Ena upload tool

templates/ena_upload_tool/archive/library construction.json

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+{
+  "metadata": {
+    "name": "library construction ENA Upload Tool",
+    "group": "ena modified for upload tool",
+    "group_order": 4,
+    "temporary_name": "4_ena_custom_library_construction",
+    "version": "1.0.0",
+    "isa_config": "genome_seq_default_v2015-07-02",
+    "isa_measurement_type": "genome sequencing",
+    "isa_technology_type": "nucleotide sequencing",
+    "isa_protocol_type": "library construction",
+    "repo_schema_id": "ENA General experiment information 2021",
+    "organism": "any",
+    "level": "assay - material"
+  },
+  "data": [
+    {
+      "iri": null,
+      "name": "Input",
+      "description": "Existing Samples in DataHub that represent input for this protocol.",
+      "dataType": "SEEK Sample Multi",
+      "required": "true",
+      "isaTag": null
+    },
+    {
+      "iri": null,
+      "name": "library construction",
+      "description": "type of assay or experimental step performed.",
+      "required": true,
+      "ontology": null,
+      "dataType": "String", //need to be autofilled with name of selected SOP for that block
+      "CVList": null, //SOPtittle
+      "isaTag": "protocol"
+    },
+    {
+      "iri": null,
+      "name": "library_construction_protocol",
+      "description": "Free form text describing the protocol by which the sequencing library was constructed.",
+      "dataType": "String",
+      "required": false,
+      "ontology": null,
+      "isaTag": "parameter_value"
+    },
+    {
+      "iri": null,
+      "name": "title",
+      "description": "Short text that can be used to call out experiment records in searches or in displays.",
+      "required": true,
+      "ontology": null,
+      "dataType": "String",
+      "CVList": null,
+      "isaTag": "otherMaterial_characteristic"
+    },
+    {
+      "iri": null,
+      "name": "design_description",
+      "description": "The design of the library including details of how it was constructed. ",
+      "required": true,
+      "ontology": null,
+      "dataType": "String",
+      "CVList": null,
+      "isaTag": "parameter_value"
+    },
+    {
+      "iri": null,
+      "name": "library_source",
+      "description": "The LIBRARY_SOURCE specifies the type of source material that is being sequenced. (SRA 1.2 documentation)",
+      "dataType": "Controlled Vocabulary",
+      "required": true,
+      "ontology": null,
+      "CVList": [
+        "GENOMIC",
+        "GENOMIC SINGLE CELL",
+        "TRANSCRIPTOMIC",
+        "TRANSCRIPTOMIC SINGLE CELL",
+        "METAGENOMIC",
+        "METATRANSCRIPTOMIC",
+        "SYNTHETIC",
+        "VIRAL RNA",
+        "OTHER"
+      ],
+      "isaTag": "parameter_value"
+    },
+    {
+      "iri": null,
+      "name": "library_strategy",
+      "description": "Sequencing technique intended for this library (SRA 1.2 documentation)",
+      "dataType": "Controlled Vocabulary",
+      "required": true,
+      "ontology": null,
+      "CVList": [
+        "WGS",
+        "WGA",
+        "WXS",
+        "RNA-Seq",
+        "ssRNA-seq",
+        "miRNA-Seq",
+        "ncRNA-Seq",
+        "FL-cDNA",
+        "EST",
+        "Hi-C",
+        "ATAC-seq",
+        "WCS",
+        "RAD-Seq",
+        "CLONE",
+        "POOLCLONE",
+        "AMPLICON",
+        "CLONEEND",
+        "FINISHING",
+        "ChIP-Seq",
+        "MNase-Seq",
+        "DNase-Hypersensitivity",
+        "Bisulfite-Seq",
+        "CTS",
+        "MRE-Seq",
+        "MeDIP-Seq",
+        "MBD-Seq",
+        "Tn-Seq",
+        "VALIDATION",
+        "FAIRE-seq",
+        "SELEX",
+        "RIP-Seq",
+        "ChIA-PET",
+        "Synthetic-Long-Read",
+        "Targeted-Capture",
+        "Tethered Chromatin Conformation Capture",
+        "OTHER",
+        "NOMe-Seq",
+        "ChM-Seq",
+        "GBS"
+      ],
+      "isaTag": "parameter_value"
+    },
+    {
+      "iri": null,
+      "name": "library_selection",
+      "description": "Whether any method was used to select for or against, enrich, or screen the material being sequenced. (SRA 1.2 documentation)",
+      "dataType": "Controlled Vocabulary",
+      "required": true,
+      "ontology": null,
+      "CVList": [
+        "RANDOM",
+        "PCR",
+        "RANDOM PCR",
+        "RT-PCR",
+        "HMPR",
+        "MF",
+        "repeat fractionation",
+        "size fractionation",
+        "MSLL",
+        "cDNA",
+        "cDNA_randomPriming",
+        "cDNA_oligo_dT",
+        "PolyA",
+        "Oligo-dT",
+        "Inverse rRNA",
+        "Inverse rRNA selection",
+        "ChIP",
+        "ChIP-Seq",
+        "MNase",
+        "DNase",
+        "Hybrid Selection",
+        "Reduced Representation",
+        "Restriction Digest",
+        "5-methylcytidine antibody",
+        "MBD2 protein methyl-CpG binding domain",
+        "CAGE",
+        "RACE",
+        "MDA",
+        "padlock probes capture method",
+        "other",
+        "unspecified"
+      ],
+      "isaTag": "parameter_value"
+    },
+    {
+      "iri": null,
+      "name": "library_layout",
+      "description": "specifies whether to expect single, paired, or other configuration of reads. In the case of paired reads, information about the relative distance and orientation is specified.",
+      "dataType": "Controlled Vocabulary",
+      "required": false,
+      "ontology": null,
+      "CVList": [
+        "SINGLE",
+        "PAIRED"
+      ],
+      "isaTag": "parameter_value"
+    },
+    {
+      "iri": null,
+      "name": "insert_size",
+      "description": "Insert size for paired reads.",
+      "dataType": "String",
+      "required": false,
+      "ontology": null,
+      "isaTag": "parameter_value"
+    },
+    {
+      "iri": null,
+      "name": "library_name",
+      "description": "Name given to the generated library",
+      "dataType": "String",
+      "title": true,
+      "required": true,
+      "ontology": null,
+      "CVList": null,
+      "isaTag": "otherMaterial"
+    },
+    {
+      "iri": null,
+      "name": "submission date",
+      "description": "Date in which experiment was submitted to ENA.",
+      "dataType": "String",
+      "required": false,
+      "ontology": null,
+      "CVList": null,
+      "isaTag": "otherMaterial_characteristic"
+    },
+    {
+      "iri": null,
+      "name": "status",
+      "description": "Status of submission to ENA.",
+      "dataType": "String",
+      "required": false,
+      "ontology": null,
+      "CVList": [
+        "add",
+        "added",
+        "modify",
+        "modified",
+        "cancel",
+        "cancelled",
+        "release",
+        "released"
+      ],
+      "isaTag": "otherMaterial_characteristic"
+    },
+    {
+      "iri": null,
+      "name": "accession",
+      "description": "ENA experiment accession code. Provided by ENA after submission.",
+      "dataType": "String",
+      "required": false,
+      "ontology": null,
+      "CVList": null,
+      "isaTag": "otherMaterial_characteristic"
+    }
+  ]
+}

templates/ena_upload_tool/archive/nucleic acid extraction.json

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+{
+  "metadata": {
+    "name": "nucleic acid extraction ENA Upload Tool",
+    "group": "ena modified for upload tool",
+    "group_order": 3,
+    "temporary_name": "3_ena_custom_nucleic_acid_extraction",
+    "version": "1.0.0",
+    "isa_config": "genome_seq_default_v2015-07-02",
+    "isa_measurement_type": "genome sequencing",
+    "isa_technology_type": "nucleotide sequencing",
+    "isa_protocol_type": "nucleic acid extraction",
+    "repo_schema_id": "ENA General experiment information 2021",
+    "organism": "any",
+    "level": "assay - material"
+  },
+  "data": [
+    {
+      "iri": null,
+      "name": "Input",
+      "description": "Existing Samples in DataHub that represent input for this protocol.",
+      "dataType": "SEEK Sample Multi",
+      "required": "true",
+      "isaTag": null
+    },
+    {
+      "iri": null,
+      "name": "nucleic acid extraction",
+      "description": "type of assay or experimental step performed.",
+      "required": true,
+      "ontology": null,
+      "dataType": "String", //need to be autofilled with name of selected SOP for that block
+      "CVList": , //SOPtittle
+      "isaTag": "protocol"
+    },
+    {
+      "iri": null,
+      "name": "sample volume or weight for DNA extraction",
+      "description": "Volume (mL) or weight (g) of sample processed for DNA extraction",
+      "required": false,
+      "ontology": null,
+      "dataType": "String", // Original regex "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?",
+      "unit": null, //Original unit options ["mL","g"],
+      "isaTag": "parameter_value"
+    },
+    {
+      "iri": null,
+      "name": "Extract Name",
+      "description": "User-defined names for each portion of extracted material.",
+      "dataType": "String",
+      "title": true,
+      "required": true,
+      "ontology": null,
+      "CVList": null,
+      "isaTag": "otherMaterial"
+    }
+  ]
+}