data/croissant.json

{
  "@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)"
        }
      ]
    },
    {
      "@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)"
        }
      ]
    }
  ]
}