negative DTI pairs with source, tier, and activity data (30.5M rows)"
},
{
"@type": "cr:FileObject",
"name": "dti_m1_balanced",
"contentUrl": "negbiodb_m1_balanced.parquet",
"encodingFormat": "application/x-parquet",
"description": "DTI M1 balanced benchmark dataset (1:1 positive:negative, 1.73M rows)"
},
{
"@type": "cr:FileObject",
"name": "ct_pairs",
"contentUrl": "ct/negbiodb_ct_pairs.parquet",
"encodingFormat": "application/x-parquet",
"description": "All clinical trial failure pairs (102,850 rows)"
},
{
"@type": "cr:FileObject",
"name": "ppi_pairs",
"contentUrl": "ppi/negbiodb_ppi_pairs.parquet",
"encodingFormat": "application/x-parquet",
"description": "All negative PPI pairs (2.2M rows)"
},
{
"@type": "cr:FileObject",
"name": "ge_pairs",
"contentUrl": "ge/negbiodb_ge_pairs.parquet",
"encodingFormat": "application/x-parquet",
"description": "All gene essentiality pairs (22.5M gene-cell-line pairs)"
},
{
"@type": "cr:FileObject",
"name": "llm_l1",
"contentUrl": "llm_benchmarks/l1_mcq.jsonl",
"encodingFormat": "application/jsonl",
"description": "L1 MCQ classification benchmark"
},
{
"@type": "cr:FileObject",
"name": "llm_l4",
"contentUrl": "llm_benchmarks/l4_tested_untested.jsonl",
"encodingFormat": "application/jsonl",
"description": "L4 tested/untested discrimination benchmark"
}
],
"recordSet": [
{
"@type": "cr:RecordSet",
"name": "dti_pairs_record",
"source": "dti_pairs",
"field": [
{
"@type": "cr:Field",
"name": "inchikey_connectivity",
"dataType": "sc:Text",
"description": "InChIKey connectivity layer (first 14 characters)"
},
{
"@type": "cr:Field",
"name": "uniprot_id",
"dataType": "sc:Text",
"description": "UniProt accession of the protein target"
},
{
"@type": "cr:Field",
"name": "activity_type",
"dataType": "sc:Text",
"description": "Activity measurement type (IC50, Ki, Kd, EC50)"
},
{
"@type": "cr:Field",
"name": "pchembl_value",
"dataType": "sc:Float",
"description": "pChEMBL value (-log10 of activity in M)"
},
{
"@type": "cr:Field",
"name": "source",
"dataType": "sc:Text",
"description": "Data source (ChEMBL, PubChem, BindingDB, DAVIS)"
},
{
"@type": "cr:Field",
"name": "tier",
"dataType": "sc:Text",
"description": "Confidence tier (gold, silver, bronze)"
}
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},
{
"@type": "cr:RecordSet",
"name": "ct_pairs_record",
"source": "ct_pairs",
"field": [
{
"@type": "cr:Field",
"name": "nct_id",
"dataType": "sc:Text",
"description": "ClinicalTrials.gov NCT identifier"
},
{
"@type": "cr:Field",
"name": "intervention_name",
"dataType": "sc:Text",
"description": "Name of the drug or intervention"
},
{
"@type": "cr:Field",
"name": "failure_category",
"dataType": "sc:Text",
"description": "Category of trial failure (safety, efficacy, enrollment, etc.)"
},
{
"@type": "cr:Field",
"name": "tier",
"dataType": "sc:Text",
"description": "Confidence tier (gold, silver, bronze, copper)"
},
{
"@type": "cr:Field",
"name": "highest_phase_reached",
"dataType": "sc:Text",
"description": "Highest clinical phase reached before failure"
}
]
},
{
"@type": "cr:RecordSet",
"name": "ppi_pairs_record",
"source": "ppi_pairs",
"field": [
{
"@type": "cr:Field",
"name": "protein_a",
"dataType": "sc:Text",
"description": "UniProt accession of first protein"
},
{
"@type": "cr:Field",
"name": "protein_b",
"dataType": "sc:Text",
"description": "UniProt accession of second protein"
},
{
"@type": "cr:Field",
"name": "source",
"dataType": "sc:Text",
"description": "Data source (IntAct, HuRI, hu.MAP, STRING)"
},
{
"@type": "cr:Field",
"name": "tier",
"dataType": "sc:Text",
"description": "Confidence tier (gold, silver, bronze)"
}
]
},
{
"@type": "cr:RecordSet",
"name": "ge_pairs_record",
"source": "ge_pairs",
"field": [
{
"@type": "cr:Field",
"name": "gene_symbol",
"dataType": "sc:Text",
"description": "HUGO gene symbol"
},
{
"@type": "cr:Field",
"name": "cell_line",
"dataType": "sc:Text",
"description": "DepMap cell line identifier"
},
{
"@type": "cr:Field",
"name": "source",
"dataType": "sc:Text",
"description": "Data source (CRISPR Chronos, RNAi DEMETER2)"
},
{
"@type": "cr:Field",
"name": "tier",
"dataType": "sc:Text",
"description": "Confidence tier (gold, silver, bronze)"
}
]
}
]
}
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