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update dataType
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@rabuono
rabuono committed Sep 28, 2021
1 parent 8c8a172 commit 0c381a9
Showing 1 changed file with 32 additions and 31 deletions.
63 changes: 32 additions & 31 deletions templates/ena/source_all_organisms_v1.0.0.json
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,8 @@
"name": "Source Name",
"description": "Sources are considered as the starting biological material used in a study.",
"dataType": "String",
"required": "true",
"title": true,
"required": true,
"isaTag": "source"
},
{
Expand All @@ -44,7 +45,7 @@
"iri": null,
"name": "cell_type",
"description": "cell type from which the sample was obtained",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -53,7 +54,7 @@
"iri": null,
"name": "dev_stage",
"description": "if the sample was obtained from an organism in a specific developmental stage, it is specified with this qualifier",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -62,7 +63,7 @@
"iri": null,
"name": "germline",
"description": "the sample described presented in the entry has not undergone somatic genomic rearrangement as part of an adaptive immune response; it is the unrearranged molecule that was inherited from the parental germline",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -71,7 +72,7 @@
"iri": null,
"name": "tissue_lib",
"description": "tissue library from which sample was obtained",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -80,7 +81,7 @@
"iri": null,
"name": "tissue_type",
"description": "tissue type from which the sample was obtained",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -89,7 +90,7 @@
"iri": null,
"name": "collection_date",
"description": "date that the specimen was collected",
"dataType": "^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$",
"dataType": "String", //original Regex "^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -98,7 +99,7 @@
"iri": null,
"name": "isolation_source",
"description": "describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -107,7 +108,7 @@
"iri": null,
"name": "lat_lon",
"description": "geographical coordinates of the location where the specimen was collected",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -116,7 +117,7 @@
"iri": null,
"name": "collected_by",
"description": "name of persons or institute who collected the specimen",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -125,7 +126,7 @@
"iri": null,
"name": "geographic location (country and/or sea)",
"description": "The geographical origin of the sample as defined by the country or sea. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).",
"dataType": "string",
"dataType": "Controlled Vocabulary",
"required": false,
"ontology": null,
"CVList": [
Expand Down Expand Up @@ -415,7 +416,7 @@
"iri": null,
"name": "geographic location (region and locality)",
"description": "The geographical origin of the sample as defined by the specific region name followed by the locality name.",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -424,7 +425,7 @@
"iri": null,
"name": "identified_by",
"description": "name of the expert who identified the specimen taxonomically",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -433,7 +434,7 @@
"iri": null,
"name": "environmental_sample",
"description": "identifies sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism",
"dataType": "string",
"dataType": "Controlled Vocabulary",
"required": false,
"ontology": null,
"CVList": ["No", "Yes"],
Expand All @@ -443,7 +444,7 @@
"iri": null,
"name": "mating_type",
"description": "mating type of the organism from which the sequence was obtained; mating type is used for prokaryotes, and for eukaryotes that undergo meiosis without sexually dimorphic gametes",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -452,7 +453,7 @@
"iri": null,
"name": "sex",
"description": "sex of the organism from which the sample was obtained",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -461,7 +462,7 @@
"iri": null,
"name": "lab_host",
"description": "scientific name of the laboratory host used to propagate the source organism from which the sample was obtained",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -470,7 +471,7 @@
"iri": null,
"name": "host scientific name",
"description": "Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -479,7 +480,7 @@
"iri": null,
"name": "bio_material",
"description": "identifier for the biological material from which the sample was obtained, with optional institution code and collection code for the place where it is currently stored.",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -488,7 +489,7 @@
"iri": null,
"name": "culture_collection",
"description": "institution code and identifier for the culture from which the sample was obtained, with optional collection code.",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -497,7 +498,7 @@
"iri": null,
"name": "specimen_voucher",
"description": "identifier for the specimen from which the sample was obtained",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -506,7 +507,7 @@
"iri": null,
"name": "cultivar",
"description": "cultivar (cultivated variety) of plant from which sample was obtained",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -515,7 +516,7 @@
"iri": null,
"name": "ecotype",
"description": "a population within a given species displaying genetically based, phenotypic traits that reflect adaptation to a local habitat.",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -524,7 +525,7 @@
"iri": null,
"name": "isolate",
"description": "individual isolate from which the sample was obtained",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -533,7 +534,7 @@
"iri": null,
"name": "sub_species",
"description": "name of sub-species of organism from which sample was obtained",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -542,7 +543,7 @@
"iri": null,
"name": "variety",
"description": "variety (= varietas, a formal Linnaean rank) of organism from which sample was derived.",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -551,7 +552,7 @@
"iri": null,
"name": "sub_strain",
"description": "name or identifier of a genetically or otherwise modified strain from which sample was obtained, derived from a parental strain (which should be annotated in the strain field; sub_strain from which sample was obtained",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -560,7 +561,7 @@
"iri": null,
"name": "cell_line",
"description": "cell line from which the sample was obtained",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -569,7 +570,7 @@
"iri": null,
"name": "serotype",
"description": "serological variety of a species characterized by its antigenic properties",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -578,7 +579,7 @@
"iri": null,
"name": "serovar",
"description": "serological variety of a species (usually a prokaryote) characterized by its antigenic properties",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand All @@ -587,7 +588,7 @@
"iri": null,
"name": "strain",
"description": "Name of the strain from which the sample was obtained.",
"dataType": "string",
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
Expand Down

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