view test-data/simple_test_case_v2.json @ 12:29648e5e83a8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 305061c25b6fcf54d960f17c2cad15c30fb2e26a-dirty
author iuc
date Wed, 27 Mar 2024 11:54:25 +0000
parents f803a68fc9e5
children
line wrap: on
line source

{
  "identifier": "",
  "title": "Test Case ENA upload tool",
  "description": "This investigation matches the test case of the ENA upload tool",
  "submissionDate": "",
  "publicReleaseDate": "",
  "ontologySourceReferences": [],
  "filename": "Test Case ENA upload tool.txt",
  "comments": [
    {
      "name": "ISAjson export time",
      "value": "2023-11-08T16:27:49Z"
    },
    {
      "name": "SEEK Project name",
      "value": "Test Project ENA upload Tool"
    },
    {
      "name": "SEEK Project ID",
      "value": "http://localhost:3000/single_pages/16"
    },
    {
      "name": "SEEK Investigation ID",
      "value": "27"
    }
  ],
  "publications": [],
  "people": [
    {
      "@id": "#people/4",
      "lastName": "De Pelseneer",
      "firstName": "Kevin",
      "midInitials": "",
      "email": "kevin.depelseneer@psb.ugent.be",
      "phone": "",
      "fax": "",
      "address": "",
      "affiliation": "",
      "roles": [
        {
          "termAccession": "",
          "termSource": "",
          "annotationValue": ""
        }
      ],
      "comments": [
        {
          "@id": "",
          "value": "",
          "name": ""
        }
      ]
    }
  ],
  "studies": [
    {
      "identifier": "",
      "title": "Study - Test Case ENA",
      "description": "",
      "submissionDate": "",
      "publicReleaseDate": "",
      "filename": "Study - Test Case ENA.txt",
      "comments": [
        {
          "@id": "#study_comment/25_13_49",
          "name": "ena_sample_alias_prefix",
          "value": "sample_alias_"
        },
        {
          "@id": "#study_comment/25_ae7461a0-6081-013c-9ed3-7a163e608de1",
          "name": "SEEK Study ID",
          "value": "25"
        },
        {
          "@id": "#study_comment/25_ae7467e0-6081-013c-9ed4-7a163e608de1",
          "name": "SEEK creation date",
          "value": "2023-10-20T11:12:23Z"
        }
      ],
      "publications": [],
      "people": [
        {
          "@id": "#people/4",
          "lastName": "De Pelseneer",
          "firstName": "Kevin",
          "midInitials": "",
          "email": "kevin.depelseneer@psb.ugent.be",
          "phone": "",
          "fax": "",
          "address": "",
          "affiliation": "",
          "roles": [
            {
              "termAccession": "",
              "termSource": "",
              "annotationValue": ""
            }
          ],
          "comments": [
            {
              "@id": "",
              "value": "",
              "name": ""
            }
          ]
        }
      ],
      "studyDesignDescriptors": [],
      "characteristicCategories": [
        {
          "@id": "#characteristic_category/geographic_location_(country_and/or_sea)_657",
          "characteristicType": {
            "annotationValue": "geographic location (country and/or sea)",
            "termAccession": "",
            "termSource": ""
          }
        },
        {
          "@id": "#characteristic_category/taxon_id_658",
          "characteristicType": {
            "annotationValue": "taxon_id",
            "termAccession": "",
            "termSource": ""
          }
        },
        {
          "@id": "#characteristic_category/title_662",
          "characteristicType": {
            "annotationValue": "title",
            "termAccession": "",
            "termSource": ""
          }
        },
        {
          "@id": "#characteristic_category/sample_description_663",
          "characteristicType": {
            "annotationValue": "sample_description",
            "termAccession": "",
            "termSource": ""
          }
        },
        {
          "@id": "#characteristic_category/collection_date_664",
          "characteristicType": {
            "annotationValue": "collection date",
            "termAccession": "",
            "termSource": ""
          }
        },
        {
          "@id": "#characteristic_category/accession_665",
          "characteristicType": {
            "annotationValue": "accession",
            "termAccession": "",
            "termSource": ""
          }
        },
        {
          "@id": "#characteristic_category/submission_date_666",
          "characteristicType": {
            "annotationValue": "submission date",
            "termAccession": "",
            "termSource": ""
          }
        },
        {
          "@id": "#characteristic_category/status_667",
          "characteristicType": {
            "annotationValue": "status",
            "termAccession": "",
            "termSource": ""
          }
        }
      ],
      "materials": {
        "sources": [
          {
            "@id": "#source/223",
            "name": "Source 1",
            "characteristics": [
              {
                "category": {
                  "@id": "#characteristic_category/geographic_location_(country_and/or_sea)_657"
                },
                "value": {
                  "annotationValue": "Argentina",
                  "termSource": "",
                  "termAccession": ""
                },
                "unit": {
                  "termSource": "",
                  "termAccession": "",
                  "comments": []
                }
              },
              {
                "category": {
                  "@id": "#characteristic_category/taxon_id_658"
                },
                "value": {
                  "annotationValue": "9606",
                  "termSource": "",
                  "termAccession": ""
                },
                "unit": {
                  "termSource": "",
                  "termAccession": "",
                  "comments": []
                }
              }
            ]
          },
          {
            "@id": "#source/226",
            "name": "Source 2",
            "characteristics": [
              {
                "category": {
                  "@id": "#characteristic_category/geographic_location_(country_and/or_sea)_657"
                },
                "value": {
                  "annotationValue": "Belgium",
                  "termSource": "",
                  "termAccession": ""
                },
                "unit": {
                  "termSource": "",
                  "termAccession": "",
                  "comments": []
                }
              },
              {
                "category": {
                  "@id": "#characteristic_category/taxon_id_658"
                },
                "value": {
                  "annotationValue": "646099",
                  "termSource": "",
                  "termAccession": ""
                },
                "unit": {
                  "termSource": "",
                  "termAccession": "",
                  "comments": []
                }
              }
            ]
          }
        ],
        "samples": [
          {
            "@id": "#sample/224",
            "name": "Sample 1",
            "derivesFrom": [
              {
                "@id": "#source/223"
              }
            ],
            "characteristics": [
              {
                "category": {
                  "@id": "#characteristic_category/title_662"
                },
                "value": {
                  "annotationValue": "sample_title_1",
                  "termSource": "",
                  "termAccession": ""
                },
                "unit": {
                  "termSource": "",
                  "termAccession": "",
                  "comments": []
                }
              },
              {
                "category": {
                  "@id": "#characteristic_category/sample_description_663"
                },
                "value": {
                  "annotationValue": "sample_description_1",
                  "termSource": "",
                  "termAccession": ""
                },
                "unit": {
                  "termSource": "",
                  "termAccession": "",
                  "comments": []
                }
              },
              {
                "category": {
                  "@id": "#characteristic_category/collection_date_664"
                },
                "value": {
                  "annotationValue": "2020-10-11",
                  "termSource": "",
                  "termAccession": ""
                },
                "unit": {
                  "termSource": "",
                  "termAccession": "",
                  "comments": []
                }
              },
              {
                "category": {
                  "@id": "#characteristic_category/accession_665"
                },
                "value": {
                  "annotationValue": "",
                  "termSource": "",
                  "termAccession": ""
                },
                "unit": {
                  "termSource": "",
                  "termAccession": "",
                  "comments": []
                }
              },
              {
                "category": {
                  "@id": "#characteristic_category/submission_date_666"
                },
                "value": {
                  "annotationValue": "",
                  "termSource": "",
                  "termAccession": ""
                },
                "unit": {
                  "termSource": "",
                  "termAccession": "",
                  "comments": []
                }
              },
              {
                "category": {
                  "@id": "#characteristic_category/status_667"
                },
                "value": {
                  "annotationValue": "add",
                  "termSource": "",
                  "termAccession": ""
                },
                "unit": {
                  "termSource": "",
                  "termAccession": "",
                  "comments": []
                }
              }
            ],
            "factorValues": [
              {
                "category": {
                  "@id": ""
                },
                "value": {
                  "annotationValue": "",
                  "termSource": "",
                  "termAccession": ""
                },
                "unit": {
                  "termSource": "",
                  "termAccession": "",
                  "comments": []
                }
              }
            ]
          },
          {
            "@id": "#sample/225",
            "name": "Sample 2",
            "derivesFrom": [
              {
                "@id": "#source/226"
              }
            ],
            "characteristics": [
              {
                "category": {
                  "@id": "#characteristic_category/title_662"
                },
                "value": {
                  "annotationValue": "sample_title_2",
                  "termSource": "",
                  "termAccession": ""
                },
                "unit": {
                  "termSource": "",
                  "termAccession": "",
                  "comments": []
                }
              },
              {
                "category": {
                  "@id": "#characteristic_category/sample_description_663"
                },
                "value": {
                  "annotationValue": "sample_description_2",
                  "termSource": "",
                  "termAccession": ""
                },
                "unit": {
                  "termSource": "",
                  "termAccession": "",
                  "comments": []
                }
              },
              {
                "category": {
                  "@id": "#characteristic_category/collection_date_664"
                },
                "value": {
                  "annotationValue": "2008-01-24",
                  "termSource": "",
                  "termAccession": ""
                },
                "unit": {
                  "termSource": "",
                  "termAccession": "",
                  "comments": []
                }
              },
              {
                "category": {
                  "@id": "#characteristic_category/accession_665"
                },
                "value": {
                  "annotationValue": "",
                  "termSource": "",
                  "termAccession": ""
                },
                "unit": {
                  "termSource": "",
                  "termAccession": "",
                  "comments": []
                }
              },
              {
                "category": {
                  "@id": "#characteristic_category/submission_date_666"
                },
                "value": {
                  "annotationValue": "",
                  "termSource": "",
                  "termAccession": ""
                },
                "unit": {
                  "termSource": "",
                  "termAccession": "",
                  "comments": []
                }
              },
              {
                "category": {
                  "@id": "#characteristic_category/status_667"
                },
                "value": {
                  "annotationValue": "add",
                  "termSource": "",
                  "termAccession": ""
                },
                "unit": {
                  "termSource": "",
                  "termAccession": "",
                  "comments": []
                }
              }
            ],
            "factorValues": [
              {
                "category": {
                  "@id": ""
                },
                "value": {
                  "annotationValue": "",
                  "termSource": "",
                  "termAccession": ""
                },
                "unit": {
                  "termSource": "",
                  "termAccession": "",
                  "comments": []
                }
              }
            ]
          }
        ]
      },
      "protocols": [
        {
          "@id": "#protocol/_25",
          "name": "sample collection",
          "protocolType": {
            "annotationValue": "sample collection",
            "termAccession": "",
            "termSource": ""
          },
          "description": "",
          "uri": "",
          "version": "",
          "parameters": [],
          "components": [
            {
              "componentName": "",
              "componentType": {
                "annotationValue": "",
                "termSource": "",
                "termAccession": ""
              }
            }
          ]
        },
        {
          "@id": "#protocol/_48",
          "name": "library construction",
          "protocolType": {
            "annotationValue": "library construction",
            "termAccession": "",
            "termSource": ""
          },
          "description": "",
          "uri": "",
          "version": "",
          "parameters": [
            {
              "@id": "#parameter/672",
              "parameterName": {
                "annotationValue": "design_description",
                "termAccession": "",
                "termSource": ""
              }
            },
            {
              "@id": "#parameter/674",
              "parameterName": {
                "annotationValue": "library_source",
                "termAccession": "",
                "termSource": ""
              }
            },
            {
              "@id": "#parameter/675",
              "parameterName": {
                "annotationValue": "library_strategy",
                "termAccession": "",
                "termSource": ""
              }
            },
            {
              "@id": "#parameter/676",
              "parameterName": {
                "annotationValue": "library_selection",
                "termAccession": "",
                "termSource": ""
              }
            },
            {
              "@id": "#parameter/677",
              "parameterName": {
                "annotationValue": "library_layout",
                "termAccession": "",
                "termSource": ""
              }
            },
            {
              "@id": "#parameter/678",
              "parameterName": {
                "annotationValue": "insert_size",
                "termAccession": "",
                "termSource": ""
              }
            },
            {
              "@id": "#parameter/679",
              "parameterName": {
                "annotationValue": "platform",
                "termAccession": "",
                "termSource": ""
              }
            },
            {
              "@id": "#parameter/680",
              "parameterName": {
                "annotationValue": "instrument_model",
                "termAccession": "",
                "termSource": ""
              }
            }
          ],
          "components": [
            {
              "componentName": "",
              "componentType": {
                "annotationValue": "",
                "termSource": "",
                "termAccession": ""
              }
            }
          ]
        },
        {
          "@id": "#protocol/_49",
          "name": "nucleic acid sequencing",
          "protocolType": {
            "annotationValue": "nucleic acid sequencing",
            "termAccession": "",
            "termSource": ""
          },
          "description": "",
          "uri": "",
          "version": "",
          "parameters": [],
          "components": [
            {
              "componentName": "",
              "componentType": {
                "annotationValue": "",
                "termSource": "",
                "termAccession": ""
              }
            }
          ]
        }
      ],
      "processSequence": [
        {
          "@id": "#process/sample_collection/224",
          "name": "",
          "executesProtocol": {
            "@id": "#protocol/_25"
          },
          "parameterValues": [],
          "performer": "",
          "date": "",
          "inputs": [
            {
              "@id": "#source/223"
            }
          ],
          "outputs": [
            {
              "@id": "#sample/224"
            }
          ]
        },
        {
          "@id": "#process/sample_collection/225",
          "name": "",
          "executesProtocol": {
            "@id": "#protocol/_25"
          },
          "parameterValues": [],
          "performer": "",
          "date": "",
          "inputs": [
            {
              "@id": "#source/226"
            }
          ],
          "outputs": [
            {
              "@id": "#sample/225"
            }
          ]
        }
      ],
      "assays": [
        {
          "@id": "#assay/48_49",
          "filename": "a_ena_stream_1.txt",
          "measurementType": {
            "annotationValue": "",
            "termSource": "",
            "termAccession": ""
          },
          "technologyType": {
            "annotationValue": "",
            "termSource": "",
            "termAccession": ""
          },
          "comments": [
            {
              "@id": "#assay_comment/25_48_49_14_50",
              "name": "ena_study_title",
              "value": "study_title_1"
            },
            {
              "@id": "#assay_comment/25_48_49_14_51",
              "name": "study_type",
              "value": "Transcriptome Analysis"
            },
            {
              "@id": "#assay_comment/25_48_49_14_52",
              "name": "new_study_type",
              "value": "This should not be submitted!"
            },
            {
              "@id": "#assay_comment/25_48_49_14_53",
              "name": "ena_study_abstract",
              "value": "study_abstract_1"
            },
            {
              "@id": "#assay_comment/25_48_49_14_54",
              "name": "assay_stream",
              "value": "Ena stream 1"
            },
            {
              "@id": "#assay_comment/25_48_49_14_55",
              "name": "ena_study_alias_prefix",
              "value": "study_alias_"
            },
            {
              "@id": "#assay_comment/25_48_49_14_56",
              "name": "ena_experiment_alias_prefix",
              "value": "experiment_alias_"
            },
            {
              "@id": "#assay_comment/25_48_49_14_57",
              "name": "ena_run_alias_prefix",
              "value": "run_alias_"
            },
            {
              "@id": "#assay_comment/48_49",
              "name": "linked_assays",
              "value": "[{\"id\":48,\"title\":\"Assay 1 - Test case ENA upload tool\"},{\"id\":49,\"title\":\"Assay 2 - Test case ENA upload tool\"}]"
            }
          ],
          "technologyPlatform": "",
          "characteristicCategories": [
            {
              "@id": "#characteristic_category/title_671",
              "characteristicType": {
                "annotationValue": "title",
                "termAccession": "",
                "termSource": ""
              }
            },
            {
              "@id": "#characteristic_category/library_name_673",
              "characteristicType": {
                "annotationValue": "library_name",
                "termAccession": "",
                "termSource": ""
              }
            },
            {
              "@id": "#characteristic_category/accession_681",
              "characteristicType": {
                "annotationValue": "accession",
                "termAccession": "",
                "termSource": ""
              }
            },
            {
              "@id": "#characteristic_category/submission_date_682",
              "characteristicType": {
                "annotationValue": "submission date",
                "termAccession": "",
                "termSource": ""
              }
            },
            {
              "@id": "#characteristic_category/status_683",
              "characteristicType": {
                "annotationValue": "status",
                "termAccession": "",
                "termSource": ""
              }
            }
          ],
          "materials": {
            "samples": [],
            "otherMaterials": [
              {
                "@id": "#other_material/227",
                "name": "library_construction_protocol_1",
                "type": "library_construction_protocol",
                "characteristics": [
                  {
                    "category": {
                      "@id": "#characteristic_category/title_671"
                    },
                    "value": {
                      "annotationValue": "experiment_title_1",
                      "termSource": "",
                      "termAccession": ""
                    },
                    "unit": {
                      "termSource": "",
                      "termAccession": "",
                      "comments": []
                    }
                  },
                  {
                    "category": {
                      "@id": "#characteristic_category/library_name_673"
                    },
                    "value": {
                      "annotationValue": "library_name_1",
                      "termSource": "",
                      "termAccession": ""
                    },
                    "unit": {
                      "termSource": "",
                      "termAccession": "",
                      "comments": []
                    }
                  },
                  {
                    "category": {
                      "@id": "#characteristic_category/accession_681"
                    },
                    "value": {
                      "annotationValue": "",
                      "termSource": "",
                      "termAccession": ""
                    },
                    "unit": {
                      "termSource": "",
                      "termAccession": "",
                      "comments": []
                    }
                  },
                  {
                    "category": {
                      "@id": "#characteristic_category/submission_date_682"
                    },
                    "value": {
                      "annotationValue": "",
                      "termSource": "",
                      "termAccession": ""
                    },
                    "unit": {
                      "termSource": "",
                      "termAccession": "",
                      "comments": []
                    }
                  },
                  {
                    "category": {
                      "@id": "#characteristic_category/status_683"
                    },
                    "value": {
                      "annotationValue": "add",
                      "termSource": "",
                      "termAccession": ""
                    },
                    "unit": {
                      "termSource": "",
                      "termAccession": "",
                      "comments": []
                    }
                  }
                ],
                "derivesFrom": [
                  {
                    "@id": "#sample/224"
                  }
                ]
              },
              {
                "@id": "#other_material/228",
                "name": "library_construction_protocol_2",
                "type": "library_construction_protocol",
                "characteristics": [
                  {
                    "category": {
                      "@id": "#characteristic_category/title_671"
                    },
                    "value": {
                      "annotationValue": "experiment_title_2",
                      "termSource": "",
                      "termAccession": ""
                    },
                    "unit": {
                      "termSource": "",
                      "termAccession": "",
                      "comments": []
                    }
                  },
                  {
                    "category": {
                      "@id": "#characteristic_category/library_name_673"
                    },
                    "value": {
                      "annotationValue": "library_name_2",
                      "termSource": "",
                      "termAccession": ""
                    },
                    "unit": {
                      "termSource": "",
                      "termAccession": "",
                      "comments": []
                    }
                  },
                  {
                    "category": {
                      "@id": "#characteristic_category/accession_681"
                    },
                    "value": {
                      "annotationValue": "",
                      "termSource": "",
                      "termAccession": ""
                    },
                    "unit": {
                      "termSource": "",
                      "termAccession": "",
                      "comments": []
                    }
                  },
                  {
                    "category": {
                      "@id": "#characteristic_category/submission_date_682"
                    },
                    "value": {
                      "annotationValue": "",
                      "termSource": "",
                      "termAccession": ""
                    },
                    "unit": {
                      "termSource": "",
                      "termAccession": "",
                      "comments": []
                    }
                  },
                  {
                    "category": {
                      "@id": "#characteristic_category/status_683"
                    },
                    "value": {
                      "annotationValue": "add",
                      "termSource": "",
                      "termAccession": ""
                    },
                    "unit": {
                      "termSource": "",
                      "termAccession": "",
                      "comments": []
                    }
                  }
                ],
                "derivesFrom": [
                  {
                    "@id": "#sample/225"
                  }
                ]
              },
              {
                "@id": "#other_material/229",
                "name": "library_construction_protocol_2",
                "type": "library_construction_protocol",
                "characteristics": [
                  {
                    "category": {
                      "@id": "#characteristic_category/title_671"
                    },
                    "value": {
                      "annotationValue": "experiment_title_3",
                      "termSource": "",
                      "termAccession": ""
                    },
                    "unit": {
                      "termSource": "",
                      "termAccession": "",
                      "comments": []
                    }
                  },
                  {
                    "category": {
                      "@id": "#characteristic_category/library_name_673"
                    },
                    "value": {
                      "annotationValue": "library_name_2",
                      "termSource": "",
                      "termAccession": ""
                    },
                    "unit": {
                      "termSource": "",
                      "termAccession": "",
                      "comments": []
                    }
                  },
                  {
                    "category": {
                      "@id": "#characteristic_category/accession_681"
                    },
                    "value": {
                      "annotationValue": "",
                      "termSource": "",
                      "termAccession": ""
                    },
                    "unit": {
                      "termSource": "",
                      "termAccession": "",
                      "comments": []
                    }
                  },
                  {
                    "category": {
                      "@id": "#characteristic_category/submission_date_682"
                    },
                    "value": {
                      "annotationValue": "",
                      "termSource": "",
                      "termAccession": ""
                    },
                    "unit": {
                      "termSource": "",
                      "termAccession": "",
                      "comments": []
                    }
                  },
                  {
                    "category": {
                      "@id": "#characteristic_category/status_683"
                    },
                    "value": {
                      "annotationValue": "add",
                      "termSource": "",
                      "termAccession": ""
                    },
                    "unit": {
                      "termSource": "",
                      "termAccession": "",
                      "comments": []
                    }
                  }
                ],
                "derivesFrom": [
                  {
                    "@id": "#sample/225"
                  }
                ]
              }
            ]
          },
          "processSequence": [
            {
              "@id": "#process/library_construction/227",
              "name": "",
              "executesProtocol": {
                "@id": "#protocol/_48"
              },
              "parameterValues": [
                {
                  "category": {
                    "@id": "#parameter/672"
                  },
                  "value": {
                    "annotationValue": "design_description_1",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/674"
                  },
                  "value": {
                    "annotationValue": "GENOMIC",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/675"
                  },
                  "value": {
                    "annotationValue": "WGA",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/676"
                  },
                  "value": {
                    "annotationValue": "RANDOM",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/677"
                  },
                  "value": {
                    "annotationValue": "PAIRED",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/678"
                  },
                  "value": {
                    "annotationValue": "250",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/679"
                  },
                  "value": {
                    "annotationValue": "LS454",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/680"
                  },
                  "value": {
                    "annotationValue": "454 GS 20",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                }
              ],
              "performer": "",
              "date": "",
              "inputs": [
                {
                  "@id": "#sample/224"
                }
              ],
              "outputs": [
                {
                  "@id": "#other_material/227"
                }
              ],
              "previousProcess": {
                "@id": "#process/sample_collection/227"
              },
              "nextProcess": {
                "@id": "#process/nucleic_acid_sequencing/227"
              }
            },
            {
              "@id": "#process/library_construction/228",
              "name": "",
              "executesProtocol": {
                "@id": "#protocol/_48"
              },
              "parameterValues": [
                {
                  "category": {
                    "@id": "#parameter/672"
                  },
                  "value": {
                    "annotationValue": "design_description_2",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/674"
                  },
                  "value": {
                    "annotationValue": "TRANSCRIPTOMIC",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/675"
                  },
                  "value": {
                    "annotationValue": "RNA-Seq",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/676"
                  },
                  "value": {
                    "annotationValue": "repeat fractionation",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/677"
                  },
                  "value": {
                    "annotationValue": "SINGLE",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/678"
                  },
                  "value": {
                    "annotationValue": "None",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/679"
                  },
                  "value": {
                    "annotationValue": "Illumina",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/680"
                  },
                  "value": {
                    "annotationValue": "Illumina Genome Analyzer",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                }
              ],
              "performer": "",
              "date": "",
              "inputs": [
                {
                  "@id": "#sample/225"
                }
              ],
              "outputs": [
                {
                  "@id": "#other_material/228"
                }
              ],
              "previousProcess": {
                "@id": "#process/sample_collection/228"
              },
              "nextProcess": {}
            },
            {
              "@id": "#process/library_construction/229",
              "name": "",
              "executesProtocol": {
                "@id": "#protocol/_48"
              },
              "parameterValues": [
                {
                  "category": {
                    "@id": "#parameter/672"
                  },
                  "value": {
                    "annotationValue": "design_description_3",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/674"
                  },
                  "value": {
                    "annotationValue": "TRANSCRIPTOMIC",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/675"
                  },
                  "value": {
                    "annotationValue": "RNA-Seq",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/676"
                  },
                  "value": {
                    "annotationValue": "repeat fractionation",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/677"
                  },
                  "value": {
                    "annotationValue": "SINGLE",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/678"
                  },
                  "value": {
                    "annotationValue": "None",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/679"
                  },
                  "value": {
                    "annotationValue": "Illumina",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                },
                {
                  "category": {
                    "@id": "#parameter/680"
                  },
                  "value": {
                    "annotationValue": "Illumina Genome Analyzer",
                    "termSource": "",
                    "termAccession": ""
                  },
                  "unit": {
                    "termSource": "",
                    "termAccession": "",
                    "comments": []
                  }
                }
              ],
              "performer": "",
              "date": "",
              "inputs": [
                {
                  "@id": "#sample/225"
                }
              ],
              "outputs": [
                {
                  "@id": "#other_material/229"
                }
              ],
              "previousProcess": {
                "@id": "#process/sample_collection/229"
              },
              "nextProcess": {
                "@id": "#process/nucleic_acid_sequencing/229"
              }
            },
            {
              "@id": "#process/nucleic_acid_sequencing/233_234",
              "name": "",
              "executesProtocol": {
                "@id": "#protocol/_49"
              },
              "parameterValues": [],
              "performer": "",
              "date": "",
              "inputs": [
                {
                  "@id": "#other_material/227"
                }
              ],
              "outputs": [
                {
                  "@id": "#data_file/233"
                },
                {
                  "@id": "#data_file/234"
                }
              ],
              "previousProcess": {
                "@id": "#process/library_construction/233"
              },
              "nextProcess": {}
            },
            {
              "@id": "#process/nucleic_acid_sequencing/235",
              "name": "",
              "executesProtocol": {
                "@id": "#protocol/_49"
              },
              "parameterValues": [],
              "performer": "",
              "date": "",
              "inputs": [
                {
                  "@id": "#other_material/229"
                }
              ],
              "outputs": [
                {
                  "@id": "#data_file/235"
                }
              ],
              "previousProcess": {
                "@id": "#process/library_construction/235"
              },
              "nextProcess": {}
            }
          ],
          "dataFiles": [
            {
              "@id": "#data_file/233",
              "name": "RD file 1a",
              "type": "Raw Data File",
              "comments": [
                {
                  "name": "file_name",
                  "value": "ENA_TEST2.R1.fastq.gz"
                },
                {
                  "name": "file_type",
                  "value": "fastq"
                },
                {
                  "name": "file checksum",
                  "value": ""
                },
                {
                  "name": "accession",
                  "value": ""
                },
                {
                  "name": "submission date",
                  "value": ""
                },
                {
                  "name": "status",
                  "value": "add"
                }
              ]
            },
            {
              "@id": "#data_file/234",
              "name": "RD file 1b",
              "type": "Raw Data File",
              "comments": [
                {
                  "name": "file_name",
                  "value": "ENA_TEST2.R2.fastq.gz"
                },
                {
                  "name": "file_type",
                  "value": "fastq"
                },
                {
                  "name": "file checksum",
                  "value": ""
                },
                {
                  "name": "accession",
                  "value": ""
                },
                {
                  "name": "submission date",
                  "value": ""
                },
                {
                  "name": "status",
                  "value": "add"
                }
              ]
            },
            {
              "@id": "#data_file/235",
              "name": "RD file 3",
              "type": "Raw Data File",
              "comments": [
                {
                  "name": "file_name",
                  "value": "ENA_TEST1.R1.fastq.gz"
                },
                {
                  "name": "file_type",
                  "value": "fastq"
                },
                {
                  "name": "file checksum",
                  "value": ""
                },
                {
                  "name": "accession",
                  "value": ""
                },
                {
                  "name": "submission date",
                  "value": ""
                },
                {
                  "name": "status",
                  "value": "add"
                }
              ]
            }
          ],
          "unitCategories": []
        }
      ],
      "factors": [],
      "unitCategories": []
    }
  ]
}