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Merge pull request #28 from rabuono/dev
Update of ENA and ArrayExpress Templates
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| String | ||
| Date time | ||
| Date | ||
| Real number | ||
| Integer | ||
| Web link | ||
| Email address | ||
| Text | ||
| ChEBI | ||
| ECN | ||
| MetaNEtX chemical | ||
| MetaNEtX reaction | ||
| MetaNEtX compartment | ||
| InChi | ||
| Boolean | ||
| SEEK Strain | ||
| SEEK Sample | ||
| SEEK Sample Multi | ||
| Controlled Vocabulary | ||
| URI | ||
| DOI | ||
| NCBI ID | ||
| SEEK Data file |
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140 changes: 140 additions & 0 deletions
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templates/arrayexpress/library construction_v1.0.0.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,140 @@ | ||
| { | ||
| "meta": { "measurement": "genome sequencing", "technology": "nucleotide sequencing" }, | ||
| "data": { | ||
| "library construction": [ | ||
| { | ||
| "name": "protocol type", | ||
| "description": "type of assay or experimental step performed.", | ||
| "required": true, | ||
| "ontology": null, | ||
| "dataType": "string", | ||
| "CVList": ["library construction"] | ||
| }, | ||
| { | ||
| "name": "library source", | ||
| "description": "The LIBRARY_SOURCE specifies the type of source material that is being sequenced. (SRA 1.2 documentation)", | ||
| "dataType": "List", | ||
| "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)", | ||
| "dataType": "List", | ||
| "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)", | ||
| "dataType": "List", | ||
| "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.", | ||
| "dataType": "List", | ||
| "required": true, | ||
| "ontology": null, | ||
| "CVList": ["SINGLE", "PAIRED"] | ||
| }, | ||
| { | ||
| "name": "library strand", | ||
| "description": "", | ||
| "dataType": "List", | ||
| "required": false, | ||
| "ontology": null, | ||
| "CVList": ["first strand", "second strand", "not applicable"] | ||
| }, | ||
| { | ||
| "name": "orientation", | ||
| "description": "", | ||
| "dataType": "List", | ||
| "required": false, | ||
| "ontology": null, | ||
| "CVList": ["5'-3'-3'-5'", "5'-3'-5'-3'"] | ||
| } | ||
| ] | ||
| } | ||
| } |
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46 changes: 46 additions & 0 deletions
46
templates/arrayexpress/nucleic acid extraction_v1.0.0.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,46 @@ | ||
| { | ||
| "meta": { "measurement": "genome sequencing", "technology": "nucleotide sequencing" }, | ||
| "data": { | ||
| "nucleic acid extraction": [ | ||
| { | ||
| "name": "protocol type", | ||
| "description": "type of assay or experimental step performed.", | ||
| "required": true, | ||
| "ontology": null, | ||
| "dataType": "string", | ||
| "CVList": ["nucleic acid extraction"] | ||
| }, | ||
| { | ||
| "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": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?", | ||
| "unit": null //need to add unit options here | ||
| }, | ||
| { | ||
| "name": "Extract Name", | ||
| "description": "User-defined names for each portion of extracted material.", | ||
| "dataType": "String", | ||
| "required": true, | ||
| "ontology": null, | ||
| "CVList": null | ||
| }, | ||
| { | ||
| "name": "Material type", | ||
| "description": "This column contains terms describing the type of each material, for examples: whole organism, organism part, cell, total RNA.", | ||
| "dataType": "List", | ||
| "required": true, | ||
| "ontology": null, | ||
| "CVList": [ | ||
| "whole organism", | ||
| "organism part", | ||
| "RNA", | ||
| "DNA", | ||
| "cell" | ||
| ] | ||
| } | ||
| ] | ||
|
|
||
| } | ||
| } |
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