{
  "$schema": "http://json-schema.org/draft-04/schema#",
  "$id": "https://schema.humancellatlas.org/type/protocol/sequencing/2.0.1/library_preparation_protocol",
  "description": "Information about how a sequencing library was created.",
  "additionalProperties": false,
  "required": [
    "describedBy",
    "schema_type",
    "protocol_core",
    "end_bias",
    "library_construction_approach",
    "strand",
    "input_nucleic_acid_molecule"
  ],
  "title": "library_preparation_protocol",
  "type": "object",
  "properties": {
    "describedBy": {
      "description": "The URL reference to the schema.",
      "type": "string",
      "pattern": "https://schema.humancellatlas.org/type/protocol/sequencing/[0-9]{1,}.[0-9]{1,}.[0-9]{1,}/library_preparation_protocol"
    },
    "schema_version": {
      "description": "The version number of the schema in major.minor.patch format.",
      "type": "string",
      "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$",
      "example": "4.6.1"
    },
    "schema_type": {
      "description": "The type of the metadata schema entity.",
      "type": "string",
      "enum": [
        "protocol"
      ]
    },
    "protocol_core": {
      "description": "Core protocol-level information.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/core/protocol/5.1.0/protocol_core"
    },
    "cell_barcode": {
      "description": "Information about cell identifier barcode.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/module/process/sequencing/5.1.0/barcode",
      "user_friendly": "Cell barcode"
    },
    "input_nucleic_acid_molecule": {
      "description": "Starting nucleic acid molecule isolated for sequencing. Should be a child term of https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0004446.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/module/ontology/5.1.1/biological_macromolecule_ontology",
      "user_friendly": "Input nucleic acid molecule"
    },
    "library_construction_approach": {
      "description": "The general approach for sequencing library construction. Should be a child term of EFO - library preparation",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/module/ontology/1.0.0/library_construction_ontology",
      "user_friendly": "Library construction approach"
    },
    "library_construction_kit": {
      "description": "Name of kit used to construct the sequencing library.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/module/process/5.2.0/purchased_reagents",
      "user_friendly": "Library construction kit"
    },
    "nucleic_acid_conversion_kit": {
      "description": "Name of kit used to convert RNA to DNA for sequencing.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/module/process/5.2.0/purchased_reagents",
      "user_friendly": "Nucleic acid conversion kit"
    },
    "end_bias": {
      "description": "The type of tag or end bias the library has. Must be one of 3 prime tag, 3 prime end bias, 5 prime tag, 5 prime end bias, or full length.",
      "type": "string",
      "example": "3_prime_tag",
      "enum": [
        "3 prime tag",
        "3 prime end bias",
        "5 prime tag",
        "5 prime end bias",
        "full length"
      ],
      "user_friendly": "End bias"
    },
    "primer": {
      "description": "Primer used for cDNA synthesis from RNA. Must be either poly-dT or random.",
      "type": "string",
      "enum": [
        "poly-dT",
        "random"
      ],
      "user_friendly": "Primer"
    },
    "strand": {
      "description": "Library strandedness. Must be one of first, second, or unstranded.",
      "type": "string",
      "enum": [
        "first",
        "second",
        "unstranded"
      ],
      "example": "unstranded",
      "user_friendly": "Strand"
    },
    "spike_in_kit": {
      "description": "Name of spike-in kit.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/module/process/5.2.0/purchased_reagents",
      "user_friendly": "Spike-in kit"
    },
    "spike_in_dilution": {
      "description": "Dilution of spike-in.",
      "type": "integer",
      "maximum": 1000000,
      "minimum": 1,
      "user_friendly": "Spike-in dilution"
    },
    "umi_barcode": {
      "description": "Information about unique molecular identifier (UMI) barcode sequences.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/module/process/sequencing/5.1.0/barcode",
      "user_friendly": "UMI barcode"
    },
    "library_preamplification_method": {
      "description": "The method used to amplify RNA prior to adaptor ligation. Should be a child term of EFO - nucleic acid preparation",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/module/ontology/1.0.0/library_amplification_ontology",
      "user_friendly": "Library pre-amplification method"
    },
    "cdna_library_amplification_method": {
      "description": "The method used to amplify a cDNA library prior to sequencing. Should be a child term of EFO - nucleic acid preparation",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/module/ontology/1.0.0/library_amplification_ontology",
      "user_friendly": "cDNA library amplification method"
    },
    "protocol_type": {
      "description": "The type of protocol. Should be a child term of https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0002694.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/module/ontology/5.1.0/process_type_ontology",
      "user_friendly": "protocol type"
    }
  }
}