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| ## Mapping | ||
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| This is the mapping between ISA-json types defined in https://isa-specs.readthedocs.io/en/latest/isajson.html and [`schema.org`](https://schema.org/)-types used by the isa-ro-crate-profile defined in https://github.com/nfdi4plants/isa-ro-crate-profile/blob/main/profile/isa_ro_crate.md . | ||
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| | ISA term | schema term | Explanation | | ||
| |----------|-------------|-------------| | ||
| |[Investigation](https://isa-specs.readthedocs.io/en/latest/isajson.html#investigation-schema-json)|[Dataset](https://schema.org/Dataset)|| | ||
| |@id|@id|| | ||
| |-|additionalType|for distinction from Study and Assay| | ||
| |fileName|url|| | ||
| |title|headline|| | ||
| |people|creator|| | ||
| |identifier|identifier|| | ||
| |description|description|| | ||
| |studies|hasPart|| | ||
| |submissionDate|dateCreated|| | ||
| |-|dateModified|| | ||
| |publicReleaseDate|datePublished|| | ||
| |publications|citation|| | ||
| |comments|comment|| | ||
| |onntologySourceReferences|mentions|| | ||
| || | ||
| |[Study](https://isa-specs.readthedocs.io/en/latest/isajson.html#study-schema-json)|[Dataset](https://schema.org/Dataset)|| | ||
| |@id|@id|| | ||
| |-|additionalType|for distinction from Investigation and Assay| | ||
| |fileName|url|| | ||
| |people|creator|| | ||
| |identifier|identifier|| | ||
| |title|headline|| | ||
| |assays|hasPart|| | ||
| |processSequence|about|| | ||
| |description|description|| | ||
| |submissionDate|dateCreated|| | ||
| |-|dateModified|| | ||
| |publicReleaseDate|datePublished|| | ||
| |publications|citation|| | ||
| |comments|comment|| | ||
| |studyDesignDescriptor|-|redundant information| | ||
| |protocols|-|redundant information| | ||
| |materials|-|redundant information| | ||
| |factors|-|redundant information| | ||
| |characteristicCategories|-|redundant information| | ||
| |unitCategories|-|redundant information| | ||
| || | ||
| |[Assay](https://isa-specs.readthedocs.io/en/latest/isajson.html#assay-schema-json)|[Dataset](https://schema.org/Dataset)|| | ||
| |@id|@id|| | ||
| |-|additionalType|for distinction from Investigation and Study| | ||
| |-|identifier|| | ||
| |processSequence|about|| | ||
| |-|creator|ARC-specific property| | ||
| |technologyType|measurementMethod|| | ||
| |technologyPlatform|measurementTechnique|| | ||
| |dataFiles|hasPart|| | ||
| |measurementType|variableMeasured|| | ||
| |comments|comment|| | ||
| |fileName|url|| | ||
| || | ||
| |[Process](https://isa-specs.readthedocs.io/en/latest/isajson.html#process-schema-json)|[bioschemas.org/LabProcess](https://bioschemas.org/LabProcess)| | ||
| |@id|@id|| | ||
| |name|name|| | ||
| |performer|agent|| | ||
| |inputs|object|| | ||
| |outputs|result|| | ||
| |executesProtocol|executesLabProtocol|| | ||
| |parameterValues|parameterValue|| | ||
| |date|endTime|| | ||
| |previousProcess|-|redundant information| | ||
| |nextProcess|-|redundant information| | ||
| |comments|disambiguatingDescription|| | ||
| || | ||
| |[Protocol](https://isa-specs.readthedocs.io/en/latest/isajson.html#protocol-schema-json)|[bioschemas.org/LabProtocol](https://bioschemas.org/LabProtocol)| | ||
| |@id|@id|| | ||
| |name|name|| | ||
| |protocolType|intendedUse|| | ||
| |description|description|| | ||
| |uri|url|| | ||
| |-|comment|ARC-specific property| | ||
| |version|version|| | ||
| |components|labEquipment|Components can be saved as `labEquipment`, `reagent`, or `computationalTool`, with `labEquipment` being the default.| | ||
| |components|reagent|Components can be saved as `labEquipment`, `reagent`, or `computationalTool`, with `labEquipment` being the default.| | ||
| |components|computationalTool|Components can be saved as `labEquipment`, `reagent`, or `computationalTool`, with `labEquipment` being the default.| | ||
| |parameters|-|redundant information| | ||
| || | ||
| |[Sample](https://isa-specs.readthedocs.io/en/latest/isajson.html#sample-schema-json)|[bioschemas.org/Sample](https://bioschemas.org/Sample)|| | ||
| |[Source](https://isa-specs.readthedocs.io/en/latest/isajson.html#source-schema-json)|[bioschemas.org/Sample](https://bioschemas.org/Sample)|| | ||
| |@id|@id|| | ||
| |name|name|| | ||
| |characteristics|additionalProperty|Characteristics and factor values can be saved as `additionalProperties`. What they represent needs to be annotated.| | ||
| |factorValues|additionalProperty|Characteristics and factor values can be saved as `additionalProperties`. What they represent needs to be annotated.| | ||
| |derivesFrom|-|redundant information| | ||
| || | ||
| |[Data](https://isa-specs.readthedocs.io/en/latest/isajson.html#data-schema-json)|'File' or '[MediaObject](https://schema.org/MediaObject)'| | ||
| |@id|@id|| | ||
| |name|name|| | ||
| |comments|comment|| | ||
| |-|encodingFormat|ARC-specific property| | ||
| |type|disambiguatingDescription|| | ||
| || | ||
| |[Person](https://isa-specs.readthedocs.io/en/latest/isajson.html#person-schema-json)|[schema.org/Person](https://schema.org/Person)| | ||
| |@id|@id|| | ||
| |firstName|givenName|| | ||
| |lastName|familyName|| | ||
| |email|email|| | ||
| |-|identifier|Can be used for identifiers stored in comment, e.g. an orcid.| | ||
| |affiliation|affiliation|The affilitation strin in ISA is converted to an Oranization object.| | ||
| |roles|jobTitle|| | ||
| |midInitials|additionalName|| | ||
| |address|address|| | ||
| |phone|telephone|| | ||
| |fax|faxNumber|| | ||
| |comments|disambiguatingDescription|Comment object in ISA has to be encoded as a string.| | ||
| || | ||
| |[Publication](https://isa-specs.readthedocs.io/en/latest/isajson.html#publication-schema-json)|[schema.org/ScholarlyArticle](https://schema.org/ScholarlyArticle)| | ||
| |@id|@id|| | ||
| |title|headline|| | ||
| |pubMedID|identifier|One or many identifiers for this article (DOI or PubMedID) can be encoded in identifier. Either as full URL or of type PropertyValue to indicate the kind of reference.| | ||
| |doi|identifier|One or many identifiers for this article (DOI or PubMedID) can be encoded in identifier. Either as full URL or of type PropertyValue to indicate the kind of reference.| | ||
| |authorList|author|| | ||
| |status|creativeWorkStatus| | ||
| |comments|comment|| | ||
| || | ||
| |[Comment](https://isa-specs.readthedocs.io/en/latest/isajson.html#comment-schema-json)|[Comment](https://schema.org/Comment)|| | ||
| |@id|@id|| | ||
| |name|name|| | ||
| |value|text|| | ||
| || | ||
| |[OntologyAnnotation](https://isa-specs.readthedocs.io/en/latest/isajson.html#ontology-annotation-schema-json)|[DefinedTerm](https://schema.org/DefinedTerm)|| | ||
| |annotationValue|name|| | ||
| |termSource|inDefinedTermSet|| | ||
| |termAccession|termCode|| | ||
| |comments|disambiguatingDescription|Comment object in ISA has to be encoded as a string.| | ||
| || | ||
| |[FactorValue](https://isa-specs.readthedocs.io/en/latest/isajson.html#factor-value-schema-json)|[schema.org/PropertyValue](https://schema.org/PropertyValue)|See details for properties [below](#key-value-unit-triples).| | ||
| |[MaterialAttributeValue](https://isa-specs.readthedocs.io/en/latest/isajson.html#material-attribute-value-schema-json)|[schema.org/PropertyValue](https://schema.org/PropertyValue)|See details for properties [below](#key-value-unit-triples).| | ||
| |[ProcessParameterValue](https://isa-specs.readthedocs.io/en/latest/isajson.html#process-parameter-value-schema-json)|[schema.org/PropertyValue](https://schema.org/PropertyValue)|See details for properties [below](#key-value-unit-triples).| | ||
| || | ||
| |[OntologySourceReference](https://isa-specs.readthedocs.io/en/latest/isajson.html#ontology-source-reference-schema-json)|-|dropped type| | ||
| |[Factor](https://isa-specs.readthedocs.io/en/latest/isajson.html#factor-schema-json)|-|dropped type| | ||
| |[Material](https://isa-specs.readthedocs.io/en/latest/isajson.html#material-schema-json)|-|dropped type| | ||
| |[ProtocolParameter](https://isa-specs.readthedocs.io/en/latest/isajson.html#protocol-parameter-schema-json)|-|dropped type| | ||
| |[MaterialAttribute](https://isa-specs.readthedocs.io/en/latest/isajson.html#material-attribute-schema-json)|-|dropped type| | ||
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| ### Key-Value-Unit Triples | ||
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| The three types `MaterialAttributeValue`, `FactorValue` and `ProcessParameterValueValue` are all encoded as a [schema.org/PropertyValue](https://schema.org/PropertyValue). | ||
| All three represent a key-value-unit triple, with the key (`category`) essentially being an ontology term (of type `Factor`,`MaterialAttribute`,`ProtocolParameter`). | ||
| The key ontology term is always encoded as a URL and a name and therefore have to be resolved on export. | ||
| The value field is encoded in a straight-forward manner. | ||
| The unit is again an ontology term that has to be resolved into a URL and a name. | ||
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| | ISA term | schema term | Explanation | | ||
| |----------|-------------|-------------| | ||
| |[MaterialAttributeValue](https://isa-specs.readthedocs.io/en/latest/isajson.html#material-attribute-value-schema-json)|[schema.org/PropertyValue](https://schema.org/PropertyValue)|| | ||
| |[FactorValue](https://isa-specs.readthedocs.io/en/latest/isajson.html#factor-value-schema-json)|[schema.org/PropertyValue](https://schema.org/PropertyValue)|| | ||
| |[ProcessParameterValue](https://isa-specs.readthedocs.io/en/latest/isajson.html#process-parameter-value-schema-json)|[schema.org/PropertyValue](https://schema.org/PropertyValue)|| | ||
| |@id|@id|| | ||
| |category|name|Name of the category.| | ||
| |value|value|Value as number or string.| | ||
| |category|propertyID|Ontology URL of the category.| | ||
| |unit|unitCode|Ontology URL of the unit.| | ||
| |unit|unitText|Name of the unit.| | ||
| |value|valueReference|Ontology URL or ontology term objetc of the value.| | ||
| |-|additionalType||Can be used to describe if the value is a factor, characteristic or parameter.| |