some updates on the profile

nfdi4plants · Jul 12, 2024 · 7a50c84 · 7a50c84
1 parent 2cfe0c4
commit 7a50c84
Showing 1 changed file with 35 additions and 29 deletions.
diff --git a/profile/isa_ro_crate_mapping.md b/profile/isa_ro_crate_mapping.md
@@ -1,6 +1,10 @@
+## Mapping
+
+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 .
+
 | ISA term | schema term | Explanation |
 |----------|-------------|-------------|
-|Investigation|Dataset||
+|[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||
@@ -16,7 +20,7 @@
 |comments|comment||
 |onntologySourceReferences|mentions||
 ||
-|Study|Dataset||
+|[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||
@@ -38,7 +42,7 @@
 |characteristicCategories|-|redundant information|
 |unitCategories|-|redundant information|
 ||
-|Assay|Dataset||
+|[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||
@@ -51,7 +55,7 @@
 |comments|comment||
 |fileName|url||
 ||
-|Process|[bioschemas.org/LabProcess](https://bioschemas.org/LabProcess)|
+|[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||
@@ -64,7 +68,7 @@
 |nextProcess|-|redundant information|
 |comments|disambiguatingDescription||
 ||
-|Protocol|[bioschemas.org/LabProtocol](https://bioschemas.org/LabProtocol)|
+|[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||
@@ -77,22 +81,22 @@
 |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)||
+|[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|'File' or 'MediaObject'|
+|[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||
 ||
-|@type |[schema.org/Person](https://schema.org/Person)|
+|[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||
@@ -106,7 +110,7 @@
 |fax|faxNumber||
 |comments|disambiguatingDescription|Comment object in ISA has to be encoded as a string.|
 ||
-|Publication|[schema.org/ScholarlyArticle](https://schema.org/ScholarlyArticle)|
+|[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.|
@@ -115,26 +119,28 @@
 |status|creativeWorkStatus|
 |comments|comment||
 ||
-|Comment|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|DefinedTerm||
+|[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|[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.|
+|[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|-|dropped type|
-|Factor|-|dropped type|
-|Material|-|dropped type|
-|ProtocolParameter|-|dropped type|
-|MaterialAttribute|-|dropped type|
+|[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|
+
+### Key-Value-Unit Triples
 
 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`).
@@ -144,14 +150,14 @@ 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)||
+|[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||
-|value|value||
-|category|propertyID||
-|unit|unitCode||
-|unit|unitText||
-|value|valueReference||
+|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.|