Samples Mapping (deprecated)
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SubtitleA specification for describing Samples in life sciencesEMBL-EBI BioSamplesMIABIS<USE CASE NAME>
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DescriptionThe Samples specification aims to tackle the problem of sample identification and linking by providing a mechanism within Bioschemas for describing samples in terms of their known identifiers (specifically, public accessions vs biobank names), their links to datasets in the public domain, and a general framework for expressing metadata attributeshttps://www.ebi.ac.uk/biosamples/samples/SAMEA2340790https://github.com/MIABIS/miabis/wiki/Data-describing-Sample<USE CASE URL>
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<Tony Burdett, Melanie Courtot, Luca Cherubin><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...>
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schema.orgbioschemas
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Property
Expected Type
DescriptionBSC DescriptionMarginalityCardinality
Controlled Vocabulary
Name
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCase
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Extends BioChemEntity
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additionalTypeURLadditionalType is defined by BioChemEntity and the value specifies the subtype. The value here is expected to be http://semanticscience.org/resource/SIO_001050 (sio:Sample) OptionalONE
http://semanticscience.org/resource/SIO_001050
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identifierTextExpected to be be a biosamples accession number OptionalONE
SAMEA2340790
Sample ID
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nameTextAn 'local' identifier assigned to each sample by the owner resource e.g. a BiobankOptionalONEERS398461
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descriptionText
A description of the sample in free text. Ideally should not contain information that could be better expressed as key/value pairs
OptionalONE
84 Mixed species samples from ENA SRA
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urlURLAn access URL for this sample, either in BioSamples or in a Biobank or elsewhere OptionalMANY
http://www.ebi.ac.uk/biosamples/samples/SAMEA2340790
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datasetUrlURLAn access URL that provides a link to a dataset that contains data about this sample OptionalMANY
http://www.ebi.ac.uk/ena/data/view/ERS398461
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additionalPropertyA property-value pair representing an additional characteristics of the entity, e.g. “Organism: Homo sapiens” or “tissue type: leaf”OptionalMANY
"additionalProperty" : [ {
"name" : "organism",
"value" : "Solanum lycopersicum",
"code" : {
"codeValue" : "http://purl.obolibrary.org/obo/NCBITaxon_4081",
"codingSystem" : null,
"@context" : "http://schema.org",
"@type" : "MedicalCode"
},
"@context" : "http://schema.org",
"@type" : "PropertyValue"
}, {
"name" : "synonym",
"value" : "S.lycLA4451_1",
"code" : null,
"@context" : "http://schema.org",
"@type" : "PropertyValue"
}, {
"name" : "synonym",
"value" : "Solanum lycopersicum; Solanum lycopersicum cv Black Cherry LA4451(?)",
"code" : null,
"@context" : "http://schema.org",
"@type" : "PropertyValue"
} ]
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PropertyValue (proposed usage)
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nameTextThe name (or 'key') of the property (see schema.org definition). Ideally this is commonly used or qualified by namespace, but may be a local property nameOptionalONE
Material type, Storage temperature, Sampled time, ... etc
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valueTextThe value of the property value node. It can be 'Text;', 'Number', 'Boolean', or 'StructuredValue'OptionalONE
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codeOntologyCodeA code that references an ontology term that describes the concept being described by this property valueOptionalMANY
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OntologyCode (new extended concept)
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see https://health-lifesci.schema.org/MedicalCode. This is a generallised extension to that framework to support the association of OntologyCodes to the PropertyValue entity
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Sheet1
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