Experiment

Schema for submitting metadata for an assay with 1 or more replicates.

{
    "title": "Experiment",
    "description": "Schema for submitting metadata for an assay with 1 or more replicates.",
    "comment": "An experiment is a special case of dataset. It includes assay metadata, replicate information and data files.",
    "id": "/profiles/experiment.json",
    "$schema": "http://json-schema.org/draft-04/schema#",
    "type": "object",
    "required": [
        "award",
        "lab",
        "assay_term_name",
        "biosample_type"
    ],
    "approvalRequired": [
        "assay_term_id",
        "biosample_term_id",
        "biosample_type"
    ],
    "identifyingProperties": [
        "uuid",
        "accession",
        "aliases"
    ],
    "additionalProperties": false,
    "mixinProperties": [
        {
            "$ref": "mixins.json#/schema_version"
        },
        {
            "$ref": "mixins.json#/uuid"
        },
        {
            "$ref": "mixins.json#/accession"
        },
        {
            "$ref": "mixins.json#/aliases"
        },
        {
            "$ref": "mixins.json#/attribution"
        },
        {
            "$ref": "mixins.json#/submitted"
        },
        {
            "$ref": "mixins.json#/notes"
        },
        {
            "$ref": "dataset.json#/properties"
        },
        {
            "$ref": "mixins.json#/references"
        },
        {
            "$ref": "mixins.json#/documents"
        },
        {
            "$ref": "mixins.json#/biosample_classification"
        },
        {
            "$ref": "mixins.json#/assay"
        },
        {
            "$ref": "mixins.json#/submitter_comment"
        }
    ],
    "dependencies": {
        "biosample_type": {
            "oneOf": [
                {
                    "properties": {
                        "biosample_type": {
                            "enum": [
                                "in vitro sample"
                            ]
                        }
                    }
                },
                {
                    "required": [
                        "biosample_term_id"
                    ],
                    "properties": {
                        "biosample_type": {
                            "enum": [
                                "primary cell",
                                "immortalized cell line",
                                "tissue",
                                "in vitro differentiated cells",
                                "induced pluripotent stem cell line",
                                "whole organisms",
                                "stem cell"
                            ]
                        }
                    }
                }
            ]
        },
        "biosample_term_id": {
            "oneOf": [
                {
                    "properties": {
                        "biosample_type": {
                            "enum": [
                                "tissue",
                                "whole organisms"
                            ]
                        },
                        "biosample_term_id": {
                            "pattern": "^(UBERON|NTR):[0-9]{2,8}$"
                        }
                    }
                },
                {
                    "properties": {
                        "biosample_type": {
                            "enum": [
                                "primary cell"
                            ]
                        },
                        "biosample_term_id": {
                            "pattern": "^(CL|NTR):[0-9]{2,8}$"
                        }
                    }
                },
                {
                    "properties": {
                        "biosample_type": {
                            "enum": [
                                "immortalized cell line",
                                "induced pluripotent stem cell line"
                            ]
                        },
                        "biosample_term_id": {
                            "pattern": "^(EFO|NTR):[0-9]{2,8}$"
                        }
                    }
                },
                {
                    "properties": {
                        "biosample_type": {
                            "enum": [
                                "stem cell",
                                "in vitro differentiated cells"
                            ]
                        },
                        "biosample_term_id": {
                            "pattern": "^(CL|EFO|NTR):[0-9]{2,8}$"
                        }
                    }
                }
            ]
        },
        "status": {
            "oneOf": [
                {
                    "required": [
                        "date_released"
                    ],
                    "properties": {
                        "status": {
                            "enum": [
                                "released",
                                "revoked"
                            ]
                        }
                    }
                },
                {
                    "not": {
                        "properties": {
                            "status": {
                                "enum": [
                                    "released",
                                    "revoked"
                                ]
                            }
                        }
                    }
                }
            ]
        },
        "internal_status": {
            "oneOf": [
                {
                    "required": [
                        "pipeline_error_detail"
                    ],
                    "properties": {
                        "internal_status": {
                            "enum": [
                                "pipeline error"
                            ]
                        }
                    }
                },
                {
                    "not": {
                        "oneOf": [
                            {
                                "required": [
                                    "pipeline_error_detail"
                                ],
                                "properties": {
                                    "internal_status": {
                                        "enum": [
                                            "unreviewed",
                                            "no available pipeline",
                                            "unrunnable",
                                            "pipeline ready",
                                            "processing",
                                            "pipeline completed",
                                            "requires lab review",
                                            "release ready"
                                        ]
                                    }
                                }
                            },
                            {
                                "properties": {
                                    "internal_status": {
                                        "enum": [
                                            "pipeline error"
                                        ]
                                    }
                                }
                            }
                        ]
                    }
                }
            ]
        }
    },
    "properties": {
        "submitter_comment": {
            "description": "Additional information specified by the submitter to be displayed as a comment on the portal.",
            "type": "string",
            "title": "Submitter comment",
            "pattern": "^(\\S+(\\s|\\S)*\\S+|\\S)$"
        },
        "assay_term_name": {
            "description": "OBI (Ontology for Biomedical Investigations) ontology term for the assay.",
            "enum": [
                "ChIP-seq",
                "RNA-seq",
                "DNase-seq",
                "eCLIP",
                "shRNA knockdown followed by RNA-seq",
                "RNA Bind-n-Seq",
                "transcription profiling by array assay",
                "DNA methylation profiling by array assay",
                "whole-genome shotgun bisulfite sequencing",
                "RRBS",
                "siRNA knockdown followed by RNA-seq",
                "RAMPAGE",
                "comparative genomic hybridization by array",
                "CAGE",
                "single cell isolation followed by RNA-seq",
                "Repli-seq",
                "microRNA-seq",
                "microRNA counts",
                "MRE-seq",
                "RIP-seq",
                "Repli-chip",
                "MeDIP-seq",
                "ChIA-PET",
                "FAIRE-seq",
                "ATAC-seq",
                "PAS-seq",
                "RIP-chip",
                "RNA-PET",
                "genotyping by high throughput sequencing assay",
                "CRISPR genome editing followed by RNA-seq",
                "protein sequencing by tandem mass spectrometry assay",
                "5C",
                "HiC",
                "TAB-seq",
                "iCLIP",
                "DNA-PET",
                "Switchgear",
                "5' RLM RACE",
                "MNase-seq",
                "5' RACE",
                "3' RACE",
                "small RNA-seq",
                "Bru-seq",
                "BruChase-seq",
                "genetic modification followed by DNase-seq",
                "CRISPRi followed by RNA-seq",
                "genotype phasing by HiC",
                "Circulome-seq",
                "whole genome sequencing assay",
                "BruUV-seq",
                "Mint-ChIP-seq",
                "single nuclei ATAC-seq",
                "icSHAPE"
            ],
            "type": "string",
            "title": "Assay name"
        },
        "biosample_term_id": {
            "@type": "@id",
            "description": "Ontology identifier describing biosample.",
            "pattern": "^(UBERON|EFO|CL|NTR|FBbt|WBbt):[0-9]{2,8}$",
            "comment": "For detailed description of ontologies used by DCC visit https://www.encodeproject.org/help/getting-started/. In cases where a new ontology term is needed, NTR (new term request) identifier would be provided by the DCC.",
            "type": "string",
            "title": "Ontology ID"
        },
        "biosample_term_name": {
            "description": "Ontology term describing biosample.",
            "comment": "The term should match the ontology identifier specified in biosample_term_id. For detailed description of ontologies used by DCC visit https://www.encodeproject.org/help/getting-started/.",
            "type": "string",
            "title": "Ontology term"
        },
        "biosample_type": {
            "description": "The categorization of the biosample.",
            "comment": "Required property. The specified category should match the type of ontology used to describe the biosample.",
            "enum": [
                "primary cell",
                "immortalized cell line",
                "tissue",
                "in vitro differentiated cells",
                "induced pluripotent stem cell line",
                "whole organisms",
                "stem cell",
                "in vitro sample"
            ],
            "type": "string",
            "title": "Biosample type"
        },
        "documents": {
            "description": "Protocols or other documents that describe the assay or the results (not data files).",
            "uniqueItems": true,
            "items": {
                "description": "A document that provides additional information (not data file).",
                "comment": "See document.json for available identifiers.",
                "type": "string",
                "title": "Document",
                "linkTo": "Document"
            },
            "type": "array",
            "title": "Documents",
            "default": []
        },
        "references": {
            "description": "The publications that provide more information about the object.",
            "uniqueItems": true,
            "items": {
                "description": "A publication that provide smore information about the object.",
                "linkTo": "Publication",
                "type": "string",
                "title": "Reference"
            },
            "type": "array",
            "title": "References",
            "default": []
        },
        "description": {
            "description": "A plain text description of the dataset.",
            "elasticsearch_mapping_index_type": {
                "description": "Defines one of three types of indexing available",
                "enum": [
                    "analyzed",
                    "not_analyzed",
                    "no"
                ],
                "type": "string",
                "title": "Field mapping index type",
                "default": "analyzed"
            },
            "type": "string",
            "title": "Description",
            "pattern": "^(\\S+(\\s|\\S)*\\S+|\\S)$|^$"
        },
        "alternate_accessions": {
            "description": "Accessions previously assigned to objects that have been merged with this object.",
            "comment": "Do not submit. Only admins are allowed to set or update this value.",
            "readonly": true,
            "items": {
                "description": "An accession previously assigned to an object that has been merged with this object.",
                "comment": "Only accessions of objects that have status equal replaced will work here.",
                "format": "accession",
                "pattern": "^(ENCSR\\d{3}[A-Z]{3})$|^(TSTSR\\d{6})$",
                "type": "string",
                "title": "Alternate Accession"
            },
            "permission": "import_items",
            "type": "array",
            "title": "Alternate accessions",
            "default": []
        },
        "status": {
            "enum": [
                "proposed",
                "started",
                "submitted",
                "ready for review",
                "deleted",
                "released",
                "revoked",
                "archived",
                "replaced"
            ],
            "type": "string",
            "title": "Status",
            "default": "proposed"
        },
        "accession": {
            "description": "A unique identifier to be used to reference the object prefixed with ENC.",
            "comment": "Do not submit. The accession is assigned by the server.",
            "serverDefault": "accession",
            "permission": "import_items",
            "accessionType": "SR",
            "format": "accession",
            "type": "string",
            "title": "Accession",
            "readonly": true
        },
        "dbxrefs": {
            "@type": "@id",
            "description": "Identifiers from external resources that may have 1-to-1 or 1-to-many relationships with ENCODE objects.",
            "rdfs:subPropertyOf": "rdfs:seeAlso",
            "uniqueItems": true,
            "items": {
                "title": "External identifier",
                "description": "An identifier from an external resource that may have 1-to-1 or 1-to-many relationships with ENCODE objects.",
                "type": "string",
                "pattern": "^(UCSC-ENCODE-mm9:wgEncodeEM\\d+|UCSC-ENCODE-hg19:wgEncodeEH\\d+|GEO:(GSM|GSE)\\d+|GEO-obsolete:(GSM|GSE)\\d+|RBPImage:[^\\s].*)$"
            },
            "type": "array",
            "title": "External identifiers",
            "default": []
        },
        "date_released": {
            "comment": "Do not submit, value is assigned whe the object is releaesd.",
            "readonly": true,
            "permission": "import_items",
            "type": "string",
            "title": "Date released",
            "anyOf": [
                {
                    "format": "date-time"
                },
                {
                    "format": "date"
                }
            ]
        },
        "schema_version": {
            "description": "The version of the JSON schema that the server uses to validate the object.",
            "comment": "Do not submit. The version used to validate the object is set by the server. The default should be set to the current version.",
            "requestMethod": [],
            "title": "Schema Version",
            "pattern": "^\\d+(\\.\\d+)*$",
            "type": "string",
            "hidden comment": "Bump the default in the subclasses.",
            "default": "13"
        },
        "internal_tags": {
            "description": "Some datasets are part of particular data collections",
            "readonly": true,
            "uniqueItems": true,
            "items": {
                "enum": [
                    "DREAM",
                    "ENCORE",
                    "ENTEx",
                    "SESCC",
                    "dbGaP",
                    "ENCYCLOPEDIAv3",
                    "ENCYCLOPEDIAv4",
                    "cre_inputv10",
                    "cre_inputv11"
                ],
                "type": "string"
            },
            "permission": "import_items",
            "type": "array",
            "title": "Internal tags",
            "default": []
        },
        "notes": {
            "description": "DCC internal notes.",
            "comment": "Do not submit. A place for the DCC to keep information that does not have a place in the schema.",
            "readonly": true,
            "pattern": "^(\\S+(\\s|\\S)*\\S+|\\S)$",
            "permission": "import_items",
            "type": "string",
            "title": "Notes"
        },
        "date_created": {
            "description": "The date the object was created.",
            "comment": "Do not submit. The date the object is created is assigned by the server.",
            "rdfs:subPropertyOf": "dc:created",
            "serverDefault": "now",
            "permission": "import_items",
            "anyOf": [
                {
                    "format": "date-time"
                },
                {
                    "format": "date"
                }
            ],
            "readonly": true,
            "type": "string",
            "title": "Date created"
        },
        "submitted_by": {
            "comment": "Do not submit. The user that created the object is assigned by the server.",
            "serverDefault": "userid",
            "rdfs:subPropertyOf": "dc:creator",
            "readonly": true,
            "permission": "import_items",
            "linkTo": "User",
            "type": "string",
            "title": "Submitted by"
        },
        "award": {
            "description": "Grant associated with the submission.",
            "comment": "Required. See award.json for list of available identifiers.",
            "type": "string",
            "title": "Grant",
            "linkTo": "Award"
        },
        "lab": {
            "description": "Lab associated with the submission.",
            "comment": "Required. See lab.json for list of available identifiers.",
            "linkSubmitsFor": true,
            "linkTo": "Lab",
            "type": "string",
            "title": "Lab"
        },
        "aliases": {
            "description": "Lab specific identifiers to reference an object.",
            "comment": "The purpose of this field is to provide a link into the lab LIMS and to facilitate shared objects.",
            "uniqueItems": true,
            "items": {
                "description": "A lab specific identifier to reference an object.",
                "comment": "Current convention is colon separated lab name and lab identifier. (e.g. john-doe:42).",
                "uniqueKey": "alias",
                "pattern": "^(?:alexander-hoffmann|alexander-rudensky|alexander-urban|ali-mortazavi|alkes-price|andrew-fire|anshul-kundaje|anton-valouev|barbara-wold|bill-noble|bin-yu|bing-ren|bradley-bernstein|brenton-graveley|chris-burge|christina-leslie|colin-dewey|david-gifford|david-gilbert|douglas-black|elliott-margulies|emery-bresnick|encode-awg|encode-consortium|encode-processing-pipeline|erez-lieberman|eric-lecuyer|eric-mendehall|ewan-birney|feng-yue|gene-yeo|george-stamatoyannopoulos|greg-cooper|gregory-crawford|guo-cheng-yuan|haiyan-huang|howard-chang|j-michael-cherry|jason-ernst|jason-lieb|jennifer-harrow|jeremy-luban|job-dekker|joe-ecker|john-lis|john-rinn|john-stamatoyannopoulos|jonathan-pritchard|joseph-costello|kenneth-offit|kevin-struhl|kevin-white|ladeana-hillier|laura-elnitski|len-pennacchio|leonard-lipovich|manolis-kellis|manuel-garber|mark-gerstein|mats-ljungman|matteo-pellegrini|michael-beer|michael-hoffman|michael-snyder|morgan-giddings|nadav-ahituv|paul-khavari|peggy-farnham|peter-bickel|peter-park|piero-carninci|rafael-irizarry|richard-myers|roadmap-epigenomics|robert-klein|robert-waterston|roderic-guigo|ross-hardison|scott-tenenbaum|sherman-weissman|souma-raychaudhuri|stephen-smale|sunduz-keles|susan-celniker|thomas-gingeras|thomas-tullius|tim-reddy|timothy-hubbard|ting-wang|tommi-jaakkola|unknown|valerie-reinke|vishwanath-iyer|w-james-kent|wei-wang|will-greenleaf|xiang-dong-fu|xiaole-shirley|xinshu-xiao|yi-xing|yijun-ruan|yin-shen|yoav-gilad|zhiping-weng|brian-oliver|david-macalpine|hugo-bellen|peter-cherbas|terry-orr-weaver|abby-dernburg|anthony-hyman|arshad-desai|david-miller|eric-lai|fabio-piano|frank-slack|gary-karpen|gregory-hannon|james-posakony|john-kim|julie-ahringer|kamran-ahmad|kris-gunsalus|lincoln-stein|michael-brent|michael-maccoss|mitzi-kuroda|nikolaus-rajewsky|norbert-perrimon|philip-green|sarah-elgin|steven-henikoff|steven-russell|susan-strome|vincenzo-pirrotta|MitaniLab|UofC-HGAC|wesley-hung|encode|modern|dnanexus|modencode|gencode|ggr|cgc|bloomington|dssc|kyoto|gtex|pgp|biochain|promocell|nichd):[a-zA-Z\\d_$.+!*,()'-]+(?:\\s[a-zA-Z\\d_$.+!*,()'-]+)*$",
                "type": "string",
                "title": "Lab alias"
            },
            "type": "array",
            "title": "Lab aliases",
            "default": []
        },
        "uuid": {
            "description": "The unique identifier associated with every object.",
            "comment": "Do not submit. The uuid is set by the server.",
            "requestMethod": "POST",
            "serverDefault": "uuid4",
            "permission": "import_items",
            "readonly": true,
            "format": "uuid",
            "type": "string",
            "title": "UUID"
        },
        "date_submitted": {
            "description": "The date that the experiment received all required replicates and files",
            "comment": "Do not submit. date_submitted will be assigned only by DCC personnel.",
            "readonly": true,
            "format": "date",
            "permission": "import_items",
            "type": "string",
            "title": "Date submitted"
        },
        "target": {
            "description": "For assays, such as ChIP-seq or RIP-seq, the name of the gene whose expression or product is under investigation for the experiment.",
            "comment": "See target.json for available identifiers.",
            "type": "string",
            "title": "Target",
            "linkTo": "Target"
        },
        "possible_controls": {
            "description": "Experiments that contain files that can serve as scientific controls for this experiment.",
            "uniqueItems": true,
            "items": {
                "title": "Control",
                "description": "An experiment that contains files that can serve as a scientific control for this experiment.",
                "comment": "See experiment.json for a list of available identifiers. Exact pairing of data files with their controls is done using file relationships.",
                "type": "string",
                "linkTo": "Experiment"
            },
            "type": "array",
            "title": "Controls",
            "default": []
        },
        "supersedes": {
            "description": "The experiment(s) that this experiment supersedes by virtue of being newer, better etc. than the one(s) it supersedes.",
            "uniqueItems": true,
            "items": {
                "comment": "See experiment.json for a list of available identifiers.",
                "type": "string",
                "linkTo": "Experiment"
            },
            "type": "array",
            "title": "Supersedes",
            "default": []
        },
        "related_files": {
            "description": "To be removed in a future release after data cleanup.",
            "readonly": true,
            "items": {
                "title": "Data file",
                "comment": "See file.json for available identifiers.",
                "type": "string",
                "linkTo": "File"
            },
            "permission": "import_items",
            "type": "array",
            "title": "Additional data files",
            "default": []
        },
        "internal_status": {
            "description": "The status of an experiment in the DCC process.",
            "comment": "unreviewed:wrangler has not evaluated, unrunnable:experiment requires more metadata to run, pipeline ready:experiment is ready for the pipeline, processing:pipeline is running, pipeline completed: pipeline has run through completion, requires lab review:there are QC concerns about this data, release ready:DCC feels that this is ready for release, pipeline error:pipeline run was started but failed for a reason that should be noted in pipeline_error_message",
            "readonly": true,
            "permission": "import_items",
            "enum": [
                "unreviewed",
                "no available pipeline",
                "unrunnable",
                "pipeline ready",
                "processing",
                "pipeline completed",
                "requires lab review",
                "release ready",
                "pipeline error"
            ],
            "type": "string",
            "title": "Internal status",
            "default": "unreviewed"
        },
        "pipeline_error_detail": {
            "description": "Explanation of why the experiment failed pipeline analysis.",
            "comment": "should be used on experiments with internal_status:pipeline error",
            "readonly": true,
            "permission": "import_items",
            "type": "string",
            "title": "Pipeline error message"
        },
        "original_files": {
            "type": "array",
            "title": "Original files",
            "items": {
                "linkFrom": "File.dataset",
                "type": [
                    "string",
                    "object"
                ]
            }
        },
        "assay_synonyms": {
            "calculatedProperty": true,
            "type": "array",
            "title": "Assay synonyms",
            "items": {
                "type": "string"
            }
        },
        "system_slims": {
            "calculatedProperty": true,
            "type": "array",
            "title": "System slims",
            "items": {
                "type": "string"
            }
        },
        "replication_type": {
            "description": "Calculated field that indicates the replication model",
            "calculatedProperty": true,
            "type": "string",
            "title": "Replication type"
        },
        "assay_term_id": {
            "description": "OBI (Ontology for Biomedical Investigations) ontology identifier for the assay.",
            "comment": "Calculated based on the choice of assay_term_name",
            "calculatedProperty": true,
            "type": "string",
            "title": "Assay ID"
        },
        "assay_slims": {
            "calculatedProperty": true,
            "type": "array",
            "title": "Assay type",
            "items": {
                "type": "string"
            }
        },
        "hub": {
            "calculatedProperty": true,
            "type": "string",
            "title": "Hub"
        },
        "@type": {
            "calculatedProperty": true,
            "type": "array",
            "title": "Type",
            "items": {
                "type": "string"
            }
        },
        "category_slims": {
            "calculatedProperty": true,
            "type": "array",
            "title": "Assay category",
            "items": {
                "type": "string"
            }
        },
        "biosample_synonyms": {
            "calculatedProperty": true,
            "type": "array",
            "title": "Biosample synonyms",
            "items": {
                "type": "string"
            }
        },
        "related_series": {
            "type": "array",
            "title": "Related series",
            "items": {
                "linkFrom": "Series.related_datasets",
                "type": [
                    "string",
                    "object"
                ]
            }
        },
        "type_slims": {
            "calculatedProperty": true,
            "type": "array",
            "title": "Assay type",
            "items": {
                "type": "string"
            }
        },
        "replicates": {
            "type": "array",
            "title": "Replicates",
            "items": {
                "linkFrom": "Replicate.experiment",
                "type": [
                    "string",
                    "object"
                ]
            }
        },
        "revoked_files": {
            "calculatedProperty": true,
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