Add GE domain, fix creator name, improve field descriptions

data/croissant.json

@@ -7,43 +7,64 @@
   },
   "@type": "sc:Dataset",
   "name": "NegBioDB",
-  "description": "A large-scale database of experimentally confirmed negative results across three biomedical domains (DTI, Clinical Trials, PPI), with dual ML/LLM benchmarks.",
+  "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": "Jungwon Jang"
+    "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"
+      "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)"
+      "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"
+      "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"
+      "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",
@@ -70,37 +91,37 @@
           "@type": "cr:Field",
           "name": "inchikey_connectivity",
           "dataType": "sc:Text",
-          "description": "inchikey connectivity"
+          "description": "InChIKey connectivity layer (first 14 characters)"
         },
         {
           "@type": "cr:Field",
           "name": "uniprot_id",
           "dataType": "sc:Text",
-          "description": "uniprot id"
+          "description": "UniProt accession of the protein target"
         },
         {
           "@type": "cr:Field",
           "name": "activity_type",
           "dataType": "sc:Text",
-          "description": "activity type"
+          "description": "Activity measurement type (IC50, Ki, Kd, EC50)"
         },
         {
           "@type": "cr:Field",
           "name": "pchembl_value",
           "dataType": "sc:Float",
-          "description": "pchembl value"
+          "description": "pChEMBL value (-log10 of activity in M)"
         },
         {
           "@type": "cr:Field",
           "name": "source",
           "dataType": "sc:Text",
-          "description": "source"
+          "description": "Data source (ChEMBL, PubChem, BindingDB, DAVIS)"
         },
         {
           "@type": "cr:Field",
           "name": "tier",
           "dataType": "sc:Text",
-          "description": "tier"
+          "description": "Confidence tier (gold, silver, bronze)"
         }
       ]
     },
@@ -113,31 +134,31 @@
           "@type": "cr:Field",
           "name": "nct_id",
           "dataType": "sc:Text",
-          "description": "nct id"
+          "description": "ClinicalTrials.gov NCT identifier"
         },
         {
           "@type": "cr:Field",
           "name": "intervention_name",
           "dataType": "sc:Text",
-          "description": "intervention name"
+          "description": "Name of the drug or intervention"
         },
         {
           "@type": "cr:Field",
           "name": "failure_category",
           "dataType": "sc:Text",
-          "description": "failure category"
+          "description": "Category of trial failure (safety, efficacy, enrollment, etc.)"
         },
         {
           "@type": "cr:Field",
           "name": "tier",
           "dataType": "sc:Text",
-          "description": "tier"
+          "description": "Confidence tier (gold, silver, bronze, copper)"
         },
         {
           "@type": "cr:Field",
           "name": "highest_phase_reached",
           "dataType": "sc:Text",
-          "description": "highest phase reached"
+          "description": "Highest clinical phase reached before failure"
         }
       ]
     },
@@ -150,27 +171,58 @@
           "@type": "cr:Field",
           "name": "protein_a",
           "dataType": "sc:Text",
-          "description": "protein a"
+          "description": "UniProt accession of first protein"
         },
         {
           "@type": "cr:Field",
           "name": "protein_b",
           "dataType": "sc:Text",
-          "description": "protein b"
+          "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": "source"
+          "description": "Data source (CRISPR Chronos, RNAi DEMETER2)"
         },
         {
           "@type": "cr:Field",
           "name": "tier",
           "dataType": "sc:Text",
-          "description": "tier"
+          "description": "Confidence tier (gold, silver, bronze)"
         }
       ]
     }
   ]
-}
+}