experiment.json

{
   "$schema": "https://json-schema.org/draft/2020-12/schema",
   "title": "MAVE experiment definition",
   "$defs": {
      "Document": {
         "type": "object",
         "additionalProperties": false,
         "description": "a written document describing a work",
         "properties": {
            "title": {
               "type": "string",
               "description": "the title of the document"
            },
            "system": {
               "type": "string",
               "description": "the name of the system the document is registered in, such as a journal or preprint server"
            },
            "date": {
               "type": "string",
               "format": "date",
               "description": "the date the document was registered"
            },
            "ref": {
               "type": "string",
               "format": "uri",
               "description": "a Universal Record Identifier for the document"
            }
         },
         "required": [
            "ref"
         ]
      },
      "Coding": {
         "type": "object",
         "additionalProperties": false,
         "properties": {
            "system": {
               "description": "identity of the terminology system",
               "type": "string",
               "format": "uri"
            },
            "version": {
               "description": "version of the terminology system",
               "type": "string"
            },
            "code": {
               "description": "a code within the terminology system",
               "type": "string",
               "pattern": "\\S+( \\S+)*"
            },
            "label": {
               "description": "a human-readable description of the concept associated with the code",
               "type": "string"
            }
         },
         "required": [
            "system",
            "code"
         ]
      },
      "Dataset": {
         "type": "object",
         "additionalProperties": false,
         "description": "a dataset available from an external source",
         "properties": {
            "system": {
               "type": "string",
               "description": "the name of the system the dataset is available from, such as a database"
            },
            "accession": {
               "type": "string",
               "description": "accession number for the dataset in the system"
            },
            "ref": {
               "type": "string",
               "format": "uri",
               "description": "a Universal Record Identifier for the dataset"
            },
            "description": {
               "description": "additional details about the dataset, such as whether it contains raw or processed data",
               "type": "string"
            }
         },
         "required": [
            "system",
            "accession"
         ]
      },
      "ReferenceSequence": {
         "type": "object",
         "additionalProperties": false,
         "properties": {
            "id": {
               "type": "string"
            },
            "sha512t24u": {
               "type": "string",
               "pattern": "[0-9A-Za-z_\\-]{32}"
            },
            "sequence": {
               "type": "string",
               "pattern": "^[A-Z*\\-]*$"
            },
            "sequenceAlphabet": {
               "type": "string",
               "enum": [
                  "DNA",
                  "RNA",
                  "protein"
               ]
            }
         }
      },
      "EndogenousLocusLibraryMethod": {
         "type": "object",
         "additionalProperties": false,
         "description": "a methodology for generating a variant library at an endogenous locus",
         "properties": {
            "type": {
               "const": "endogenous locus library",
               "default": "endogenous locus library"
            },
            "system": {
               "type": "string",
               "description": "the system used to generate the library",
               "enum": [
                  "SpCas9",
                  "SaCas9",
                  "AsCas12a",
                  "RfsCas13d"
               ]
            },
            "mechanism": {
               "description": "the functional mechanism of the library generation method",
               "type": "string",
               "enum": [
                  "nuclease",
                  "base editor",
                  "prime editor"
               ]
            },
            "description": {
               "description": "additional details about the variant library generation method",
               "type": "string"
            }
         },
         "required": [
            "type",
            "system",
            "mechanism"
         ]
      },
      "InVitroConstructLibraryMethod": {
         "type": "object",
         "additionalProperties": false,
         "description": "a methodology for generating and integrating an exogenous variant library",
         "properties": {
            "type": {
               "const": "in-vitro construct library",
               "default": "in-vitro construct library"
            },
            "system": {
               "type": "string",
               "description": "the type of method used to generate the library",
               "enum": [
                  "oligo-directed mutagenic PCR",
                  "error-prone PCR",
                  "nicking mutagenesis",
                  "microarray synthesis",
                  "site-directed mutagenesis",
                  "doped oligo synthesis",
                  "oligo pool synthesis",
                  "proprietary method",
                  "other"
               ]
            },
            "integration": {
               "description": "the mechanism for integration or expression of an exogenous construct",
               "type": "string",
               "enum": [
                  "native locus replacement",
                  "extra-local construct insertion",
                  "random locus viral integration",
                  "episomal delivery",
                  "plasmid (not integrated)",
                  "transfection of RNA"
               ]
            },
            "description": {
               "description": "additional details about the variant library generation method",
               "type": "string"
            }
         },
         "if": {
            "properties": {
               "system": {
                  "const": "other"
               }
            }
         },
         "then": {
            "required": [
               "type",
               "system",
               "description"
            ]
         },
         "else": {
            "required": [
               "type",
               "system"
            ]
         }
      },
      "VariantLibrary": {
         "type": "object",
         "additionalProperties": false,
         "description": "a collection of sequence variants that are derived from a common target sequence",
         "properties": {
            "targetSequences": {
               "description": "the collection of sequences used as references from which all variants in the library are defined",
               "type": "array",
               "items": {
                  "$ref": "#/$defs/ReferenceSequence"
               },
               "minItems": 1
            },
            "scope": {
               "description": "the functional scope of DNA elements introduced into the library. DNA elements can have known or unknown functions. Example functions include a gene, an exon or set of exons included in a transcript, a set of enhancers, a set of repressors, etc.",
               "type": "object",
               "properties": {
                  "type": {
                     "description": "the scope type for elements introduced into the library",
                     "type": "string",
                     "enum": [
                        "coding",
                        "intronic",
                        "non-coding, regulatory",
                        "non-coding, other"
                     ]
                  },
                  "description": {
                     "type": "string",
                     "description": "additional details about the DNA element scope. For example, distinguishing the mode of variant programming/engineering (e.g. all SNV, indels, ClinVar variants etc)."
                  }
               },
               "if": {
                  "properties": {
                     "type": {
                        "const": "non-coding, other"
                     }
                  }
               },
               "then": {
                  "required": [
                     "description"
                  ]
               }
            },
            "generationMethod": {
               "description": "the method used for generating the library",
               "oneOf": [
                  {
                     "$ref": "#/$defs/EndogenousLocusLibraryMethod"
                  },
                  {
                     "$ref": "#/$defs/InVitroConstructLibraryMethod"
                  }
               ]
            },
            "deliveryMethod": {
               "description": "how the variant library was delivered to the model system for phenotype evaluation.",
               "type": "object",
               "properties": {
                  "type": {
                     "type": "string",
                     "enum": [
                        "electroporation",
                        "nucleofection",
                        "chemical-based transfection",
                        "adeno-associated virus transduction",
                        "lentivirus transduction",
                        "chemical or heat shock transformation",
                        "other"
                     ]
                  },
                  "description": {
                     "type": "string",
                     "description": "additional details about the delivery method"
                  }
               },
               "required": [
                  "type"
               ]
            }
         },
         "required": [
            "scope",
            "targetSequences",
            "generationMethod",
            "deliveryMethod"
         ]
      },
      "phenotypicAssay": {
         "description": "a physical adjudication of a model system that allows for systematic interrogation of a functional read-out for a large amount of genetic variants.",
         "type": "object",
         "additionalProperties": false,
         "properties": {
            "dimensionality": {
               "type": "object",
               "description": "dimensionality of phenotyping assay. Describes how many phenotypes and of what complexity are included in the map.",
               "properties": {
                  "type": {
                     "description": "a coding defining the dimensionality of the assay as single or multiple functional readouts.",
                     "type": "string",
                     "enum": [
                        "single-dimensional data",
                        "high-dimensional data",
                        "combined functional data"
                     ]
                  },
                  "description": {
                     "type": "string",
                     "description": "additional details about the dimensionality of the assay"
                  }
               },
               "required": [
                  "type"
               ]
            },
            "replication": {
               "type": "object",
               "description": "replication of phenotyping assay. Describes what kind of replication was performed.",
               "properties": {
                  "type": {
                     "description": "a coding defining the kind of replication performed.",
                     "type": "string",
                     "enum": [
                        "biological",
                        "technical",
                        "biological and technical",
                        "no replication"
                     ]
                  },
                  "description": {
                     "type": "string",
                     "description": "additional details about the replicate structure of the assay, including number of replicates"
                  }
               },
               "required": [
                  "type"
               ]
            },
            "method": {
               "description": "the assay method, defining the molecular properties interrogated.",
               "type": "object",
               "properties": {
                  "type": {
                     "type": "string",
                     "enum": [
                        "promoter activity detection by reporter gene assay",
                        "bulk RNA-sequencing",
                        "single-cell RNA sequencing assay",
                        "fluorescence in-situ hybridization (FISH) assay",
                        "flow cytometry assay",
                        "imaging mass cytometry assay",
                        "systematic evolution of ligands by exponential enrichment assay",
                        "single cell imaging",
                        "multiplexed fluorescent antibody imaging",
                        "binding assay",
                        "cell proliferation assay",
                        "survival assessment assay",
                        "other"
                     ]
                  },
                  "description": {
                     "type": "string",
                     "description": "additional details about the assay method."
                  }
               },
               "required": [
                  "type"
               ]
            },
            "relevance": {
               "description": "the disease or biological processes the assay is relevant to.",
               "type": "array",
               "items": {
                  "$ref": "#/$defs/Coding"
               },
               "minItems": 1
            },
            "modelSystem": {
               "description": "the model system context that influences expression of the phenotype.",
               "type": "object",
               "properties": {
                  "type": {
                     "description": "the model system.",
                     "type": "string",
                     "enum": [
                        "immortalized human cells",
                        "murine primary cells",
                        "induced pluripotent stem cells from human male",
                        "induced pluripotent stem cells from human female",
                        "patient derived primary cells (e.g. T-cells, adipocytes)",
                        "yeast",
                        "bacteria",
                        "bacteriophage",
                        "molecular display",
                        "other"
                     ]
                  },
                  "description": {
                     "type": "string",
                     "description": "additional details about the model system."
                  },
                  "codings": {
                     "description": "relevant ontology terms or identifiers for the model system.",
                     "type": "array",
                     "items": {
                        "$ref": "#/$defs/Coding"
                     },
                     "minItems": 1
                  }
               }
            },
            "profilingStrategy": {
               "description": "the strategy used to profile the variant library",
               "type": "string",
               "enum": [
                  "direct sequencing",
                  "shotgun sequencing",
                  "barcode sequencing"
               ]
            },
            "sequencingReadType": {
               "description": "the sequencing method used",
               "type": "string",
               "enum": [
                  "single-segment (short read)",
                  "single-segment (long read)",
                  "multi-segment"
               ]
            }
         },
         "required": [
            "dimensionality",
            "method",
            "relevance",
            "modelSystem",
            "profilingStrategy",
            "sequencingReadType",
            "replication"
         ]
      }
   },
   "type": "object",
   "additionalProperties": false,
   "properties": {
      "title": {
         "description": "the title of the MAVE experiment",
         "type": "string"
      },
      "abstract": {
         "description": "an abstract describing the MAVE experiment",
         "type": "string"
      },
      "document": {
         "description": "the primary document describing this experiment",
         "$ref": "#/$defs/Document"
      },
      "datasets": {
         "description": "datasets associated with this experiment",
         "type": "array",
         "items": {
            "$ref": "#/$defs/Dataset"
         },
         "minItems": 1
      },
      "variantLibrary": {
         "description": "characteristics of the variant library generation process",
         "$ref": "#/$defs/VariantLibrary"
      },
      "phenotypicAssay": {
         "$ref": "#/$defs/phenotypicAssay"
      }
   },
   "required": [
      "title",
      "abstract",
      "variantLibrary",
      "phenotypicAssay"
   ]
}