Update benchmark to 1515 queries with complete qrels

cell_culture/queries_raw.json

@@ -6025,45 +6025,6 @@
     ],
     "explore_field": null
   },
-  "cell_culture_R3_pos_000200": {
-    "query": "Find experiments in which SH-SY5Y cells are cultured in MEM supplemented with 10% fetal bovine serum.",
-    "domain": "cell_culture",
-    "type": "reproduction",
-    "type_id": "R3",
-    "constraint_count": 4,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "culture_medium.basal_medium",
-        "op": "=",
-        "value": "MEM"
-      },
-      {
-        "field": "culture_medium.serum.concentration",
-        "op": "=",
-        "value": "10%",
-        "parsed": {
-          "kind": "point",
-          "number": 10.0,
-          "unit": "%",
-          "raw": "10%"
-        }
-      },
-      {
-        "field": "culture_medium.serum.identity",
-        "op": "=",
-        "value": "fetal bovine serum"
-      },
-      {
-        "field": "cultured_cells.cell_type",
-        "op": "=",
-        "value": "SH-SY5Y"
-      }
-    ],
-    "explore_field": null
-  },
   "cell_culture_R3_pos_000043": {
     "query": "Find experiments in which MC3T3-E1 cells are cultured in MEM supplemented with 10% fetal bovine serum.",
     "domain": "cell_culture",
@@ -8952,4 +8913,4 @@
     ],
     "explore_field": null
   }
-}
+}

electrochemistry/qrels_stage1.json

@@ -2154,4 +2154,4 @@
   "electrochemistry_R5_pos_000305": {
     "31959": 1
   }
-}
+}

electrochemistry/queries_raw.json

@@ -479,40 +479,6 @@
     ],
     "explore_field": null
   },
-  "electrochemistry_R1_pos_000201": {
-    "query": "Find electrochemical experiments targeting benzaldehyde in 1 mM Na2SO4 electrolyte.",
-    "domain": "electrochemistry",
-    "type": "reproduction",
-    "type_id": "R1",
-    "constraint_count": 3,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "electrolytes.chemical",
-        "op": "=",
-        "value": "Na2SO4"
-      },
-      {
-        "field": "electrolytes.concentration",
-        "op": "=",
-        "value": "1 mM",
-        "parsed": {
-          "kind": "point",
-          "number": 1.0,
-          "unit": "mm",
-          "raw": "1 mM"
-        }
-      },
-      {
-        "field": "target_species",
-        "op": "=",
-        "value": "benzaldehyde"
-      }
-    ],
-    "explore_field": null
-  },
   "electrochemistry_R2_pos_000415": {
     "query": "Find cyclic voltammetry experiments targeting Li+ in PC electrolyte.",
     "domain": "electrochemistry",
@@ -618,50 +584,6 @@
     ],
     "explore_field": null
   },
-  "electrochemistry_R5_pos_000027": {
-    "query": "Find cyclic voltammetry experiments targeting K3[Fe(CN)6] in 5 mM KCl electrolyte at room temperature.",
-    "domain": "electrochemistry",
-    "type": "reproduction",
-    "type_id": "R5",
-    "constraint_count": 5,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "electrolytes.chemical",
-        "op": "=",
-        "value": "KCl"
-      },
-      {
-        "field": "electrolytes.concentration",
-        "op": "=",
-        "value": "5 mM",
-        "parsed": {
-          "kind": "point",
-          "number": 5.0,
-          "unit": "mm",
-          "raw": "5 mM"
-        }
-      },
-      {
-        "field": "measurement_method",
-        "op": "=",
-        "value": "CV"
-      },
-      {
-        "field": "target_species",
-        "op": "=",
-        "value": "K3[Fe(CN)6]"
-      },
-      {
-        "field": "temperature",
-        "op": "=",
-        "value": "room temperature"
-      }
-    ],
-    "explore_field": null
-  },
   "electrochemistry_R5_pos_000023": {
     "query": "Find electrochemical impedance spectroscopy experiments targeting [Fe(CN)6]3-/4- in 100 mM KCl at room temperature.",
     "domain": "electrochemistry",
@@ -856,56 +778,6 @@
     ],
     "explore_field": null
   },
-  "electrochemistry_R5_pos_000264": {
-    "query": "Find cyclic voltammetry experiments targeting K3[Fe(CN)6] in 100 mM K3[Fe(CN)6] at a scan rate of 0.05 V/s.",
-    "domain": "electrochemistry",
-    "type": "reproduction",
-    "type_id": "R5",
-    "constraint_count": 5,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "electrolytes.chemical",
-        "op": "=",
-        "value": "K3[Fe(CN)6]"
-      },
-      {
-        "field": "electrolytes.concentration",
-        "op": "=",
-        "value": "100 mM",
-        "parsed": {
-          "kind": "point",
-          "number": 100.0,
-          "unit": "mm",
-          "raw": "100 mM"
-        }
-      },
-      {
-        "field": "measurement_method",
-        "op": "=",
-        "value": "CV"
-      },
-      {
-        "field": "scan_rate",
-        "op": "=",
-        "value": "0.05 V/s",
-        "parsed": {
-          "kind": "point",
-          "number": 0.05,
-          "unit": "v/s",
-          "raw": "0.05 V/s"
-        }
-      },
-      {
-        "field": "target_species",
-        "op": "=",
-        "value": "K3[Fe(CN)6]"
-      }
-    ],
-    "explore_field": null
-  },
   "electrochemistry_R5_pos_000005": {
     "query": "Find cyclic voltammetry experiments on K3[Fe(CN)6] in K3[Fe(CN)6] electrolyte at room temperature with scan rates of 10-100 mV/s.",
     "domain": "electrochemistry",
@@ -949,56 +821,6 @@
     ],
     "explore_field": null
   },
-  "electrochemistry_R5_pos_000258": {
-    "query": "Find cyclic voltammetry experiments targeting aniline in 100 mM H2SO4 at a scan rate of 10 mV/s.",
-    "domain": "electrochemistry",
-    "type": "reproduction",
-    "type_id": "R5",
-    "constraint_count": 5,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "electrolytes.chemical",
-        "op": "=",
-        "value": "H2SO4"
-      },
-      {
-        "field": "electrolytes.concentration",
-        "op": "=",
-        "value": "100 mM",
-        "parsed": {
-          "kind": "point",
-          "number": 100.0,
-          "unit": "mm",
-          "raw": "100 mM"
-        }
-      },
-      {
-        "field": "measurement_method",
-        "op": "=",
-        "value": "CV"
-      },
-      {
-        "field": "scan_rate",
-        "op": "=",
-        "value": "10 mV/s",
-        "parsed": {
-          "kind": "point",
-          "number": 10.0,
-          "unit": "mv/s",
-          "raw": "10 mV/s"
-        }
-      },
-      {
-        "field": "target_species",
-        "op": "=",
-        "value": "aniline"
-      }
-    ],
-    "explore_field": null
-  },
   "electrochemistry_R5_pos_000179": {
     "query": "Find cyclic voltammetry experiments targeting K3[Fe(CN)6] in 5 mM K3[Fe(CN)6] electrolyte at a scan rate of 10 mV/s.",
     "domain": "electrochemistry",
@@ -1248,56 +1070,6 @@
     ],
     "explore_field": null
   },
-  "electrochemistry_R5_pos_000062": {
-    "query": "Find cyclic voltammetry experiments targeting K3[Fe(CN)6] in 100 mM K3[Fe(CN)6] electrolyte at a scan rate of 40 mV/s.",
-    "domain": "electrochemistry",
-    "type": "reproduction",
-    "type_id": "R5",
-    "constraint_count": 5,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "electrolytes.chemical",
-        "op": "=",
-        "value": "K3[Fe(CN)6]"
-      },
-      {
-        "field": "electrolytes.concentration",
-        "op": "=",
-        "value": "100 mM",
-        "parsed": {
-          "kind": "point",
-          "number": 100.0,
-          "unit": "mm",
-          "raw": "100 mM"
-        }
-      },
-      {
-        "field": "measurement_method",
-        "op": "=",
-        "value": "CV"
-      },
-      {
-        "field": "scan_rate",
-        "op": "=",
-        "value": "40 mV/s",
-        "parsed": {
-          "kind": "point",
-          "number": 40.0,
-          "unit": "mv/s",
-          "raw": "40 mV/s"
-        }
-      },
-      {
-        "field": "target_species",
-        "op": "=",
-        "value": "K3[Fe(CN)6]"
-      }
-    ],
-    "explore_field": null
-  },
   "electrochemistry_R5_pos_000206": {
     "query": "Find cyclic voltammetry experiments targeting the K3[Fe(CN)6]/K4[Fe(CN)6] redox couple in 5 mM K3[Fe(CN)6] electrolyte at a scan rate of 50 mV/s.",
     "domain": "electrochemistry",
@@ -1680,45 +1452,6 @@
     ],
     "explore_field": null
   },
-  "electrochemistry_R4_pos_000426": {
-    "query": "Find electrochemical impedance spectroscopy experiments targeting [Fe(CN)6]3-/4- in 5 mM KNO3 electrolyte.",
-    "domain": "electrochemistry",
-    "type": "reproduction",
-    "type_id": "R4",
-    "constraint_count": 4,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "electrolytes.chemical",
-        "op": "=",
-        "value": "KNO3"
-      },
-      {
-        "field": "electrolytes.concentration",
-        "op": "=",
-        "value": "5 mM",
-        "parsed": {
-          "kind": "point",
-          "number": 5.0,
-          "unit": "mm",
-          "raw": "5 mM"
-        }
-      },
-      {
-        "field": "measurement_method",
-        "op": "=",
-        "value": "EIS"
-      },
-      {
-        "field": "target_species",
-        "op": "=",
-        "value": "[Fe(CN)6]3-/4-"
-      }
-    ],
-    "explore_field": null
-  },
   "electrochemistry_R4_pos_000410": {
     "query": "Find electrochemical experiments using electrolysis to target CO2 in 0.5 M KCl electrolyte.",
     "domain": "electrochemistry",
@@ -4555,34 +4288,6 @@
     ],
     "explore_field": "electrolytes.chemical"
   },
-  "electrochemistry_EI_NEG_neg_000863": {
-    "query": "What electrolyte other than NaOH is used for electrochemical glucose experiments with a Cu sheet working electrode?",
-    "domain": "electrochemistry",
-    "type": "input_exploration",
-    "type_id": "EI_NEG",
-    "constraint_count": 3,
-    "has_numeric": false,
-    "has_negation": true,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "electrolytes.chemical",
-        "op": "!=",
-        "value": "NaOH"
-      },
-      {
-        "field": "target_species",
-        "op": "=",
-        "value": "glucose"
-      },
-      {
-        "field": "working_electrode",
-        "op": "=",
-        "value": "Cu sheet"
-      }
-    ],
-    "explore_field": "electrolytes.chemical"
-  },
   "electrochemistry_EI_NEG_neg_001988": {
     "query": "What electrolyte chemical other than NaCl is used for cyclic voltammetry of CH3OH at 100 mV/s and 24 °C?",
     "domain": "electrochemistry",
@@ -6438,45 +6143,6 @@
     ],
     "explore_field": null
   },
-  "electrochemistry_R4_pos_000772": {
-    "query": "Find electrochemical experiments targeting CO2 at a Pb working electrode in 0.7 M H2SO4 electrolyte.",
-    "domain": "electrochemistry",
-    "type": "reproduction",
-    "type_id": "R4",
-    "constraint_count": 4,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "electrolytes.chemical",
-        "op": "=",
-        "value": "H2SO4"
-      },
-      {
-        "field": "electrolytes.concentration",
-        "op": "=",
-        "value": "0.7 M",
-        "parsed": {
-          "kind": "point",
-          "number": 0.7,
-          "unit": "m",
-          "raw": "0.7 M"
-        }
-      },
-      {
-        "field": "target_species",
-        "op": "=",
-        "value": "CO2"
-      },
-      {
-        "field": "working_electrode",
-        "op": "=",
-        "value": "Pb"
-      }
-    ],
-    "explore_field": null
-  },
   "electrochemistry_R4_pos_000211": {
     "query": "Find cyclic voltammetry experiments targeting [Fe(CN)6]3-/[Fe(CN)6]4- in PBS at a scan rate of 100 mV/s.",
     "domain": "electrochemistry",
@@ -6516,40 +6182,6 @@
     ],
     "explore_field": null
   },
-  "electrochemistry_R1_pos_000376": {
-    "query": "Find electrochemical experiments targeting V(IV) in 2 M VOSO4 electrolyte.",
-    "domain": "electrochemistry",
-    "type": "reproduction",
-    "type_id": "R1",
-    "constraint_count": 3,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "electrolytes.chemical",
-        "op": "=",
-        "value": "VOSO4"
-      },
-      {
-        "field": "electrolytes.concentration",
-        "op": "=",
-        "value": "2 M",
-        "parsed": {
-          "kind": "point",
-          "number": 2.0,
-          "unit": "m",
-          "raw": "2 M"
-        }
-      },
-      {
-        "field": "target_species",
-        "op": "=",
-        "value": "V(IV)"
-      }
-    ],
-    "explore_field": null
-  },
   "electrochemistry_R4_pos_000062": {
     "query": "Find cyclic voltammetry experiments targeting the [Fe(CN)6]3-/4- redox couple in K4[Fe(CN)6] electrolyte at scan rates of 20-250 mV/s.",
     "domain": "electrochemistry",
@@ -7253,56 +6885,6 @@
     ],
     "explore_field": "electrolytes.chemical"
   },
-  "electrochemistry_R5_pos_000106": {
-    "query": "Find cyclic voltammetry experiments targeting V(III) in 0.2 M H2SO4 at a scan rate of 2 mV/s.",
-    "domain": "electrochemistry",
-    "type": "reproduction",
-    "type_id": "R5",
-    "constraint_count": 5,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "electrolytes.chemical",
-        "op": "=",
-        "value": "H2SO4"
-      },
-      {
-        "field": "electrolytes.concentration",
-        "op": "=",
-        "value": "0.2 M",
-        "parsed": {
-          "kind": "point",
-          "number": 0.2,
-          "unit": "m",
-          "raw": "0.2 M"
-        }
-      },
-      {
-        "field": "measurement_method",
-        "op": "=",
-        "value": "CV"
-      },
-      {
-        "field": "scan_rate",
-        "op": "=",
-        "value": "2 mV/s",
-        "parsed": {
-          "kind": "point",
-          "number": 2.0,
-          "unit": "mv/s",
-          "raw": "2 mV/s"
-        }
-      },
-      {
-        "field": "target_species",
-        "op": "=",
-        "value": "V(III)"
-      }
-    ],
-    "explore_field": null
-  },
   "electrochemistry_R5_pos_000014": {
     "query": "Find cyclic voltammetry experiments targeting O2 in 0.5 M H2SO4 at 25 °C.",
     "domain": "electrochemistry",
@@ -7424,4 +7006,4 @@
     ],
     "explore_field": null
   }
-}
+}

immunotechnology/qrels_stage1.json

@@ -2911,4 +2911,4 @@
     "86039": 1,
     "8939": 1
   }
-}
+}

immunotechnology/queries_raw.json

@@ -9585,4 +9585,4 @@
     ],
     "explore_field": null
   }
-}
+}

inorganic_materials/queries_raw.json

@@ -683,45 +683,6 @@
     ],
     "explore_field": null
   },
-  "inorganic_materials_R3_pos_000014": {
-    "query": "Find synthesis protocols for Al2O3 prepared from alumina with 2 wt% MgO as an additive.",
-    "domain": "inorganic_materials",
-    "type": "reproduction",
-    "type_id": "R3",
-    "constraint_count": 4,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "dopant_or_additive.amount",
-        "op": "=",
-        "value": "2 wt%",
-        "parsed": {
-          "kind": "point",
-          "number": 2.0,
-          "unit": "wt%",
-          "raw": "2 wt%"
-        }
-      },
-      {
-        "field": "dopant_or_additive.identity",
-        "op": "=",
-        "value": "MgO"
-      },
-      {
-        "field": "precursors",
-        "op": "=",
-        "value": "alumina"
-      },
-      {
-        "field": "target_material",
-        "op": "=",
-        "value": "Al2O3"
-      }
-    ],
-    "explore_field": null
-  },
   "inorganic_materials_R4_pos_000009": {
     "query": "Find synthesis protocols for CuO/TiO2 prepared from Cu(NO3)2·6H2O with a calcination step at a heating rate of 10 °C/min.",
     "domain": "inorganic_materials",
@@ -1402,40 +1363,6 @@
     ],
     "explore_field": null
   },
-  "inorganic_materials_R1_pos_000136": {
-    "query": "Find synthesis protocols for Al2O3 with 2 wt% MgO additive.",
-    "domain": "inorganic_materials",
-    "type": "reproduction",
-    "type_id": "R1",
-    "constraint_count": 3,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "dopant_or_additive.amount",
-        "op": "=",
-        "value": "2 wt%",
-        "parsed": {
-          "kind": "point",
-          "number": 2.0,
-          "unit": "wt%",
-          "raw": "2 wt%"
-        }
-      },
-      {
-        "field": "dopant_or_additive.identity",
-        "op": "=",
-        "value": "MgO"
-      },
-      {
-        "field": "target_material",
-        "op": "=",
-        "value": "Al2O3"
-      }
-    ],
-    "explore_field": null
-  },
   "inorganic_materials_R2_pos_000002": {
     "query": "Find synthesis protocols for BaTiO3 using polyvinyl alcohol as an additive and including a calcination step.",
     "domain": "inorganic_materials",
@@ -2472,56 +2399,6 @@
     ],
     "explore_field": null
   },
-  "inorganic_materials_R5_pos_000005": {
-    "query": "Find hot-press sintering experiments for RGO/Ni-17Mo alloy composite using reduced graphene oxide as an additive, a heating rate of 100 °C/min, and a sintering time of 0.1667 h.",
-    "domain": "inorganic_materials",
-    "type": "reproduction",
-    "type_id": "R5",
-    "constraint_count": 5,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "dopant_or_additive.identity",
-        "op": "=",
-        "value": "reduced graphene oxide"
-      },
-      {
-        "field": "heating_rate",
-        "op": "=",
-        "value": "100 °C/min",
-        "parsed": {
-          "kind": "point",
-          "number": 100.0,
-          "unit": "°c/min",
-          "raw": "100 °C/min"
-        }
-      },
-      {
-        "field": "sintering.time",
-        "op": "=",
-        "value": "0.1667 h",
-        "parsed": {
-          "kind": "point",
-          "number": 0.1667,
-          "unit": "h",
-          "raw": "0.1667 h"
-        }
-      },
-      {
-        "field": "synthesis_route",
-        "op": "=",
-        "value": "hot-press sintering"
-      },
-      {
-        "field": "target_material",
-        "op": "=",
-        "value": "RGO/Ni-17Mo alloy composite"
-      }
-    ],
-    "explore_field": null
-  },
   "inorganic_materials_EM2_pos_000012": {
     "query": "What synthesis route is used to prepare LiCoO2 in air?",
     "domain": "inorganic_materials",
@@ -6235,45 +6112,6 @@
     ],
     "explore_field": null
   },
-  "inorganic_materials_R3_pos_000015": {
-    "query": "Find synthesis protocols for Al2O3 prepared from alumina with 1.5 wt% SiO2 as an additive.",
-    "domain": "inorganic_materials",
-    "type": "reproduction",
-    "type_id": "R3",
-    "constraint_count": 4,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "dopant_or_additive.amount",
-        "op": "=",
-        "value": "1.5 wt%",
-        "parsed": {
-          "kind": "point",
-          "number": 1.5,
-          "unit": "wt%",
-          "raw": "1.5 wt%"
-        }
-      },
-      {
-        "field": "dopant_or_additive.identity",
-        "op": "=",
-        "value": "SiO2"
-      },
-      {
-        "field": "precursors",
-        "op": "=",
-        "value": "alumina"
-      },
-      {
-        "field": "target_material",
-        "op": "=",
-        "value": "Al2O3"
-      }
-    ],
-    "explore_field": null
-  },
   "inorganic_materials_EI2_pos_000168": {
     "query": "What precursors are used to prepare BaTiO3 sintered at 1000 °C?",
     "domain": "inorganic_materials",
@@ -7108,45 +6946,6 @@
     ],
     "explore_field": "dopant_or_additive.identity"
   },
-  "inorganic_materials_R4_pos_000060": {
-    "query": "Find hot-press sintering experiments for RGO/Ni-17Mo alloy composites containing 0.5 vol% reduced graphene oxide.",
-    "domain": "inorganic_materials",
-    "type": "reproduction",
-    "type_id": "R4",
-    "constraint_count": 4,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "dopant_or_additive.amount",
-        "op": "=",
-        "value": "0.5 vol%",
-        "parsed": {
-          "kind": "point",
-          "number": 0.5,
-          "unit": "vol%",
-          "raw": "0.5 vol%"
-        }
-      },
-      {
-        "field": "dopant_or_additive.identity",
-        "op": "=",
-        "value": "reduced graphene oxide"
-      },
-      {
-        "field": "synthesis_route",
-        "op": "=",
-        "value": "hot-press sintering"
-      },
-      {
-        "field": "target_material",
-        "op": "=",
-        "value": "RGO/Ni-17Mo alloy composite"
-      }
-    ],
-    "explore_field": null
-  },
   "inorganic_materials_EI_NEG_neg_000190": {
     "query": "What dopant or additive other than Y2O3 is used for BaTiO3 subjected to calcination?",
     "domain": "inorganic_materials",
@@ -7506,40 +7305,6 @@
     ],
     "explore_field": null
   },
-  "inorganic_materials_R1_pos_000083": {
-    "query": "Find synthesis protocols for preparing CaO from CaCO3 with a main sintering step at 800 °C.",
-    "domain": "inorganic_materials",
-    "type": "reproduction",
-    "type_id": "R1",
-    "constraint_count": 3,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "precursors",
-        "op": "=",
-        "value": "CaCO3"
-      },
-      {
-        "field": "sintering.temperature",
-        "op": "=",
-        "value": "800 °C",
-        "parsed": {
-          "kind": "point",
-          "number": 800.0,
-          "unit": "c",
-          "raw": "800 °C"
-        }
-      },
-      {
-        "field": "target_material",
-        "op": "=",
-        "value": "CaO"
-      }
-    ],
-    "explore_field": null
-  },
   "inorganic_materials_R4_pos_000002": {
     "query": "Find spark plasma sintering experiments for Si3N4 with Y2O3 additive under N2 atmosphere.",
     "domain": "inorganic_materials",
@@ -7835,40 +7600,6 @@
     ],
     "explore_field": null
   },
-  "inorganic_materials_R1_pos_000137": {
-    "query": "Find synthesis protocols for Al2O3 with 1.5 wt% SiO2 additive.",
-    "domain": "inorganic_materials",
-    "type": "reproduction",
-    "type_id": "R1",
-    "constraint_count": 3,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "dopant_or_additive.amount",
-        "op": "=",
-        "value": "1.5 wt%",
-        "parsed": {
-          "kind": "point",
-          "number": 1.5,
-          "unit": "wt%",
-          "raw": "1.5 wt%"
-        }
-      },
-      {
-        "field": "dopant_or_additive.identity",
-        "op": "=",
-        "value": "SiO2"
-      },
-      {
-        "field": "target_material",
-        "op": "=",
-        "value": "Al2O3"
-      }
-    ],
-    "explore_field": null
-  },
   "inorganic_materials_R4_pos_000037": {
     "query": "Find spark plasma sintering experiments for (Hf0.2Nb0.2Ta0.2Mo0.2Ti0.2)B2 with graphite as an additive and a sintering time of 0.3333 h.",
     "domain": "inorganic_materials",

organic_synthesis/queries_raw.json

@@ -363,34 +363,6 @@
     ],
     "explore_field": null
   },
-  "organic_synthesis_R1_pos_000200": {
-    "query": "Find Suzuki coupling experiments using CuI as the catalyst in 1,4-dioxane.",
-    "domain": "organic_synthesis",
-    "type": "reproduction",
-    "type_id": "R1",
-    "constraint_count": 3,
-    "has_numeric": false,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "catalysts.name",
-        "op": "=",
-        "value": "CuI"
-      },
-      {
-        "field": "solvents",
-        "op": "=",
-        "value": "1,4-dioxane"
-      },
-      {
-        "field": "transformation_type",
-        "op": "=",
-        "value": "Suzuki coupling"
-      }
-    ],
-    "explore_field": null
-  },
   "organic_synthesis_R1_pos_000339": {
     "query": "Find asymmetric Diels-Alder reaction experiments using (E)-cinnamaldehyde as a substrate in H2O.",
     "domain": "organic_synthesis",
@@ -877,44 +849,6 @@
     ],
     "explore_field": null
   },
-  "organic_synthesis_R5_pos_000045": {
-    "query": "Find thermal Sonogashira coupling experiments using allylpalladium chloride dimer as the catalyst, DABCO as the base, and acetonitrile as the solvent.",
-    "domain": "organic_synthesis",
-    "type": "reproduction",
-    "type_id": "R5",
-    "constraint_count": 5,
-    "has_numeric": false,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "activation_mode",
-        "op": "=",
-        "value": "thermal"
-      },
-      {
-        "field": "bases",
-        "op": "=",
-        "value": "DABCO"
-      },
-      {
-        "field": "catalysts.name",
-        "op": "=",
-        "value": "allylpalladium chloride dimer"
-      },
-      {
-        "field": "solvents",
-        "op": "=",
-        "value": "acetonitrile"
-      },
-      {
-        "field": "transformation_type",
-        "op": "=",
-        "value": "Sonogashira coupling"
-      }
-    ],
-    "explore_field": null
-  },
   "organic_synthesis_R5_pos_000040": {
     "query": "Find thermal Sonogashira coupling experiments using CuI as catalyst, diisopropylamine as base, and THF as solvent.",
     "domain": "organic_synthesis",
@@ -1257,44 +1191,6 @@
     ],
     "explore_field": null
   },
-  "organic_synthesis_R5_pos_000012": {
-    "query": "Find thermal CuAAC reactions of azides carried out in ethanol with sodium ascorbate.",
-    "domain": "organic_synthesis",
-    "type": "reproduction",
-    "type_id": "R5",
-    "constraint_count": 5,
-    "has_numeric": false,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "activation_mode",
-        "op": "=",
-        "value": "thermal"
-      },
-      {
-        "field": "additives",
-        "op": "=",
-        "value": "sodium ascorbate"
-      },
-      {
-        "field": "solvents",
-        "op": "=",
-        "value": "ethanol"
-      },
-      {
-        "field": "substrates",
-        "op": "=",
-        "value": "azide"
-      },
-      {
-        "field": "transformation_type",
-        "op": "=",
-        "value": "CuAAC"
-      }
-    ],
-    "explore_field": null
-  },
   "organic_synthesis_R5_pos_000088": {
     "query": "Find thermal Suzuki-Miyaura coupling experiments using Pd(amphos)Cl2 as the catalyst, NaHCO3 as the base, and toluene as the solvent.",
     "domain": "organic_synthesis",
@@ -1371,120 +1267,6 @@
     ],
     "explore_field": null
   },
-  "organic_synthesis_R5_pos_000072": {
-    "query": "Find thermal Suzuki coupling experiments using CuI as the catalyst, K2CO3 as the base, and 1,4-dioxane as the solvent.",
-    "domain": "organic_synthesis",
-    "type": "reproduction",
-    "type_id": "R5",
-    "constraint_count": 5,
-    "has_numeric": false,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "activation_mode",
-        "op": "=",
-        "value": "thermal"
-      },
-      {
-        "field": "bases",
-        "op": "=",
-        "value": "K2CO3"
-      },
-      {
-        "field": "catalysts.name",
-        "op": "=",
-        "value": "CuI"
-      },
-      {
-        "field": "solvents",
-        "op": "=",
-        "value": "1,4-dioxane"
-      },
-      {
-        "field": "transformation_type",
-        "op": "=",
-        "value": "Suzuki coupling"
-      }
-    ],
-    "explore_field": null
-  },
-  "organic_synthesis_R5_pos_000007": {
-    "query": "Find thermal A3 coupling reactions using Cu3 NC (NHC) as the catalyst, 4 Å molecular sieves as an additive, and DCM as the solvent.",
-    "domain": "organic_synthesis",
-    "type": "reproduction",
-    "type_id": "R5",
-    "constraint_count": 5,
-    "has_numeric": false,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "activation_mode",
-        "op": "=",
-        "value": "thermal"
-      },
-      {
-        "field": "additives",
-        "op": "=",
-        "value": "4 Å molecular sieves"
-      },
-      {
-        "field": "catalysts.name",
-        "op": "=",
-        "value": "Cu3 NC (NHC)"
-      },
-      {
-        "field": "solvents",
-        "op": "=",
-        "value": "DCM"
-      },
-      {
-        "field": "transformation_type",
-        "op": "=",
-        "value": "A3 coupling"
-      }
-    ],
-    "explore_field": null
-  },
-  "organic_synthesis_R5_pos_000100": {
-    "query": "Find thermal Sonogashira coupling experiments of an alkyne in acetonitrile using DABCO as the base.",
-    "domain": "organic_synthesis",
-    "type": "reproduction",
-    "type_id": "R5",
-    "constraint_count": 5,
-    "has_numeric": false,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "activation_mode",
-        "op": "=",
-        "value": "thermal"
-      },
-      {
-        "field": "bases",
-        "op": "=",
-        "value": "DABCO"
-      },
-      {
-        "field": "solvents",
-        "op": "=",
-        "value": "acetonitrile"
-      },
-      {
-        "field": "substrates",
-        "op": "=",
-        "value": "alkyne"
-      },
-      {
-        "field": "transformation_type",
-        "op": "=",
-        "value": "Sonogashira coupling"
-      }
-    ],
-    "explore_field": null
-  },
   "organic_synthesis_R5_pos_000064": {
     "query": "Find thermal Suzuki coupling reactions using Pd(PPh3)4 as catalyst, Na2CO3 as base, and methanol as solvent.",
     "domain": "organic_synthesis",
@@ -1637,44 +1419,6 @@
     ],
     "explore_field": null
   },
-  "organic_synthesis_R5_pos_000013": {
-    "query": "Find thermal CuAAC experiments using tripropargylamine in H2O with sodium ascorbate.",
-    "domain": "organic_synthesis",
-    "type": "reproduction",
-    "type_id": "R5",
-    "constraint_count": 5,
-    "has_numeric": false,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "activation_mode",
-        "op": "=",
-        "value": "thermal"
-      },
-      {
-        "field": "additives",
-        "op": "=",
-        "value": "sodium ascorbate"
-      },
-      {
-        "field": "solvents",
-        "op": "=",
-        "value": "H2O"
-      },
-      {
-        "field": "substrates",
-        "op": "=",
-        "value": "tripropargylamine"
-      },
-      {
-        "field": "transformation_type",
-        "op": "=",
-        "value": "CuAAC"
-      }
-    ],
-    "explore_field": null
-  },
   "organic_synthesis_R5_pos_000134": {
     "query": "Find thermal Suzuki coupling experiments using N-(prop-2-yn-1-yl)benzamide as a substrate with KOAc in 1,4-dioxane.",
     "domain": "organic_synthesis",
@@ -1751,44 +1495,6 @@
     ],
     "explore_field": null
   },
-  "organic_synthesis_R5_pos_000135": {
-    "query": "Find thermal Suzuki coupling experiments using (4-methoxyphenyl)boronic acid in 1,4-dioxane with KOAc as the base.",
-    "domain": "organic_synthesis",
-    "type": "reproduction",
-    "type_id": "R5",
-    "constraint_count": 5,
-    "has_numeric": false,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "activation_mode",
-        "op": "=",
-        "value": "thermal"
-      },
-      {
-        "field": "bases",
-        "op": "=",
-        "value": "KOAc"
-      },
-      {
-        "field": "solvents",
-        "op": "=",
-        "value": "1,4-dioxane"
-      },
-      {
-        "field": "substrates",
-        "op": "=",
-        "value": "(4-methoxyphenyl)boronic acid"
-      },
-      {
-        "field": "transformation_type",
-        "op": "=",
-        "value": "Suzuki coupling"
-      }
-    ],
-    "explore_field": null
-  },
   "organic_synthesis_R5_pos_000055": {
     "query": "Find thermal Suzuki-Miyaura coupling experiments using Pd(dppf)Cl2 as catalyst, K2CO3 as base, and H2O as solvent.",
     "domain": "organic_synthesis",
@@ -2469,39 +2175,6 @@
     ],
     "explore_field": null
   },
-  "organic_synthesis_R4_pos_000140": {
-    "query": "Find thermal Suzuki coupling reactions using CuI as the catalyst in H2O.",
-    "domain": "organic_synthesis",
-    "type": "reproduction",
-    "type_id": "R4",
-    "constraint_count": 4,
-    "has_numeric": false,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "activation_mode",
-        "op": "=",
-        "value": "thermal"
-      },
-      {
-        "field": "catalysts.name",
-        "op": "=",
-        "value": "CuI"
-      },
-      {
-        "field": "solvents",
-        "op": "=",
-        "value": "H2O"
-      },
-      {
-        "field": "transformation_type",
-        "op": "=",
-        "value": "Suzuki coupling"
-      }
-    ],
-    "explore_field": null
-  },
   "organic_synthesis_R4_pos_000278": {
     "query": "Find thermal Suzuki-Miyaura coupling experiments using (2-methoxypyrimidin-5-yl)boronic acid in 1,4-dioxane.",
     "domain": "organic_synthesis",
@@ -2601,39 +2274,6 @@
     ],
     "explore_field": null
   },
-  "organic_synthesis_R4_pos_000074": {
-    "query": "Find thermal Sonogashira coupling experiments using allylpalladium chloride dimer as the catalyst in acetonitrile.",
-    "domain": "organic_synthesis",
-    "type": "reproduction",
-    "type_id": "R4",
-    "constraint_count": 4,
-    "has_numeric": false,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "activation_mode",
-        "op": "=",
-        "value": "thermal"
-      },
-      {
-        "field": "catalysts.name",
-        "op": "=",
-        "value": "allylpalladium chloride dimer"
-      },
-      {
-        "field": "solvents",
-        "op": "=",
-        "value": "acetonitrile"
-      },
-      {
-        "field": "transformation_type",
-        "op": "=",
-        "value": "Sonogashira coupling"
-      }
-    ],
-    "explore_field": null
-  },
   "organic_synthesis_R3_pos_000059": {
     "query": "Find Suzuki coupling experiments using 1,3,5-tribromobenzene as the substrate, colloidal Pd as the catalyst, and KOH as the base.",
     "domain": "organic_synthesis",
@@ -6625,39 +6265,6 @@
     ],
     "explore_field": null
   },
-  "organic_synthesis_R4_pos_000034": {
-    "query": "Find thermal Sonogashira coupling experiments using allylpalladium chloride dimer as the catalyst and DABCO as the base.",
-    "domain": "organic_synthesis",
-    "type": "reproduction",
-    "type_id": "R4",
-    "constraint_count": 4,
-    "has_numeric": false,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "activation_mode",
-        "op": "=",
-        "value": "thermal"
-      },
-      {
-        "field": "bases",
-        "op": "=",
-        "value": "DABCO"
-      },
-      {
-        "field": "catalysts.name",
-        "op": "=",
-        "value": "allylpalladium chloride dimer"
-      },
-      {
-        "field": "transformation_type",
-        "op": "=",
-        "value": "Sonogashira coupling"
-      }
-    ],
-    "explore_field": null
-  },
   "organic_synthesis_R1_pos_000342": {
     "query": "Find asymmetric Diels–Alder reaction experiments using cyclopentadiene in DMF.",
     "domain": "organic_synthesis",
@@ -8023,39 +7630,6 @@
     ],
     "explore_field": null
   },
-  "organic_synthesis_R4_pos_000159": {
-    "query": "Find thermal A3 coupling reactions using Cu3 NC (NHC) as the catalyst in DCM.",
-    "domain": "organic_synthesis",
-    "type": "reproduction",
-    "type_id": "R4",
-    "constraint_count": 4,
-    "has_numeric": false,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "activation_mode",
-        "op": "=",
-        "value": "thermal"
-      },
-      {
-        "field": "catalysts.name",
-        "op": "=",
-        "value": "Cu3 NC (NHC)"
-      },
-      {
-        "field": "solvents",
-        "op": "=",
-        "value": "DCM"
-      },
-      {
-        "field": "transformation_type",
-        "op": "=",
-        "value": "A3 coupling"
-      }
-    ],
-    "explore_field": null
-  },
   "organic_synthesis_R1_pos_000118": {
     "query": "Find Stille coupling experiments using Pd(PPh3)2Cl2 as the catalyst in tetrahydrofuran.",
     "domain": "organic_synthesis",

polymer_materials/qrels_stage1.json

@@ -1776,4 +1776,4 @@
     "44377": 1,
     "44378": 1
   }
-}
+}

polymer_materials/queries_raw.json

@@ -154,44 +154,6 @@
     ],
     "explore_field": null
   },
-  "polymer_materials_R4_pos_000005": {
-    "query": "Find curing experiments using a UV lamp at 320-400 nm with Darocur 1173 to cure the PM-2 polymer system.",
-    "domain": "polymer_materials",
-    "type": "reproduction",
-    "type_id": "R4",
-    "constraint_count": 4,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": true,
-    "constraints": [
-      {
-        "field": "light_source_type",
-        "op": "=",
-        "value": "UV lamp"
-      },
-      {
-        "field": "photoinitiators.name",
-        "op": "=",
-        "value": "Darocur 1173"
-      },
-      {
-        "field": "polymer_system",
-        "op": "=",
-        "value": "PM-2"
-      },
-      {
-        "field": "wavelength",
-        "op": "between",
-        "range": {
-          "lower": 320.0,
-          "upper": 400.0,
-          "unit": "nm"
-        },
-        "surface": "320-400 nm"
-      }
-    ],
-    "explore_field": null
-  },
   "polymer_materials_R3_pos_000006": {
     "query": "Find photocuring experiments using HEMA with PEGDA as a crosslinking agent and TPO as the photoinitiator under 385-420 nm irradiation.",
     "domain": "polymer_materials",
@@ -1123,40 +1085,6 @@
     ],
     "explore_field": null
   },
-  "polymer_materials_R1_pos_000127": {
-    "query": "Find photocuring experiments using TEGDMA with BAPO at 0.5 wt% as the photoinitiator.",
-    "domain": "polymer_materials",
-    "type": "reproduction",
-    "type_id": "R1",
-    "constraint_count": 3,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "photoinitiators.loading",
-        "op": "=",
-        "value": "0.5 wt%",
-        "parsed": {
-          "kind": "point",
-          "number": 0.5,
-          "unit": "wt%",
-          "raw": "0.5 wt%"
-        }
-      },
-      {
-        "field": "photoinitiators.name",
-        "op": "=",
-        "value": "BAPO"
-      },
-      {
-        "field": "polymer_system",
-        "op": "=",
-        "value": "TEGDMA"
-      }
-    ],
-    "explore_field": null
-  },
   "polymer_materials_R1_pos_000043": {
     "query": "Find photocuring experiments using GelAGE with LAP as the photoinitiator under 405 nm irradiation.",
     "domain": "polymer_materials",
@@ -2319,40 +2247,6 @@
     ],
     "explore_field": null
   },
-  "polymer_materials_R1_pos_000090": {
-    "query": "Find photocuring experiments using BisGMA with EDB as the photoinitiator at 0.1 wt%.",
-    "domain": "polymer_materials",
-    "type": "reproduction",
-    "type_id": "R1",
-    "constraint_count": 3,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "photoinitiators.loading",
-        "op": "=",
-        "value": "0.1 wt%",
-        "parsed": {
-          "kind": "point",
-          "number": 0.1,
-          "unit": "wt%",
-          "raw": "0.1 wt%"
-        }
-      },
-      {
-        "field": "photoinitiators.name",
-        "op": "=",
-        "value": "EDB"
-      },
-      {
-        "field": "polymer_system",
-        "op": "=",
-        "value": "BisGMA"
-      }
-    ],
-    "explore_field": null
-  },
   "polymer_materials_R1_pos_000003": {
     "query": "Find fabrication protocols using 5 wt% PEGNB with PEG4SH as the crosslinking agent.",
     "domain": "polymer_materials",
@@ -3201,40 +3095,6 @@
     ],
     "explore_field": null
   },
-  "polymer_materials_R1_pos_000098": {
-    "query": "Find photocuring experiments using TEGDMA with 0.50 wt% BAPO as the photoinitiator.",
-    "domain": "polymer_materials",
-    "type": "reproduction",
-    "type_id": "R1",
-    "constraint_count": 3,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "photoinitiators.loading",
-        "op": "=",
-        "value": "0.50 wt%",
-        "parsed": {
-          "kind": "point",
-          "number": 0.5,
-          "unit": "wt%",
-          "raw": "0.50 wt%"
-        }
-      },
-      {
-        "field": "photoinitiators.name",
-        "op": "=",
-        "value": "BAPO"
-      },
-      {
-        "field": "polymer_system",
-        "op": "=",
-        "value": "TEGDMA"
-      }
-    ],
-    "explore_field": null
-  },
   "polymer_materials_EC3_pos_000054": {
     "query": "What polymer concentration is used for GelMA photocrosslinked with LAP at 0.05% w/v?",
     "domain": "polymer_materials",
@@ -8394,40 +8254,6 @@
     ],
     "explore_field": null
   },
-  "polymer_materials_R1_pos_000113": {
-    "query": "Find photocuring experiments using PMMA with TI as the photoinitiator at 0.15 wt%.",
-    "domain": "polymer_materials",
-    "type": "reproduction",
-    "type_id": "R1",
-    "constraint_count": 3,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "photoinitiators.loading",
-        "op": "=",
-        "value": "0.15 wt%",
-        "parsed": {
-          "kind": "point",
-          "number": 0.15,
-          "unit": "wt%",
-          "raw": "0.15 wt%"
-        }
-      },
-      {
-        "field": "photoinitiators.name",
-        "op": "=",
-        "value": "TI"
-      },
-      {
-        "field": "polymer_system",
-        "op": "=",
-        "value": "PMMA"
-      }
-    ],
-    "explore_field": null
-  },
   "polymer_materials_R1_pos_000048": {
     "query": "Find photopolymerization experiments using PDHAA with Darocur 1173 as the photoinitiator under 320-400 nm irradiation.",
     "domain": "polymer_materials",
@@ -8556,40 +8382,6 @@
     ],
     "explore_field": null
   },
-  "polymer_materials_R1_pos_000092": {
-    "query": "Find photocuring experiments using TEGDMA with EDB as the photoinitiator at 0.1 wt%.",
-    "domain": "polymer_materials",
-    "type": "reproduction",
-    "type_id": "R1",
-    "constraint_count": 3,
-    "has_numeric": true,
-    "has_negation": false,
-    "has_range": false,
-    "constraints": [
-      {
-        "field": "photoinitiators.loading",
-        "op": "=",
-        "value": "0.1 wt%",
-        "parsed": {
-          "kind": "point",
-          "number": 0.1,
-          "unit": "wt%",
-          "raw": "0.1 wt%"
-        }
-      },
-      {
-        "field": "photoinitiators.name",
-        "op": "=",
-        "value": "EDB"
-      },
-      {
-        "field": "polymer_system",
-        "op": "=",
-        "value": "TEGDMA"
-      }
-    ],
-    "explore_field": null
-  },
   "polymer_materials_R1_pos_000025": {
     "query": "Find photocuring experiments using 20% w/v GelMA with LAP as the photoinitiator.",
     "domain": "polymer_materials",
@@ -9352,4 +9144,4 @@
     ],
     "explore_field": null
   }
-}
+}