Skip to content

Commit

Permalink
Merge pull request #7 from ELIXIR-Belgium/main
Browse files Browse the repository at this point in the history 
sync
  • Loading branch information
@rabuono
rabuono authored Apr 6, 2021
2 parents 09ec585 + fe743a4 commit a55a38b
Show file tree
Hide file tree
Showing 16 changed files with 2,513 additions and 82 deletions.
145 changes: 145 additions & 0 deletions templates/arrayexpress/library construction_v1.1.0.json
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,145 @@
{
"metadata": {
"name": "library construction",
"group": "arrayexpress",
"group_order": 3,
"temporary_name": "3_arrayexpress_library_construction",
"template_version": "1.1.0",
"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'"]
}
]
}
52 changes: 52 additions & 0 deletions templates/arrayexpress/nucleic acid extraction_v1.1.0.json
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,52 @@
{
"metadata": {
"name": "nucleic acid extraction",
"group": "arrayexpress",
"group_order": 2,
"temporary_name": "2_arrayexpress_nucleic_acid_extraction",
"template_version": "1.1.0",
"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": "NA",
"organism": "any",
"level": "assay"
},
"data": [
{
"name": "protocol type",
"description": "type of assay or experimental step performed.",
"required": true,
"ontology": null,
"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,
"unit": null
},
{
"name": "Extract Name",
"description": "User-defined names for each portion of extracted material.",
"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.",
"required": true,
"ontology": null,
"CVList": [
"whole organism",
"organism part",
"RNA",
"DNA",
"cell"
]
}
]
}
115 changes: 115 additions & 0 deletions templates/arrayexpress/nucleic acid sequencing_v1.1.0.json
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,115 @@
{
"metadata": {
"name": "nucleic acid sequencing",
"group": "arrayexpress",
"group_order": 4,
"temporary_name": "4_arrayexpress_nucleic_acid_sequencing",
"template_version": "1.1.0",
"isa_config": "genome_seq_default_v2015-07-02",
"isa_measurement_type": "genome sequencing",
"isa_technology_type": "nucleotide sequencing",
"isa_protocol_type": "nucleic acid sequencing",
"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": ["nucleic acid sequencing"]
},
{
"name": "sequencing instrument",
"description": "a parameter to report the sequencing instrument model and make",
"required": "false",
"ontology": null,
"CVList": [
"454 GS",
"454 GS 20",
"454 GS FLX",
"454 GS FLX+",
"454 GS FLX Titanium",
"454 GS Junior",
"HiSeq X Five",
"HiSeq X Ten",
"Illumina Genome Analyzer",
"Illumina Genome Analyzer II",
"Illumina Genome Analyzer IIx",
"Illumina HiScanSQ",
"Illumina HiSeq 1000",
"Illumina HiSeq 1500",
"Illumina HiSeq 2000",
"Illumina HiSeq 2500",
"Illumina HiSeq 3000",
"Illumina HiSeq 4000",
"Illumina iSeq 100",
"Illumina MiSeq",
"Illumina MiniSeq",
"Illumina NovaSeq 6000",
"NextSeq 500",
"NextSeq 550",
"PacBio RS",
"PacBio RS II",
"Sequel",
"Ion Torrent PGM",
"Ion Torrent Proton",
"Ion Torrent S5",
"Ion Torrent S5 XL",
"AB 3730xL Genetic Analyzer",
"AB 3730 Genetic Analyzer",
"AB 3500xL Genetic Analyzer",
"AB 3500 Genetic Analyzer",
"AB 3130xL Genetic Analyzer",
"AB 3130 Genetic Analyzer",
"AB 310 Genetic Analyzer",
"MinION",
"GridION",
"PromethION",
"BGISEQ-500",
"DNBSEQ-T7",
"DNBSEQ-G400",
"DNBSEQ-G50",
"DNBSEQ-G400 FAST",
"unspecified"
]
},
{
"name": "quality scorer",
"description": "Name and version of the quality scoring software.",
"required": "false",
"ontology": null,
"CVList": null
},
{
"name": "base caller",
"description": "Name and version of the base or color calling software.",
"required": "false",
"ontology": null,
"CVList": null
},
{
"name": "Assay Name",
"description": "User-defined name for an assay.",
"required": true,
"ontology": null,
"CVList": null
},
{
"name": "Technology type",
"description": "",
"required": true,
"ontology": null,
"CVList": ["sequencing assay"]
},
{
"name": "Raw Data File",
"description": "or Array Data File: Name (or URI) of the raw data file generated by an assay.",
"required": true,
"ontology": null,
"CVList": null
}
]
}
Loading

0 comments on commit a55a38b

Please sign in to comment.