From 37d0b80517fc8d2ec59c7f0dd07826af8d4d315e Mon Sep 17 00:00:00 2001
From: Philippe Rocca-Serra <proccaserra@gmail.com>
Date: Fri, 19 Jul 2024 13:42:50 +0100
Subject: [PATCH] implementation of the swat4ls mapping work into a context
 file

---
 .../w3c/isa_assay_w3c_context.jsonld          | 67 +++++++++++++++
 .../w3c/isa_data_w3c_context.jsonld           | 27 ++++++
 .../w3c/isa_factor_w3c_context.jsonld         | 25 ++++++
 .../w3c/isa_material_w3c_context.jsonld       | 35 ++++++++
 .../w3c/isa_organization_w3c_context.jsonld   | 30 +++++++
 .../w3c/isa_person_w3c_context.jsonld         | 45 ++++++++++
 ...process_parameter_value_w3c_context.jsonld | 25 ++++++
 .../w3c/isa_process_w3c_context.jsonld        | 54 ++++++++++++
 .../w3c/isa_protocol_w3c_context.jsonld       | 51 ++++++++++++
 .../w3c/isa_publication_w3c_context.jsonld    | 17 ++++
 .../w3c/isa_sample_w3c_context.jsonld         | 35 ++++++++
 .../w3c/isa_source_w3c_context.jsonld         | 27 ++++++
 .../w3c/isa_study_w3c_context.jsonld          | 83 +++++++++++++++++++
 13 files changed, 521 insertions(+)
 create mode 100644 isatools/resources/json-context/w3c/isa_assay_w3c_context.jsonld
 create mode 100644 isatools/resources/json-context/w3c/isa_data_w3c_context.jsonld
 create mode 100644 isatools/resources/json-context/w3c/isa_factor_w3c_context.jsonld
 create mode 100644 isatools/resources/json-context/w3c/isa_material_w3c_context.jsonld
 create mode 100644 isatools/resources/json-context/w3c/isa_organization_w3c_context.jsonld
 create mode 100644 isatools/resources/json-context/w3c/isa_person_w3c_context.jsonld
 create mode 100644 isatools/resources/json-context/w3c/isa_process_parameter_value_w3c_context.jsonld
 create mode 100644 isatools/resources/json-context/w3c/isa_process_w3c_context.jsonld
 create mode 100644 isatools/resources/json-context/w3c/isa_protocol_w3c_context.jsonld
 create mode 100644 isatools/resources/json-context/w3c/isa_publication_w3c_context.jsonld
 create mode 100644 isatools/resources/json-context/w3c/isa_sample_w3c_context.jsonld
 create mode 100644 isatools/resources/json-context/w3c/isa_source_w3c_context.jsonld
 create mode 100644 isatools/resources/json-context/w3c/isa_study_w3c_context.jsonld

diff --git a/isatools/resources/json-context/w3c/isa_assay_w3c_context.jsonld b/isatools/resources/json-context/w3c/isa_assay_w3c_context.jsonld
new file mode 100644
index 00000000..ac075bbd
--- /dev/null
+++ b/isatools/resources/json-context/w3c/isa_assay_w3c_context.jsonld
@@ -0,0 +1,67 @@
+{
+  "@context": {
+    "@language": "en",
+    "prov": "http://www.w3.org/ns/prov#",
+    "foaf": "http://xmlns.com/foaf/0.1/",
+    "sosa": "http://www.w3.org/ns/sosa/",
+    "dcterms": "http://purl.org/dc/terms/",
+    "xsd": "http://www.w3.org/2001/XMLSchema#",
+    "Assay": "prov:Activity",
+    "identifier": {
+      "@id": "prov:id",
+      "@type": "@id"
+    },
+    "name": {
+      "@id": "?:?",
+      "@type": "xsd:string"
+    },
+    "description": {
+      "@id": "dcterms:description",
+      "@type": "xsd:string"
+    },
+    "filename": {
+      "@id": "prov:atLocation",
+      "@type": "prov:Location"
+    },
+    "measurementType": {
+      "@id": "prov:type",
+      "@type": ["xsd:string","sosa:ObservableProperty"]
+    },
+    "technologyType": {
+      "@id": "prov:type",
+      "@type": "xsd:string"
+    },
+    "technologyPlatform": {
+      "@id": "prov:instrument",
+      "@type": "prov:Agent"
+    },
+    "materials": {
+      "@id": "prov:used",
+      "@type": "prov:Entity"
+    },
+    "othermaterials": {
+      "@id": "prov:used",
+      "@type": "prov:Entity"
+    },
+    "characteristicCategories": {
+      "@id": "prov:type",
+      "@type": ["xsd:string","sosa:ObservableProperty"]
+    },
+    "dataFiles": {
+      "@id": "prov:atLocation",
+      "@type": "prov:Location"
+    },
+    "processSequence": {
+      "@id": "prov:wasAssociatedWith",
+      "@type": "prov:Activity"
+    },
+    "unitCategories": {
+      "@id": "prov:type",
+      "@type": "qudt:Unit"
+    },
+    "comments": {
+      "@id": "rdfs:comment",
+      "@type": "xsd:string"
+    }
+  }
+}
diff --git a/isatools/resources/json-context/w3c/isa_data_w3c_context.jsonld b/isatools/resources/json-context/w3c/isa_data_w3c_context.jsonld
new file mode 100644
index 00000000..4dd95e03
--- /dev/null
+++ b/isatools/resources/json-context/w3c/isa_data_w3c_context.jsonld
@@ -0,0 +1,27 @@
+{
+  "@context": {
+    "@language": "en",
+    "prov": "http://www.w3.org/ns/prov#",
+    "foaf": "http://xmlns.com/foaf/0.1/",
+    "dcterms": "http://purl.org/dc/terms/",
+    "dcat": "https://www.w3.org/TR/vocab-dcat-3/",
+    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+    "Data": "dcat:Dataset",
+    "type": {
+      "@id": "prov:type",
+      "@type": "xsd:string"
+    },
+    "identifier": {
+      "@id": "prod:id",
+      "@type": "xsd:uri"
+    },
+    "name": {
+      "@id": "rdfs:Label",
+      "@type": "xsd:string"
+    },
+    "comments": {
+      "@id": "rdfs:comment",
+      "@type": "xsd:string"
+    }
+  }
+}
\ No newline at end of file
diff --git a/isatools/resources/json-context/w3c/isa_factor_w3c_context.jsonld b/isatools/resources/json-context/w3c/isa_factor_w3c_context.jsonld
new file mode 100644
index 00000000..ade53096
--- /dev/null
+++ b/isatools/resources/json-context/w3c/isa_factor_w3c_context.jsonld
@@ -0,0 +1,25 @@
+{
+  "@context": {
+    "@language": "en",
+    "prov": "http://www.w3.org/ns/prov#",
+    "sosa": "http://www.w3.org/ns/sosa/",
+    "xsd": "http://www.w3.org/2001/XMLSchema#",
+    "Factor": "sosa:ObservableProperty?",
+    "identifier": {
+      "@id": "prov:id",
+      "@type": "@id"
+    },
+    "factorName": {
+      "@id": "?:?",
+      "@type": "xsd:string"
+    },
+    "factorType": {
+      "@id": "prov:type",
+      "@type": "xsd:uri"
+    }
+  },
+    "comments": {
+      "@id": "rdfs:comment",
+      "@type": "xsd:string"
+    }
+}
diff --git a/isatools/resources/json-context/w3c/isa_material_w3c_context.jsonld b/isatools/resources/json-context/w3c/isa_material_w3c_context.jsonld
new file mode 100644
index 00000000..9e8dfbde
--- /dev/null
+++ b/isatools/resources/json-context/w3c/isa_material_w3c_context.jsonld
@@ -0,0 +1,35 @@
+{
+  "@context": {
+    "@language": "en",
+    "prov": "http://www.w3.org/ns/prov#",
+    "foaf": "http://xmlns.com/foaf/0.1/",
+    "dcterms": "http://purl.org/dc/terms/",
+    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+    "xsd": "http://www.w3.org/2001/XMLSchema#",
+    "Material": "prov:Entity",
+    "type": {
+      "@id": "prov:type",
+      "@type": "prov:value"
+    },
+    "identifier": {
+      "@id": "prov:id",
+      "@type": "@id"
+    },
+    "name": {
+      "@id": "rdfls:Label",
+      "@type": "xsd:string"
+    },
+    "characteristics": {
+      "@id": "prov:type",
+      "@type": "prov:value"
+    },
+    "roles": {
+      "@id": "prov:hadRole",
+      "@type": "prov:Role"
+    },
+    "derivesFrom": {
+      "@id": "prov:wasDerivedFrom",
+      "@type": "prov:Entity"
+    }
+  }
+}
\ No newline at end of file
diff --git a/isatools/resources/json-context/w3c/isa_organization_w3c_context.jsonld b/isatools/resources/json-context/w3c/isa_organization_w3c_context.jsonld
new file mode 100644
index 00000000..b1c65f2f
--- /dev/null
+++ b/isatools/resources/json-context/w3c/isa_organization_w3c_context.jsonld
@@ -0,0 +1,30 @@
+{
+  "@context": {
+    "@language": "en",
+    "prov": "http://www.w3.org/ns/prov#",
+    "foaf": "http://xmlns.com/foaf/0.1/",
+    "dcterms": "http://purl.org/dc/terms/",
+    "xsd": "http://www.w3.org/2001/XMLSchema#",
+    "Organization": "prov:Organization",
+    "identifier": {
+      "@id": "prov:id",
+      "@type": "@id"
+    },
+    "name": {
+      "@id": "foaf:name",
+      "@type": "xsd:string"
+    },
+    "description": {
+      "@id": "dcterms:description",
+      "@type": "xsd:string"
+    },
+    "postalAddress": {
+      "@id": "prov:atLocation",
+      "@type": "prov:Location"
+    },
+    "roles": {
+      "@id": "prov:hadRole",
+      "@type": "prov:Role"
+    }
+  }
+}
\ No newline at end of file
diff --git a/isatools/resources/json-context/w3c/isa_person_w3c_context.jsonld b/isatools/resources/json-context/w3c/isa_person_w3c_context.jsonld
new file mode 100644
index 00000000..2d150138
--- /dev/null
+++ b/isatools/resources/json-context/w3c/isa_person_w3c_context.jsonld
@@ -0,0 +1,45 @@
+{
+  "@context": {
+    "@language": "en",
+    "prov": "http://www.w3.org/ns/prov#",
+    "foaf": "http://xmlns.com/foaf/0.1/",
+    "xsd": "http://www.w3.org/2001/XMLSchema#",
+    "Person": "prov:Person",
+    "identifier": {
+      "@id": "prov:id",
+      "@type": "@id"
+    },
+    "firstName": {
+      "@id": "foaf:firstName",
+      "@type": "string"
+    },
+    "lastName": {
+      "@id": "foaf:lastName",
+      "@type": "string"
+    },
+    "midInitials": {
+      "@id": "foaf:name",
+      "@type": "string"
+    },
+    "email": {
+      "@id": "foaf:mbox",
+      "@type": "uri"
+    },
+    "phone": {
+      "@id": "foaf:phone",
+      "@type": "string"
+    },
+    "fax": {
+      "@id": "",
+      "@type": "string"
+    },
+    "affiliation": {
+      "@id": "foaf:member",
+      "@type": "prov:Organization"
+    },
+    "roles": {
+      "@id": "prov:hadRole",
+      "@type": "prov:Role"
+    }
+  }
+}
\ No newline at end of file
diff --git a/isatools/resources/json-context/w3c/isa_process_parameter_value_w3c_context.jsonld b/isatools/resources/json-context/w3c/isa_process_parameter_value_w3c_context.jsonld
new file mode 100644
index 00000000..5fdc03d7
--- /dev/null
+++ b/isatools/resources/json-context/w3c/isa_process_parameter_value_w3c_context.jsonld
@@ -0,0 +1,25 @@
+{
+  "@context": {
+    "@language": "en",
+    "prov": "http://www.w3.org/ns/prov#",
+    "dcterms": "http://purl.org/dc/terms/",
+    "sdmx-measure": "http://purl.org/linked-data/sdmx/2009/measure#",
+    "qudt": "http://qudt.org/schema/qudt",
+    "cube" : "http://purl.org/linked-data/cube#",
+    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+    "xsd": "http://www.w3.org/2001/XMLSchema#",
+    "ParameterValue": "qb:MeasureProperty",
+    "category": {
+      "@id": "prov:type",
+      "@type": "xsd:string"
+    },
+    "value": {
+      "@id": "prov:value",
+      "@type": ["xsd:string","xsd:float"]
+    },
+    "unit": {
+      "@id": "qudt:unit",
+      "@type": "qudt:Unit"
+    }
+  }
+}
diff --git a/isatools/resources/json-context/w3c/isa_process_w3c_context.jsonld b/isatools/resources/json-context/w3c/isa_process_w3c_context.jsonld
new file mode 100644
index 00000000..c611d728
--- /dev/null
+++ b/isatools/resources/json-context/w3c/isa_process_w3c_context.jsonld
@@ -0,0 +1,54 @@
+{
+  "@context": {
+    "@language": "en",
+    "prov": "http://www.w3.org/ns/prov#",
+    "foaf": "http://xmlns.com/foaf/0.1/",
+    "dcterms": "http://purl.org/dc/terms/",
+    "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#",
+    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+    "xsd": "http://www.w3.org/2001/XMLSchema#",
+    "Process": "prov:Activity",
+    "identifier": {
+      "@id": "prov:id",
+      "@type": "@id"
+    },
+    "name": {
+      "@id": "rdfls:Label",
+      "@type": "xsd:string"
+    },
+    "description": {
+      "@id": "dcterms:description",
+      "@type": "xsd:string"
+    },
+    "date": {
+      "@id": "prov:wasStartedate",
+      "@type": "xsd:date"
+    },
+    "executesProtocol": {
+      "@id": "prov:wasAssociatedWith",
+      "@type": "prov:Plan"
+    },
+    "parameterValues": {
+      "@id": "prov:type",
+      "@type": "prov:value"
+    },
+    "previousProcess": {
+      "@id": "xkos:previous",
+      "@type": "prov:Activity"
+    },
+    "nextProcess": {
+      "@id": "xkos:next",
+      "@type": "prov:Activity"
+    },
+    "inputs": "prov:used",
+    "outputs": "prov:generated",
+    "performer": {
+      "@id": "prov:wasAttributedTo",
+      "@type": "prov:Person"
+    },
+    "comments": {
+      "@id": "rdfs:comment",
+      "@type": "xsd:string"
+    }
+  }
+}
diff --git a/isatools/resources/json-context/w3c/isa_protocol_w3c_context.jsonld b/isatools/resources/json-context/w3c/isa_protocol_w3c_context.jsonld
new file mode 100644
index 00000000..9a8f9dd8
--- /dev/null
+++ b/isatools/resources/json-context/w3c/isa_protocol_w3c_context.jsonld
@@ -0,0 +1,51 @@
+{
+  "@context": {
+    "@language": "en",
+    "prov": "http://www.w3.org/ns/prov#",
+    "foaf": "http://xmlns.com/foaf/0.1/",
+    "dcterms": "http://purl.org/dc/terms/",
+    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+    "xsd": "http://www.w3.org/2001/XMLSchema#",
+    "Protocol": "prov:Plan",
+    "filename": {
+      "@id": "prov:atLocation",
+      "@type": "prov:Location"
+    },
+    "identifier": {
+      "@id": "prov:id",
+      "@type": "@id"
+    },
+    "title": {
+      "@id": "dcterms:title",
+      "@type": "xsd:string"
+    },
+    "description": {
+      "@id": "dcterms:description",
+      "@type": "xsd:string"
+    },
+    "version": {
+      "@id": "dcterms:hasVersion",
+      "@type": "prov:value"
+    },
+    "components": {
+      "@id": "prov:agent",
+      "@type": ["prov:Agent","prov:SoftwareAgent"]
+    },
+    "parameters": {
+      "@id": "prov:type",
+      "@type": "prov:?"
+    },
+    "uri": {
+      "@id": "prov:atLocation",
+      "@type": "prov:Location"
+    },
+    "publications": {
+      "@id": "prov:wasAssociatedWith",
+      "@type": "prov:Communication"
+    },
+    "comments": {
+      "@id": "rdfs:comment",
+      "@type": "xsd:string"
+    }
+  }
+}
diff --git a/isatools/resources/json-context/w3c/isa_publication_w3c_context.jsonld b/isatools/resources/json-context/w3c/isa_publication_w3c_context.jsonld
new file mode 100644
index 00000000..640cb071
--- /dev/null
+++ b/isatools/resources/json-context/w3c/isa_publication_w3c_context.jsonld
@@ -0,0 +1,17 @@
+{
+  "@context": {
+    "@language": "en",
+    "prov": "http://www.w3.org/ns/prov#",
+    "dcterms": "http://purl.org/dc/terms/",
+    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+    "xsd": "http://www.w3.org/2001/XMLSchema#",
+    "Publication": "prov:Communication",
+    "identifier": "prov:id",
+    "pubMedID": "prov:id",
+    "doi": "prov:id",
+    "title": "dcterms:title",
+    "status": "",
+    "authorList": "prov:Bundle",
+    "comments": "rdfs:comment"
+  }
+}
diff --git a/isatools/resources/json-context/w3c/isa_sample_w3c_context.jsonld b/isatools/resources/json-context/w3c/isa_sample_w3c_context.jsonld
new file mode 100644
index 00000000..47cab0bd
--- /dev/null
+++ b/isatools/resources/json-context/w3c/isa_sample_w3c_context.jsonld
@@ -0,0 +1,35 @@
+{
+  "@context": {
+    "@language": "en",
+    "prov": "http://www.w3.org/ns/prov#",
+    "foaf": "http://xmlns.com/foaf/0.1/",
+    "dcterms": "http://purl.org/dc/terms/",
+    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+    "xsd": "http://www.w3.org/2001/XMLSchema#",
+    "Sample": "prov:Entity",
+    "identifier": {
+      "@id": "prov:id",
+      "@type": "@id"
+    },
+    "name": {
+      "@id": "rdfls:Label",
+      "@type": "xsd:string"
+    },
+    "characteristics": {
+      "@id": "prov:type",
+      "@type": "prov:value"
+    },
+    "roles": {
+      "@id": "prov:hadRole",
+      "@type": "prov:Role"
+    },
+    "factorValues": {
+        "@id": "prov:type",
+        "@type": "sdo:value"
+    },
+    "derivesFrom": {
+      "@id": "prov:wasDerivedFrom",
+      "@type": "prov:Entity"
+    }
+  }
+}
\ No newline at end of file
diff --git a/isatools/resources/json-context/w3c/isa_source_w3c_context.jsonld b/isatools/resources/json-context/w3c/isa_source_w3c_context.jsonld
new file mode 100644
index 00000000..4cbeb495
--- /dev/null
+++ b/isatools/resources/json-context/w3c/isa_source_w3c_context.jsonld
@@ -0,0 +1,27 @@
+{
+  "@context": {
+    "@language": "en",
+    "prov": "http://www.w3.org/ns/prov#",
+    "foaf": "http://xmlns.com/foaf/0.1/",
+    "dcterms": "http://purl.org/dc/terms/",
+    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+    "xsd": "http://www.w3.org/2001/XMLSchema#",
+    "Source": "prov:Entity",
+    "identifier": {
+      "@id": "prov:id",
+      "@type": "@id"
+    },
+    "name": {
+      "@id": "rdfls:Label",
+      "@type": "xsd:string"
+    },
+    "characteristics": {
+      "@id": "prov:type",
+      "@type": "prov:value"
+    },
+    "roles": {
+      "@id": "prov:hadRole",
+      "@type": "prov:Role"
+    }
+  }
+}
\ No newline at end of file
diff --git a/isatools/resources/json-context/w3c/isa_study_w3c_context.jsonld b/isatools/resources/json-context/w3c/isa_study_w3c_context.jsonld
new file mode 100644
index 00000000..e53f3c64
--- /dev/null
+++ b/isatools/resources/json-context/w3c/isa_study_w3c_context.jsonld
@@ -0,0 +1,83 @@
+{
+  "@context": {
+    "@language": "en",
+    "materials": "@nest",
+    "prov": "http://www.w3.org/ns/prov#",
+    "sosa": "http://www.w3.org/ns/sosa/",
+    "foaf": "http://xmlns.com/foaf/0.1/",
+    "dcterms": "http://purl.org/dc/terms/",
+    "dcat": "https://www.w3.org/TR/vocab-dcat-3/",
+    "qudt": "http://qudt.org/schema/qudt",
+    "cube" : "http://purl.org/linked-data/cube#",
+    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+    "xsd": "http://www.w3.org/2001/XMLSchema#",
+    "Study": "dcat:Dataset",
+    "filename": {
+      "@id": "prov:atLocation",
+      "@type": "prov:Location"
+    },
+    "identifier": {
+      "@id": "prov:id",
+      "@type": "@id"
+    },
+    "title": {
+      "@id": "dcterms:title",
+      "@type": "xsd:string"
+    },
+    "description": {
+      "@id": "dcterms:description",
+      "@type": "xsd:string"
+    },
+    "submissionDate": {
+      "@id": "prov:startedAtTime",
+      "@type": "xsd:date"
+    },
+    "publicReleaseDate": {
+      "@id": "prov:generatedAtTime",
+      "@type": "xsd:date"
+    },
+    "publications": {
+      "@id": "prov:wasAssociatedWith",
+      "@type": "prov:Communication"
+    },
+    "people": {
+      "@id": "wasAttributedTo",
+      "@type": "prov:Person"
+    },
+    "studyDesignDescriptors": {
+      "@id": "prov:type",
+      "@type": "prov:value"
+    },
+    "protocols": {
+      "@id": "rov:wasAssociatedWith",
+      "@type": "prov:Plan"
+    },
+    "sources": "prov:Entity",
+    "samples": "prov:Entity",
+    "otherMaterials": "prov:Entity",
+    "processSequence": {
+      "@id": "prov:wasAssociatedWith",
+      "@type": "prov:Activity"
+    },
+    "assays": {
+      "@id": "prov:wasAssociatedWith",
+      "@type": "prov:Activity"
+    },
+    "factors": {
+      "@id": "cube:dimension",
+      "@type": "cube:DimensionProperty"
+    },
+    "characteristicCategories": {
+      "@id": "prov:type",
+      "@type": ["xsd:string","sosa:ObservableProperty"]
+    },
+    "unitCategories": {
+      "@id": "prov:type",
+      "@type": "qudt:Unit"
+    },
+    "comments": {
+      "@id": "rdfs:comment",
+      "@type": "xsd:string"
+    }
+  }
+}
\ No newline at end of file