JSON Schema

The JSON schema for FROG version 1 is available from frog-schema-version-1.json

{
  "$defs": {
    "Creator": {
      "description": "Creator/curator in ModelHistory and other COMBINE formats.\n\nExtended by optional orcid.",
      "properties": {
        "familyName": {
          "title": "Familyname",
          "type": "string"
        },
        "givenName": {
          "title": "Givenname",
          "type": "string"
        },
        "email": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Email"
        },
        "organization": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Organization"
        },
        "site": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Site"
        },
        "orcid": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "title": "Orcid"
        }
      },
      "required": [
        "familyName",
        "givenName"
      ],
      "title": "Creator",
      "type": "object"
    },
    "FrogFVA": {
      "description": "Definition of FROG FVA.",
      "properties": {
        "fva": {
          "items": {
            "$ref": "#/$defs/FrogFVASingle"
          },
          "title": "Fva",
          "type": "array"
        }
      },
      "required": [
        "fva"
      ],
      "title": "FrogFVA",
      "type": "object"
    },
    "FrogFVASingle": {
      "description": "Frog FVA.",
      "properties": {
        "model": {
          "title": "Model",
          "type": "string"
        },
        "objective": {
          "title": "Objective",
          "type": "string"
        },
        "reaction": {
          "title": "Reaction",
          "type": "string"
        },
        "flux": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "title": "Flux"
        },
        "status": {
          "$ref": "#/$defs/StatusCode"
        },
        "minimum": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "title": "Minimum"
        },
        "maximum": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "title": "Maximum"
        },
        "fraction_optimum": {
          "title": "Fraction Optimum",
          "type": "number"
        }
      },
      "required": [
        "model",
        "objective",
        "reaction",
        "flux",
        "status",
        "minimum",
        "maximum",
        "fraction_optimum"
      ],
      "title": "FrogFVASingle",
      "type": "object"
    },
    "FrogGeneDeletion": {
      "description": "Frog gene deletion.",
      "properties": {
        "model": {
          "title": "Model",
          "type": "string"
        },
        "objective": {
          "title": "Objective",
          "type": "string"
        },
        "gene": {
          "title": "Gene",
          "type": "string"
        },
        "status": {
          "$ref": "#/$defs/StatusCode"
        },
        "value": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "title": "Value"
        }
      },
      "required": [
        "model",
        "objective",
        "gene",
        "status",
        "value"
      ],
      "title": "FrogGeneDeletion",
      "type": "object"
    },
    "FrogGeneDeletions": {
      "description": "Definition of FROG Gene deletions.",
      "properties": {
        "deletions": {
          "items": {
            "$ref": "#/$defs/FrogGeneDeletion"
          },
          "title": "Deletions",
          "type": "array"
        }
      },
      "required": [
        "deletions"
      ],
      "title": "FrogGeneDeletions",
      "type": "object"
    },
    "FrogMetaData": {
      "description": "FROG metadata.",
      "properties": {
        "model.location": {
          "description": "Location of the model in the COMBINE archive for which the FROG analysis was performed.",
          "title": "Model.Location",
          "type": "string"
        },
        "model.md5": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "description": "MD5 hash of model",
          "title": "Model.Md5"
        },
        "frog_id": {
          "description": "Id for the FROG analysis. All frog_ids within an archive must be unique.",
          "title": "Frog Id",
          "type": "string"
        },
        "frog.software": {
          "$ref": "#/$defs/Tool",
          "description": "Software used to run FROG (e.g. 'fbc_curation')"
        },
        "frog.curators": {
          "description": "Curators which executed the FROG analysis.",
          "items": {
            "$ref": "#/$defs/Creator"
          },
          "title": "Frog.Curators",
          "type": "array"
        },
        "software": {
          "$ref": "#/$defs/Tool",
          "description": "Software used to run FBC (e.g. 'COBRA', 'cobrapy')."
        },
        "solver": {
          "$ref": "#/$defs/Tool",
          "description": "Solver used to solve LP problem (e.g. 'CPLEX', 'GUROBI', 'GLPK')."
        },
        "environment": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "description": "Execution environment such as Linux.",
          "title": "Environment"
        }
      },
      "required": [
        "model.location",
        "model.md5",
        "frog_id",
        "frog.software",
        "frog.curators",
        "software",
        "solver",
        "environment"
      ],
      "title": "FrogMetaData",
      "type": "object"
    },
    "FrogObjective": {
      "description": "Frog Objective.",
      "properties": {
        "model": {
          "title": "Model",
          "type": "string"
        },
        "objective": {
          "title": "Objective",
          "type": "string"
        },
        "status": {
          "$ref": "#/$defs/StatusCode"
        },
        "value": {
          "title": "Value",
          "type": "number"
        }
      },
      "required": [
        "model",
        "objective",
        "status",
        "value"
      ],
      "title": "FrogObjective",
      "type": "object"
    },
    "FrogObjectives": {
      "description": "Definition of FROG Objectives.",
      "properties": {
        "objectives": {
          "items": {
            "$ref": "#/$defs/FrogObjective"
          },
          "title": "Objectives",
          "type": "array"
        }
      },
      "required": [
        "objectives"
      ],
      "title": "FrogObjectives",
      "type": "object"
    },
    "FrogReactionDeletion": {
      "description": "Frog reaction deletion.",
      "properties": {
        "model": {
          "title": "Model",
          "type": "string"
        },
        "objective": {
          "title": "Objective",
          "type": "string"
        },
        "reaction": {
          "title": "Reaction",
          "type": "string"
        },
        "status": {
          "$ref": "#/$defs/StatusCode"
        },
        "value": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "title": "Value"
        }
      },
      "required": [
        "model",
        "objective",
        "reaction",
        "status",
        "value"
      ],
      "title": "FrogReactionDeletion",
      "type": "object"
    },
    "FrogReactionDeletions": {
      "description": "Definition of FROG Reaction deletions.",
      "properties": {
        "deletions": {
          "items": {
            "$ref": "#/$defs/FrogReactionDeletion"
          },
          "title": "Deletions",
          "type": "array"
        }
      },
      "required": [
        "deletions"
      ],
      "title": "FrogReactionDeletions",
      "type": "object"
    },
    "StatusCode": {
      "description": "Status code for simulation results.",
      "enum": [
        "optimal",
        "infeasible"
      ],
      "title": "StatusCode",
      "type": "string"
    },
    "Tool": {
      "description": "Tool description.",
      "properties": {
        "name": {
          "description": "Name of tool/software/library.",
          "title": "Name",
          "type": "string"
        },
        "version": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "description": "Version of tool/software/library.",
          "title": "Version"
        },
        "url": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "description": "URL of tool/software/library.",
          "title": "Url"
        }
      },
      "required": [
        "name",
        "version",
        "url"
      ],
      "title": "Tool",
      "type": "object"
    }
  },
  "description": "Definition of the FROG standard.",
  "properties": {
    "metadata": {
      "$ref": "#/$defs/FrogMetaData"
    },
    "objectives": {
      "$ref": "#/$defs/FrogObjectives"
    },
    "fva": {
      "$ref": "#/$defs/FrogFVA"
    },
    "reaction_deletions": {
      "$ref": "#/$defs/FrogReactionDeletions"
    },
    "gene_deletions": {
      "$ref": "#/$defs/FrogGeneDeletions"
    }
  },
  "required": [
    "metadata",
    "objectives",
    "fva",
    "reaction_deletions",
    "gene_deletions"
  ],
  "title": "FrogReport",
  "type": "object"
}