completed mapping table

nfdi4plants · Jul 5, 2024 · 2cfe0c4 · 2cfe0c4
1 parent 9084d56
commit 2cfe0c4
Showing 1 changed file with 110 additions and 5 deletions.
diff --git a/profile/isa_ro_crate_mapping.md b/profile/isa_ro_crate_mapping.md
@@ -1,8 +1,8 @@
 | ISA term | schema term | Explanation |
 |----------|-------------|-------------|
-|Investigation|Dataset|for distinction from Study and Assay|
+|Investigation|Dataset||
 |@id|@id||
-|-|additionalType||
+|-|additionalType|for distinction from Study and Assay|
 |fileName|url||
 |title|headline||
 |people|creator||
@@ -42,11 +42,116 @@
 |@id|@id||
 |-|additionalType|for distinction from Investigation and Study|
 |-|identifier||
-|processSequence|about|
-|-|creator|
+|processSequence|about||
+|-|creator|ARC-specific property|
 |technologyType|measurementMethod||
 |technologyPlatform|measurementTechnique||
 |dataFiles|hasPart||
 |measurementType|variableMeasured||
 |comments|comment||
-|fileName|url||
+|fileName|url||
+||
+|Process|[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|[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|[bioschemas.org/Sample](https://bioschemas.org/Sample)||
+|Source|[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|'File' or 'MediaObject'|
+|@id|@id||
+|name|name||
+|comments|comment||
+|-|encodingFormat|ARC-specific property|
+|type|disambiguatingDescription||
+||
+|@type |[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|[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|Comment||
+|@id|@id||
+|name|name||
+|value|text||
+||
+|OntologyAnnotation|DefinedTerm||
+|annotationValue|name||
+|termSource|inDefinedTermSet||
+|termAccession|termCode||
+|comments|disambiguatingDescription|Comment object in ISA has to be encoded as a string.|
+||
+|FactorValue|[schema.org/PropertyValue](https://schema.org/PropertyValue)|See details for properties below.|
+|MaterialAttributeValue|[schema.org/PropertyValue](https://schema.org/PropertyValue)|See details for properties below.|
+|ProcessParameterValue|[schema.org/PropertyValue](https://schema.org/PropertyValue)|See details for properties below.|
+||
+|OntologySourceReference|-|dropped type|
+|Factor|-|dropped type|
+|Material|-|dropped type|
+|ProtocolParameter|-|dropped type|
+|MaterialAttribute|-|dropped type|
+
+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.
+
+| ISA term | schema term | Explanation |
+|----------|-------------|-------------|
+|MaterialAttributeValue|[schema.org/PropertyValue](https://schema.org/PropertyValue)||
+|FactorValue|[schema.org/PropertyValue](https://schema.org/PropertyValue)||
+|ProcessParameterValue|[schema.org/PropertyValue](https://schema.org/PropertyValue)||
+|@id|@id||
+|category|name||
+|value|value||
+|category|propertyID||
+|unit|unitCode||
+|unit|unitText||
+|value|valueReference||
+|-|additionalType||Can be used to describe if the value is a factor, characteristic or parameter.|