{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://aptatlas.org/data/choose_engine_spec.schema.json",
  "title": "Help Me Choose engine specification",
  "description": "Every constant the Help Me Choose engine uses.",
  "type": "object",
  "required": [
    "schema",
    "name",
    "title",
    "version",
    "last_updated",
    "licence",
    "licence_url",
    "citation",
    "archive_doi",
    "third_party",
    "data"
  ],
  "additionalProperties": false,
  "properties": {
    "schema": {
      "type": "string",
      "description": "URL of this schema for this release"
    },
    "name": {
      "const": "choose_engine_spec"
    },
    "title": {
      "type": "string"
    },
    "version": {
      "type": "string",
      "pattern": "^\\d+\\.\\d+$",
      "description": "APT release"
    },
    "last_updated": {
      "type": "string",
      "pattern": "^\\d{4}-\\d{2}-\\d{2}$"
    },
    "licence": {
      "const": "CC-BY-4.0"
    },
    "licence_url": {
      "type": "string"
    },
    "citation": {
      "type": "string"
    },
    "archive_doi": {
      "type": "string"
    },
    "third_party": {
      "type": "array",
      "description": "Sources this file draws on that carry their own licence.",
      "items": {
        "type": "object",
        "required": [
          "name",
          "licence",
          "url",
          "relationship",
          "note"
        ],
        "additionalProperties": false,
        "properties": {
          "name": {
            "type": "string"
          },
          "licence": {
            "type": "string",
            "description": "SPDX identifier"
          },
          "url": {
            "type": "string"
          },
          "relationship": {
            "enum": [
              "source",
              "derived"
            ]
          },
          "note": {
            "type": "string"
          },
          "fields": {
            "type": "array",
            "items": {
              "type": "string"
            },
            "description": "JSONPath, relative to data, of fields derived from this source"
          },
          "fields_derived_in_part": {
            "type": "array",
            "items": {
              "type": "string"
            },
            "description": "JSONPath, relative to data, of fields computed partly from the fields above"
          }
        }
      }
    },
    "data": {
      "type": "object",
      "properties": {
        "engine_version": {
          "type": "string"
        },
        "generated_from": {
          "type": "string"
        },
        "source_locations": {
          "type": "object",
          "properties": {
            "scoring_function": {
              "type": "string"
            },
            "goal_adjustments": {
              "type": "string"
            },
            "hard_filters": {
              "type": "string"
            },
            "sample_flexibility_overrides": {
              "type": "string"
            },
            "priority_miss_penalty": {
              "type": "string"
            },
            "data": {
              "type": "string"
            }
          },
          "required": [
            "scoring_function",
            "goal_adjustments",
            "hard_filters",
            "sample_flexibility_overrides",
            "priority_miss_penalty",
            "data"
          ],
          "additionalProperties": false
        },
        "platform_ids": {
          "type": "array",
          "items": {
            "type": "string"
          }
        },
        "ptm_capable": {
          "type": "array",
          "items": {
            "type": "string"
          }
        },
        "absolute_quant_capable": {
          "type": "array",
          "items": {
            "type": "string"
          }
        },
        "cost_efficiency_bands": {
          "type": "object",
          "properties": {
            "basis": {
              "type": "string"
            },
            "bands": {
              "type": "object",
              "properties": {
                "1": {
                  "type": "string"
                },
                "2": {
                  "type": "string"
                },
                "3": {
                  "type": "string"
                },
                "4": {
                  "type": "string"
                },
                "5": {
                  "type": "string"
                }
              },
              "required": [
                "1",
                "2",
                "3",
                "4",
                "5"
              ],
              "additionalProperties": false
            },
            "band_note": {
              "type": "string"
            }
          },
          "required": [
            "basis",
            "bands",
            "band_note"
          ],
          "additionalProperties": false
        },
        "slider_dimensions": {
          "type": "object",
          "properties": {
            "cost": {
              "type": "string"
            },
            "coverage": {
              "type": "string"
            },
            "precision": {
              "type": "string"
            },
            "specificity": {
              "type": "string"
            },
            "sensitivity": {
              "type": "string"
            },
            "throughput": {
              "type": "string"
            },
            "pqtl": {
              "type": "string"
            }
          },
          "required": [
            "cost",
            "coverage",
            "precision",
            "specificity",
            "sensitivity",
            "throughput",
            "pqtl"
          ],
          "additionalProperties": false
        },
        "goals": {
          "type": "array",
          "items": {
            "type": "string"
          }
        },
        "sample_types": {
          "type": "array",
          "items": {
            "type": "string"
          }
        },
        "study_sizes": {
          "type": "array",
          "items": {
            "type": "string"
          }
        },
        "weight_range": {
          "type": "array",
          "items": {
            "type": "integer"
          }
        },
        "goal_adjustments": {
          "type": "object",
          "additionalProperties": {
            "type": "object",
            "properties": {
              "coverage": {
                "type": "integer"
              },
              "specificity": {
                "type": "integer"
              },
              "throughput": {
                "type": "integer"
              },
              "sensitivity": {
                "type": "integer"
              },
              "precision": {
                "type": "integer"
              },
              "cost": {
                "type": "integer"
              }
            },
            "required": [],
            "additionalProperties": false
          }
        },
        "size_boost": {
          "type": "object",
          "properties": {
            "formula": {
              "type": "string"
            },
            "SIZE_BOOST_SCALE": {
              "type": "number"
            },
            "note_v3.0": {
              "type": "string"
            }
          },
          "required": [
            "formula",
            "SIZE_BOOST_SCALE",
            "note_v3.0"
          ],
          "additionalProperties": false
        },
        "context_boosts": {
          "type": "object",
          "properties": {
            "csf_sensitivity": {
              "type": "object",
              "properties": {
                "condition": {
                  "type": "string"
                },
                "value": {
                  "type": "integer"
                },
                "applies_to": {
                  "type": "string"
                }
              },
              "required": [
                "condition",
                "value",
                "applies_to"
              ],
              "additionalProperties": false
            },
            "cns_focus_sensitivity": {
              "type": "object",
              "properties": {
                "condition": {
                  "type": "string"
                },
                "value": {
                  "type": "string"
                },
                "applies_to": {
                  "type": "string"
                }
              },
              "required": [
                "condition",
                "value",
                "applies_to"
              ],
              "additionalProperties": false
            },
            "cns_focus_specificity": {
              "type": "object",
              "properties": {
                "condition": {
                  "type": "string"
                },
                "value": {
                  "type": "string"
                },
                "applies_to": {
                  "type": "string"
                }
              },
              "required": [
                "condition",
                "value",
                "applies_to"
              ],
              "additionalProperties": false
            },
            "longitudinal_precision": {
              "type": "object",
              "properties": {
                "condition": {
                  "type": "string"
                },
                "value": {
                  "type": "integer"
                },
                "applies_to": {
                  "type": "string"
                }
              },
              "required": [
                "condition",
                "value",
                "applies_to"
              ],
              "additionalProperties": false
            }
          },
          "required": [
            "csf_sensitivity",
            "cns_focus_sensitivity",
            "cns_focus_specificity",
            "longitudinal_precision"
          ],
          "additionalProperties": false
        },
        "context_boost_provenance_note": {
          "type": "string"
        },
        "effective_weight_formula": {
          "type": "string"
        },
        "priority_miss_penalty": {
          "type": "object",
          "properties": {
            "rule": {
              "type": "string"
            },
            "changed_in_v3.0": {
              "type": "string"
            },
            "note": {
              "type": "string"
            },
            "fix_d": {
              "type": "string"
            }
          },
          "required": [
            "rule",
            "changed_in_v3.0",
            "note",
            "fix_d"
          ],
          "additionalProperties": false
        },
        "quantification_weight": {
          "type": "object",
          "properties": {
            "yes": {
              "type": "integer"
            },
            "nice": {
              "type": "integer"
            },
            "no": {
              "type": "integer"
            },
            "applies_to": {
              "type": "string"
            }
          },
          "required": [
            "yes",
            "nice",
            "no",
            "applies_to"
          ],
          "additionalProperties": false
        },
        "sample_flexibility_weight": {
          "type": "object",
          "properties": {
            "base_by_sample_type": {
              "type": "object",
              "properties": {
                "tissue": {
                  "type": "integer"
                },
                "cell_culture": {
                  "type": "integer"
                },
                "multiple": {
                  "type": "integer"
                },
                "csf": {
                  "type": "integer"
                },
                "default": {
                  "type": "integer"
                }
              },
              "required": [
                "tissue",
                "cell_culture",
                "multiple",
                "csf",
                "default"
              ],
              "additionalProperties": false
            },
            "note_v3.0": {
              "type": "string"
            },
            "per_platform_overrides": {
              "type": "object",
              "properties": {
                "tissue": {
                  "type": "object",
                  "properties": {
                    "nulisa": {
                      "type": "integer"
                    },
                    "nomic-omni": {
                      "type": "integer"
                    },
                    "seer-proteograph": {
                      "type": "integer"
                    },
                    "olink-explore-ht": {
                      "type": "integer"
                    },
                    "illumina-protein-prep": {
                      "type": "integer"
                    },
                    "biognosys-truediscovery": {
                      "type": "string"
                    }
                  },
                  "required": [
                    "nulisa",
                    "nomic-omni",
                    "seer-proteograph",
                    "olink-explore-ht",
                    "illumina-protein-prep",
                    "biognosys-truediscovery"
                  ],
                  "additionalProperties": false
                },
                "tissue_rationale": {
                  "type": "string"
                },
                "cell_culture": {
                  "type": "object",
                  "properties": {
                    "nomic-omni": {
                      "type": "integer"
                    }
                  },
                  "required": [
                    "nomic-omni"
                  ],
                  "additionalProperties": false
                },
                "cell_culture_rationale": {
                  "type": "string"
                }
              },
              "required": [
                "tissue",
                "tissue_rationale",
                "cell_culture",
                "cell_culture_rationale"
              ],
              "additionalProperties": false
            }
          },
          "required": [
            "base_by_sample_type",
            "note_v3.0",
            "per_platform_overrides"
          ],
          "additionalProperties": false
        },
        "protein_target_weight": {
          "type": "object",
          "properties": {
            "value": {
              "type": "integer"
            },
            "condition": {
              "type": "string"
            },
            "hard_filter": {
              "type": "string"
            },
            "simulation_coverage_note": {
              "type": "string"
            }
          },
          "required": [
            "value",
            "condition",
            "hard_filter",
            "simulation_coverage_note"
          ],
          "additionalProperties": false
        },
        "hard_filters": {
          "type": "array",
          "items": {
            "type": "object",
            "properties": {
              "id": {
                "type": "string"
              },
              "condition": {
                "type": "string"
              },
              "excludes": {
                "type": "string"
              }
            },
            "required": [
              "id",
              "condition",
              "excludes"
            ],
            "additionalProperties": false
          }
        },
        "calibration": {
          "type": "object",
          "properties": {
            "total_weight": {
              "type": "string"
            },
            "min_possible_raw": {
              "type": "string"
            },
            "max_possible_raw": {
              "type": "string"
            },
            "display_pct": {
              "type": "string"
            }
          },
          "required": [
            "total_weight",
            "min_possible_raw",
            "max_possible_raw",
            "display_pct"
          ],
          "additionalProperties": false
        },
        "rounding_rule": {
          "type": "object",
          "properties": {
            "spec": {
              "type": "string"
            },
            "why_this_is_called_out": {
              "type": "string"
            }
          },
          "required": [
            "spec",
            "why_this_is_called_out"
          ],
          "additionalProperties": false
        },
        "tie_band": {
          "type": "integer"
        },
        "tie_band_note": {
          "type": "string"
        },
        "win_statistics_definition": {
          "type": "string"
        },
        "prevalence_weighting": {
          "type": "object",
          "properties": {
            "rationale": {
              "type": "string"
            },
            "goal_prevalence": {
              "type": "object",
              "properties": {
                "discovery": {
                  "type": "number"
                },
                "disease_char": {
                  "type": "number"
                },
                "population": {
                  "type": "number"
                },
                "drug_target": {
                  "type": "number"
                },
                "validation": {
                  "type": "number"
                },
                "pharmacoproteomics": {
                  "type": "integer"
                }
              },
              "required": [
                "discovery",
                "disease_char",
                "population",
                "drug_target",
                "validation",
                "pharmacoproteomics"
              ],
              "additionalProperties": false
            },
            "sample_type_prevalence": {
              "type": "object",
              "properties": {
                "plasma": {
                  "type": "number"
                },
                "multiple": {
                  "type": "number"
                },
                "serum": {
                  "type": "number"
                },
                "csf": {
                  "type": "number"
                },
                "tissue": {
                  "type": "number"
                },
                "cell_culture": {
                  "type": "number"
                }
              },
              "required": [
                "plasma",
                "multiple",
                "serum",
                "csf",
                "tissue",
                "cell_culture"
              ],
              "additionalProperties": false
            },
            "study_size_prevalence": {
              "type": "object",
              "properties": {
                "small": {
                  "type": "number"
                },
                "medium": {
                  "type": "number"
                },
                "large": {
                  "type": "number"
                },
                "xlarge": {
                  "type": "number"
                }
              },
              "required": [
                "small",
                "medium",
                "large",
                "xlarge"
              ],
              "additionalProperties": false
            },
            "cns_focus_prevalence": {
              "type": "number"
            },
            "longitudinal_prevalence": {
              "type": "number"
            },
            "toggle_prevalence_note": {
              "type": "string"
            },
            "source": {
              "type": "string"
            },
            "scope_note": {
              "type": "string"
            },
            "superseded_methodology": {
              "type": "string"
            }
          },
          "required": [
            "rationale",
            "goal_prevalence",
            "sample_type_prevalence",
            "study_size_prevalence",
            "cns_focus_prevalence",
            "longitudinal_prevalence",
            "toggle_prevalence_note",
            "source",
            "scope_note",
            "superseded_methodology"
          ],
          "additionalProperties": false
        },
        "baseline_grid": {
          "type": "object",
          "properties": {
            "description": {
              "type": "string"
            },
            "n": {
              "type": "string"
            },
            "outright_win_pct": {
              "type": "object",
              "properties": {
                "seer-proteograph": {
                  "type": "number"
                },
                "illumina-protein-prep": {
                  "type": "number"
                },
                "nomic-omni": {
                  "type": "number"
                },
                "nulisa": {
                  "type": "number"
                },
                "olink-explore-ht": {
                  "type": "number"
                },
                "biognosys-truediscovery": {
                  "type": "number"
                }
              },
              "required": [
                "seer-proteograph",
                "illumina-protein-prep",
                "nomic-omni",
                "nulisa",
                "olink-explore-ht",
                "biognosys-truediscovery"
              ],
              "additionalProperties": false
            },
            "co_recommended_pct": {
              "type": "object",
              "properties": {
                "seer-proteograph": {
                  "type": "number"
                },
                "illumina-protein-prep": {
                  "type": "number"
                },
                "olink-explore-ht": {
                  "type": "number"
                },
                "nomic-omni": {
                  "type": "number"
                },
                "nulisa": {
                  "type": "number"
                },
                "biognosys-truediscovery": {
                  "type": "number"
                }
              },
              "required": [
                "seer-proteograph",
                "illumina-protein-prep",
                "olink-explore-ht",
                "nomic-omni",
                "nulisa",
                "biognosys-truediscovery"
              ],
              "additionalProperties": false
            },
            "tie_group_size_distribution": {
              "type": "object",
              "properties": {
                "1_outright_win": {
                  "type": "number"
                },
                "2_way_tie": {
                  "type": "number"
                },
                "3_way_tie": {
                  "type": "number"
                },
                "4_way_tie": {
                  "type": "number"
                },
                "5_way_tie": {
                  "type": "number"
                },
                "6_way_tie": {
                  "type": "number"
                }
              },
              "required": [
                "1_outright_win",
                "2_way_tie",
                "3_way_tie",
                "4_way_tie",
                "5_way_tie",
                "6_way_tie"
              ],
              "additionalProperties": false
            }
          },
          "required": [
            "description",
            "n",
            "outright_win_pct",
            "co_recommended_pct",
            "tie_group_size_distribution"
          ],
          "additionalProperties": false
        },
        "baseline_grid_uniform_legacy": {
          "type": "object",
          "properties": {
            "description": {
              "type": "string"
            },
            "n": {
              "type": "integer"
            },
            "outright_win_pct": {
              "type": "object",
              "properties": {
                "nomic-omni": {
                  "type": "number"
                },
                "illumina-protein-prep": {
                  "type": "number"
                },
                "seer-proteograph": {
                  "type": "number"
                },
                "nulisa": {
                  "type": "number"
                },
                "biognosys-truediscovery": {
                  "type": "number"
                },
                "olink-explore-ht": {
                  "type": "number"
                }
              },
              "required": [
                "nomic-omni",
                "illumina-protein-prep",
                "seer-proteograph",
                "nulisa",
                "biognosys-truediscovery",
                "olink-explore-ht"
              ],
              "additionalProperties": false
            },
            "co_recommended_pct": {
              "type": "object",
              "properties": {
                "illumina-protein-prep": {
                  "type": "number"
                },
                "seer-proteograph": {
                  "type": "number"
                },
                "olink-explore-ht": {
                  "type": "number"
                },
                "nomic-omni": {
                  "type": "number"
                },
                "biognosys-truediscovery": {
                  "type": "number"
                },
                "nulisa": {
                  "type": "number"
                }
              },
              "required": [
                "illumina-protein-prep",
                "seer-proteograph",
                "olink-explore-ht",
                "nomic-omni",
                "biognosys-truediscovery",
                "nulisa"
              ],
              "additionalProperties": false
            },
            "tie_group_size_distribution": {
              "type": "object",
              "properties": {
                "1_outright_win": {
                  "type": "number"
                },
                "2_way_tie": {
                  "type": "number"
                },
                "3_way_tie": {
                  "type": "number"
                },
                "4_way_tie": {
                  "type": "number"
                },
                "5_way_tie": {
                  "type": "number"
                },
                "6_way_tie": {
                  "type": "number"
                }
              },
              "required": [
                "1_outright_win",
                "2_way_tie",
                "3_way_tie",
                "4_way_tie",
                "5_way_tie",
                "6_way_tie"
              ],
              "additionalProperties": false
            }
          },
          "required": [
            "description",
            "n",
            "outright_win_pct",
            "co_recommended_pct",
            "tie_group_size_distribution"
          ],
          "additionalProperties": false
        },
        "secondary_check": {
          "type": "object",
          "properties": {
            "description": {
              "type": "string"
            },
            "n": {
              "type": "integer"
            },
            "outright_win_pct": {
              "type": "object",
              "properties": {
                "seer-proteograph": {
                  "type": "number"
                },
                "nomic-omni": {
                  "type": "number"
                },
                "illumina-protein-prep": {
                  "type": "number"
                },
                "olink-explore-ht": {
                  "type": "number"
                },
                "nulisa": {
                  "type": "number"
                },
                "biognosys-truediscovery": {
                  "type": "integer"
                }
              },
              "required": [
                "seer-proteograph",
                "nomic-omni",
                "illumina-protein-prep",
                "olink-explore-ht",
                "nulisa",
                "biognosys-truediscovery"
              ],
              "additionalProperties": false
            },
            "co_recommended_pct": {
              "type": "object",
              "properties": {
                "seer-proteograph": {
                  "type": "number"
                },
                "olink-explore-ht": {
                  "type": "number"
                },
                "nomic-omni": {
                  "type": "number"
                },
                "illumina-protein-prep": {
                  "type": "number"
                },
                "nulisa": {
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