{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://aptatlas.org/data/helpMeCombine.schema.json",
  "title": "Help Me Combine data",
  "description": "Inputs to the pairing engine.",
  "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": "helpMeCombine"
    },
    "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": {
        "universe": {
          "type": "object",
          "properties": {
            "drug_targets": {
              "type": "integer"
            },
            "drug_targets_on_a_platform": {
              "type": "integer"
            },
            "approved_phase4": {
              "type": "integer"
            },
            "proteome_canonical": {
              "type": "integer"
            },
            "proteome_atlas_union": {
              "type": "integer"
            },
            "fda_approved_biomarkers": {
              "type": "integer"
            },
            "atlas_fetch_date": {
              "type": "string"
            },
            "chembl_fetch_date": {
              "type": "string"
            },
            "fda_biomarker_source": {
              "type": "string"
            }
          },
          "required": [
            "drug_targets",
            "drug_targets_on_a_platform",
            "approved_phase4",
            "proteome_canonical",
            "proteome_atlas_union",
            "fda_approved_biomarkers",
            "atlas_fetch_date",
            "chembl_fetch_date",
            "fda_biomarker_source"
          ],
          "additionalProperties": false
        },
        "coverage_modes": {
          "type": "array",
          "items": {
            "type": "object",
            "properties": {
              "key": {
                "type": "string"
              },
              "label": {
                "type": "string"
              },
              "denominator": {
                "type": [
                  "integer",
                  "null"
                ]
              },
              "default": {
                "type": "boolean"
              },
              "note": {
                "type": "string"
              }
            },
            "required": [
              "key",
              "label",
              "denominator"
            ],
            "additionalProperties": false
          }
        },
        "quality_dimensions": {
          "type": "object",
          "properties": {
            "proteome_coverage": {
              "type": "integer"
            },
            "precision": {
              "type": "integer"
            },
            "specificity": {
              "type": "integer"
            },
            "sensitivity": {
              "type": "integer"
            },
            "cost_efficiency": {
              "type": "integer"
            },
            "throughput": {
              "type": "integer"
            },
            "quantification_type": {
              "type": "integer"
            },
            "sample_flexibility": {
              "type": "integer"
            },
            "evidence_depth": {
              "type": "integer"
            },
            "pqtl_accuracy": {
              "type": "integer"
            }
          },
          "required": [
            "proteome_coverage",
            "precision",
            "specificity",
            "sensitivity",
            "cost_efficiency",
            "throughput",
            "quantification_type",
            "sample_flexibility",
            "evidence_depth",
            "pqtl_accuracy"
          ],
          "additionalProperties": false
        },
        "composite_axes": {
          "type": "array",
          "items": {
            "type": "object",
            "properties": {
              "key": {
                "type": "string"
              },
              "default_weight": {
                "type": "number"
              },
              "note": {
                "type": "string"
              },
              "invert": {
                "type": "boolean"
              }
            },
            "required": [
              "key",
              "default_weight"
            ],
            "additionalProperties": false
          }
        },
        "class_balance_rule": {
          "type": "string"
        },
        "quality_axis_dims_used": {
          "type": "array",
          "items": {
            "type": "string"
          }
        },
        "dedup_note": {
          "type": "string"
        },
        "no_feasibility_penalty": {
          "type": "string"
        },
        "platforms": {
          "type": "object",
          "additionalProperties": {
            "type": "object",
            "properties": {
              "display_name": {
                "type": "string"
              },
              "coverage_gene_set_size": {
                "type": "integer"
              },
              "coverage": {
                "type": "object",
                "properties": {
                  "drug_targets": {
                    "type": "number"
                  },
                  "proteome_canonical": {
                    "type": "number"
                  },
                  "proteome_atlas_union": {
                    "type": "number"
                  },
                  "fda_biomarkers": {
                    "type": "number"
                  }
                },
                "required": [
                  "drug_targets",
                  "proteome_canonical",
                  "proteome_atlas_union",
                  "fda_biomarkers"
                ],
                "additionalProperties": false
              },
              "ptm_proteoform_capable": {
                "type": "boolean"
              },
              "app_scores": {
                "type": "object",
                "properties": {
                  "proteome_coverage": {
                    "type": "integer"
                  },
                  "precision": {
                    "type": "integer"
                  },
                  "specificity": {
                    "type": "integer"
                  },
                  "sensitivity": {
                    "type": "integer"
                  },
                  "cost_efficiency": {
                    "type": "integer"
                  },
                  "throughput": {
                    "type": "integer"
                  },
                  "quantification_type": {
                    "type": "integer"
                  },
                  "sample_flexibility": {
                    "type": "integer"
                  },
                  "evidence_depth": {
                    "type": "integer"
                  },
                  "pqtl_accuracy": {
                    "type": "integer"
                  }
                },
                "required": [
                  "proteome_coverage",
                  "precision",
                  "specificity",
                  "sensitivity",
                  "cost_efficiency",
                  "throughput",
                  "quantification_type",
                  "sample_flexibility",
                  "evidence_depth",
                  "pqtl_accuracy"
                ],
                "additionalProperties": false
              },
              "sample_volume_uL": {
                "type": "integer"
              },
              "cost_tier_rel": {
                "type": "number"
              }
            },
            "required": [
              "display_name",
              "coverage_gene_set_size",
              "coverage",
              "ptm_proteoform_capable",
              "app_scores",
              "sample_volume_uL",
              "cost_tier_rel"
            ],
            "additionalProperties": false
          }
        },
        "pairs": {
          "type": "array",
          "items": {
            "type": "object",
            "properties": {
              "a": {
                "type": "string"
              },
              "b": {
                "type": "string"
              },
              "coverage_pct": {
                "type": "number"
              },
              "coverage_ci_lo": {
                "type": "number"
              },
              "coverage_ci_hi": {
                "type": "number"
              },
              "coverage_pct_canonical": {
                "type": "number"
              },
              "coverage_pct_atlas_union": {
                "type": "number"
              },
              "coverage_pct_fda": {
                "type": "number"
              },
              "coverage_fda_ci_lo": {
                "type": "number"
              },
              "coverage_fda_ci_hi": {
                "type": "number"
              },
              "net_new_targets": {
                "type": "integer"
              },
              "net_new_pct": {
                "type": "number"
              },
              "quality_intrinsic": {
                "type": "number"
              },
              "quality_maturity": {
                "type": "number"
              },
              "class_balance": {
                "type": "number"
              },
              "total_cost": {
                "type": "number"
              },
              "joint_volume_uL": {
                "type": "integer"
              },
              "composite": {
                "type": "number"
              },
              "pareto_nondominated": {
                "type": "boolean"
              },
              "top3_pct": {
                "type": "number"
              },
              "mean_regret": {
                "type": "number"
              },
              "win_pct_secondary": {
                "type": "number"
              },
              "tier": {
                "type": "integer"
              }
            },
            "required": [
              "a",
              "b",
              "coverage_pct",
              "coverage_ci_lo",
              "coverage_ci_hi",
              "coverage_pct_canonical",
              "coverage_pct_atlas_union",
              "coverage_pct_fda",
              "coverage_fda_ci_lo",
              "coverage_fda_ci_hi",
              "net_new_targets",
              "net_new_pct",
              "quality_intrinsic",
              "quality_maturity",
              "class_balance",
              "total_cost",
              "joint_volume_uL",
              "composite",
              "pareto_nondominated",
              "top3_pct",
              "mean_regret",
              "win_pct_secondary",
              "tier"
            ],
            "additionalProperties": false
          }
        },
        "ms_note": {
          "type": "string"
        },
        "fairness_note": {
          "type": "string"
        },
        "quality_axes": {
          "type": "object",
          "properties": {
            "intrinsic": {
              "type": "object",
              "properties": {
                "dims": {
                  "type": "array",
                  "items": {
                    "type": "string"
                  }
                },
                "default_weight": {
                  "type": "integer"
                },
                "label": {
                  "type": "string"
                },
                "note": {
                  "type": "string"
                }
              },
              "required": [
                "dims",
                "default_weight",
                "label",
                "note"
              ],
              "additionalProperties": false
            },
            "maturity": {
              "type": "object",
              "properties": {
                "dims": {
                  "type": "array",
                  "items": {
                    "type": "string"
                  }
                },
                "default_weight": {
                  "type": "integer"
                },
                "label": {
                  "type": "string"
                },
                "note": {
                  "type": "string"
                }
              },
              "required": [
                "dims",
                "default_weight",
                "label",
                "note"
              ],
              "additionalProperties": false
            }
          },
          "required": [
            "intrinsic",
            "maturity"
          ],
          "additionalProperties": false
        },
        "quality_custom_weighting": {
          "type": "string"
        },
        "naming_note": {
          "type": "string"
        },
        "ranking_sensitivity_note": {
          "type": "string"
        },
        "default_philosophy": {
          "type": "string"
        },
        "complementarity_note": {
          "type": "string"
        },
        "anchor_recommendations": {
          "type": "object",
          "additionalProperties": {
            "type": "object",
            "properties": {
              "anchor_solo_pct": {
                "type": "number"
              },
              "single_suffices": {
                "type": "boolean"
              },
              "tiered_partners": {
                "type": "array",
                "items": {
                  "type": "object",
                  "properties": {
                    "partner": {
                      "type": "string"
                    },
                    "pair_coverage_pct": {
                      "type": "number"
                    },
                    "net_new_targets": {
                      "type": "integer"
                    },
                    "composite": {
                      "type": "number"
                    },
                    "top3_pct": {
                      "type": "number"
                    },
                    "mean_regret": {
                      "type": "number"
                    },
                    "pareto": {
                      "type": "boolean"
                    },
                    "coverage_gain_pp": {
                      "type": "number"
                    },
                    "tier": {
                      "type": "integer"
                    }
                  },
                  "required": [
                    "partner",
                    "pair_coverage_pct",
                    "net_new_targets",
                    "composite",
                    "top3_pct",
                    "mean_regret",
                    "pareto",
                    "coverage_gain_pp",
                    "tier"
                  ],
                  "additionalProperties": false
                }
              }
            },
            "required": [
              "anchor_solo_pct",
              "single_suffices",
              "tiered_partners"
            ],
            "additionalProperties": false
          }
        },
        "interaction_modes": {
          "type": "object",
          "properties": {
            "anchor_mode": {
              "type": "object",
              "properties": {
                "description": {
                  "type": "string"
                },
                "default_first_platform": {
                  "type": "string"
                }
              },
              "required": [
                "description",
                "default_first_platform"
              ],
              "additionalProperties": false
            },
            "discovery_mode": {
              "type": "object",
              "properties": {
                "description": {
                  "type": "string"
                },
                "trigger": {
                  "type": "string"
                }
              },
              "required": [
                "description",
                "trigger"
              ],
              "additionalProperties": false
            },
            "single_suffices_flag": {
              "type": "string"
            }
          },
          "required": [
            "anchor_mode",
            "discovery_mode",
            "single_suffices_flag"
          ],
          "additionalProperties": false
        },
        "fairness_analyses": {
          "type": "object",
          "properties": {
            "coverage_confidence_intervals": {
              "type": "object",
              "properties": {
                "method": {
                  "type": "string"
                },
                "key_result": {
                  "type": "string"
                },
                "table": {
                  "type": "string"
                }
              },
              "required": [
                "method",
                "key_result",
                "table"
              ],
              "additionalProperties": false
            },
            "pareto_frontier": {
              "type": "object",
              "properties": {
                "non_dominated": {
                  "type": "integer"
                },
                "total": {
                  "type": "integer"
                },
                "dominated": {
                  "type": "array",
                  "items": {
                    "type": "string"
                  }
                },
                "note": {
                  "type": "string"
                }
              },
              "required": [
                "non_dominated",
                "total",
                "dominated",
                "note"
              ],
              "additionalProperties": false
            },
            "quality_score_robustness": {
              "type": "object",
              "properties": {
                "method": {
                  "type": "string"
                },
                "key_result": {
                  "type": "string"
                }
              },
              "required": [
                "method",
                "key_result"
              ],
              "additionalProperties": false
            },
            "robustness_metric": {
              "type": "object",
              "properties": {
                "primary": {
                  "type": "array",
                  "items": {
                    "type": "string"
                  }
                },
                "secondary": {
                  "type": "string"
                },
                "why": {
                  "type": "string"
                },
                "headline": {
                  "type": "string"
                }
              },
              "required": [
                "primary",
                "secondary",
                "why",
                "headline"
              ],
              "additionalProperties": false
            }
          },
          "required": [
            "coverage_confidence_intervals",
            "pareto_frontier",
            "quality_score_robustness",
            "robustness_metric"
          ],
          "additionalProperties": false
        },
        "recommendation_output": {
          "type": "object",
          "properties": {
            "mode": {
              "type": "string"
            },
            "tiers": {
              "type": "object",
              "properties": {
                "1": {
                  "type": "string"
                },
                "2": {
                  "type": "string"
                },
                "3": {
                  "type": "string"
                },
                "4": {
                  "type": "string"
                }
              },
              "required": [
                "1",
                "2",
                "3",
                "4"
              ],
              "additionalProperties": false
            },
            "rule": {
              "type": "string"
            },
            "consortium_note": {
              "type": "string"
            }
          },
          "required": [
            "mode",
            "tiers",
            "rule",
            "consortium_note"
          ],
          "additionalProperties": false
        },
        "engine_version": {
          "type": "string"
        }
      },
      "required": [
        "universe",
        "coverage_modes",
        "quality_dimensions",
        "composite_axes",
        "class_balance_rule",
        "quality_axis_dims_used",
        "dedup_note",
        "no_feasibility_penalty",
        "platforms",
        "pairs",
        "ms_note",
        "fairness_note",
        "quality_axes",
        "quality_custom_weighting",
        "naming_note",
        "ranking_sensitivity_note",
        "default_philosophy",
        "complementarity_note",
        "anchor_recommendations",
        "interaction_modes",
        "fairness_analyses",
        "recommendation_output",
        "engine_version"
      ],
      "additionalProperties": false
    }
  }
}