Replicate

Schema for submitting an experimental replicate.

{
    "title": "Replicate",
    "description": "Schema for submitting an experimental replicate.",
    "id": "/profiles/replicate.json",
    "$schema": "http://json-schema.org/draft-04/schema#",
    "type": "object",
    "required": [
        "experiment",
        "biological_replicate_number",
        "technical_replicate_number"
    ],
    "approvalRequired": [
        "library"
    ],
    "identifyingProperties": [
        "uuid",
        "aliases"
    ],
    "additionalProperties": false,
    "mixinProperties": [
        {
            "$ref": "mixins.json#/schema_version"
        },
        {
            "$ref": "mixins.json#/uuid"
        },
        {
            "$ref": "mixins.json#/aliases"
        },
        {
            "$ref": "mixins.json#/standard_status"
        },
        {
            "$ref": "mixins.json#/submitted"
        },
        {
            "$ref": "mixins.json#/notes"
        }
    ],
    "dependencies": {
        "rbns_protein_concentration": [
            "rbns_protein_concentration_units"
        ],
        "rbns_protein_concentration_units": [
            "rbns_protein_concentration"
        ]
    },
    "properties": {
        "notes": {
            "type": "string",
            "readonly": true,
            "comment": "Do not submit. A place for the DCC to keep information that does not have a place in the schema.",
            "permission": "import_items",
            "pattern": "^(\\S+(\\s|\\S)*\\S+|\\S)$",
            "title": "Notes",
            "description": "DCC internal notes."
        },
        "submitted_by": {
            "type": "string",
            "readonly": true,
            "comment": "Do not submit. The user that created the object is assigned by the server.",
            "permission": "import_items",
            "serverDefault": "userid",
            "linkTo": "User",
            "rdfs:subPropertyOf": "dc:creator",
            "title": "Submitted by"
        },
        "date_created": {
            "type": "string",
            "readonly": true,
            "comment": "Do not submit. The date the object is created is assigned by the server.",
            "permission": "import_items",
            "rdfs:subPropertyOf": "dc:created",
            "title": "Date created",
            "serverDefault": "now",
            "anyOf": [
                {
                    "format": "date-time"
                },
                {
                    "format": "date"
                }
            ],
            "description": "The date the object was created."
        },
        "status": {
            "type": "string",
            "default": "in progress",
            "title": "Status",
            "enum": [
                "in progress",
                "deleted",
                "released",
                "preliminary",
                "proposed",
                "archived",
                "revoked"
            ]
        },
        "aliases": {
            "type": "array",
            "default": [],
            "uniqueItems": true,
            "comment": "The purpose of this field is to provide a link into the lab LIMS and to facilitate shared objects.",
            "description": "Lab specific identifiers to reference an object.",
            "title": "Lab aliases",
            "items": {
                "type": "string",
                "comment": "Current convention is colon separated lab name and lab identifier. (e.g. john-doe:42).",
                "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_$.+!*,()'-]+(?:\\s[a-zA-Z\\d_$.+!*,()'-]+)*$",
                "uniqueKey": "alias",
                "title": "Lab alias",
                "description": "A lab specific identifier to reference an object."
            }
        },
        "uuid": {
            "type": "string",
            "readonly": true,
            "comment": "Do not submit. The uuid is set by the server.",
            "permission": "import_items",
            "requestMethod": "POST",
            "format": "uuid",
            "title": "UUID",
            "serverDefault": "uuid4",
            "description": "The unique identifier associated with every object."
        },
        "schema_version": {
            "type": "string",
            "default": "8",
            "comment": "Do not submit. The version used to validate the object is set by the server. The default should be set to the current version.",
            "requestMethod": [],
            "pattern": "^\\d+(\\.\\d+)*$",
            "title": "Schema Version",
            "description": "The version of the JSON schema that the server uses to validate the object."
        },
        "antibody": {
            "type": "string",
            "linkTo": "AntibodyLot",
            "title": "Antibody",
            "description": "For Immunoprecipitation assays, the antibody used.",
            "comment": "See antibody_lot.json for available identifiers."
        },
        "biological_replicate_number": {
            "type": "integer",
            "default": 1,
            "title": "Biological replicate",
            "description": "Data collection under the same methods using a different biological source, measuring the variability in the biological source."
        },
        "technical_replicate_number": {
            "type": "integer",
            "default": 1,
            "title": "Technical replicate",
            "description": "Data collection under the same methods using the same biological source, measuring the variability in the method."
        },
        "experiment": {
            "type": "string",
            "linkTo": "Experiment",
            "title": "Experiment",
            "description": "The experiment the replicate belongs to.",
            "comment": "See experiment.json for available identifiers."
        },
        "library": {
            "type": "string",
            "linkTo": "Library",
            "title": "Library",
            "description": "The nucleic acid library used in this replicate.",
            "comment": "See library.json for available identifiers."
        },
        "rbns_protein_concentration": {
            "type": "integer",
            "title": "RBNS protein concentration",
            "description": "For use only with RNA Bind-n-Seq replicates to indicate the protein concentration.",
            "comment": "Only for use with RBNS replicates."
        },
        "rbns_protein_concentration_units": {
            "type": "string",
            "enum": [
                "nM",
                "pM"
            ],
            "title": "RBNS protein concentration units",
            "comment": "The unit for the dependant rbns_protein_concentration."
        },
        "@id": {
            "type": "string",
            "calculatedProperty": true,
            "title": "ID"
        },
        "@type": {
            "type": "array",
            "calculatedProperty": true,
            "title": "Type",
            "items": {
                "type": "string"
            }
        }
    },
    "boost_values": {
        "experiment.accession": 1,
        "experiment.alternate_accessions": 1,
        "aliases": 1,
        "library.biosample.accession": 1,
        "library.biosample.alternate_accessions": 1,
        "library.biosample.aliases": 1,
        "library.biosample.subcellular_fraction_term_name": 1,
        "library.biosample.donor.accession": 1,
        "library.biosample.donor.alternate_accessions": 1,
        "library.biosample.donor.organism.name": 1,
        "antibody.accession": 1,
        "antibody.alternate_accessions": 1,
        "antibody.lot_id": 1,
        "antibody.lot_id_alias": 1,
        "antibody.product_id": 1,
        "antibody.aliases": 1
    },
    "changelog": "/profiles/changelogs/replicate.md",
    "@type": [
        "JSONSchema"
    ]
}