Add example template file

ELIXIR-Belgium · Mar 11, 2021 · 6407386 · 6407386
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commit 6407386
Showing 1 changed file with 156 additions and 0 deletions.
diff --git a/templates/template.example.json b/templates/template.example.json
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+{
+  "metadata": {
+    "name": "library_construction",
+    "group": "ena",
+    "group_order": 3,
+    "temporary_name": "3_ena_library_construction",
+    "template_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"
+  },
+  "data": [
+    {
+      "name": "protocol type",
+      "description": "type of assay or experimental step performed.",
+      "required": true,
+      "ontology": null,
+      "CVList": ["library construction"]
+    },
+    {
+      "name": "library source",
+      "description": "The LIBRARY_SOURCE specifies the type of source material that is being sequenced. (SRA 1.2 documentation)",
+      "required": true,
+      "ontology": null,
+      "CVList": [
+        "GENOMIC",
+        "GENOMIC SINGLE CELL",
+        "TRANSCRIPTOMIC",
+        "TRANSCRIPTOMIC SINGLE CELL",
+        "METAGENOMIC",
+        "METATRANSCRIPTOMIC",
+        "SYNTHETIC",
+        "VIRAL RNA",
+        "OTHER"
+      ]
+    },
+    {
+      "name": "library strategy",
+      "description": "Sequencing technique intended for this library (SRA 1.2 documentation)",
+      "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",
+        "OTHER"
+      ]
+    },
+    {
+      "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)",
+      "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"
+      ]
+    },
+    {
+      "name": "library layout",
+      "description": "specifies whether to expect single, paired, or other configuration of reads.",
+      "required": true,
+      "ontology": null,
+      "CVList": ["SINGLE", "PAIRED"]
+    },
+    {
+      "name": "library strand",
+      "description": "",
+      "required": false,
+      "ontology": null,
+      "CVList": ["first strand", "second strand", "not applicable"]
+    },
+    {
+      "name": "orientation",
+      "description": "",
+      "required": false,
+      "ontology": null,
+      "CVList": ["5'-3'-3'-5'", "5'-3'-5'-3'"]
+    },
+    {
+      "name": "organism part",
+      "description": "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. E.g Drosophila melanogaster.",
+      "required": true,
+      "ontology": {
+        "name": "efo",
+        "version": "1",
+        "description": "ontologyDescription",
+        "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000635"
+      }
+    }
+  ]
+}