pre-refactor

linkml · Jun 14, 2024 · 88af46c · 88af46c
1 parent 5ba789c
commit 88af46c
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Showing 15 changed files with 4,240 additions and 2,850 deletions.
diff --git a/project/excel/linkml_common.xlsx b/project/excel/linkml_common.xlsx
diff --git a/project/graphql/linkml_common.graphql b/project/graphql/linkml_common.graphql
@@ -712,8 +712,10 @@ type Measurement
     isOngoingAsOf: TimePoint
     id: Uriorcurie!
     name: String
-    quantityMeasured: Quantity
+    observationSubject: Entity
     variableMeasured: Variable
+    measuredUsing: PhysicalDevice
+    quantityMeasured: Quantity
   }
 
 type MiningFacility
@@ -784,6 +786,9 @@ type Observation
     isOngoingAsOf: TimePoint
     id: Uriorcurie!
     name: String
+    observationSubject: Entity
+    variableMeasured: Variable
+    measuredUsing: PhysicalDevice
   }
 
 type Organization
@@ -954,6 +959,22 @@ type Publication
     name: String
   }
 
+type QualitativeObservation
+  {
+    type: String
+    startsAt: TimePoint
+    endsAt: TimePoint
+    happensAt: TimePoint
+    hasInterval: TemporalInterval
+    hasDuration: Duration
+    isOngoingAsOf: TimePoint
+    id: Uriorcurie!
+    name: String
+    observationSubject: Entity
+    variableMeasured: Variable
+    measuredUsing: PhysicalDevice
+  }
+
 type Quantity
   {
     type: String

diff --git a/project/jsonld/linkml_common.context.jsonld b/project/jsonld/linkml_common.context.jsonld
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-06-13T22:19:59",
+      "generation_date": "2024-06-13T22:32:40",
       "source": "linkml_common.yaml"
    },
    "@context": {
@@ -333,10 +333,6 @@
          "@type": "@id",
          "@id": "quantity_measured"
       },
-      "variable_measured": {
-         "@type": "@id",
-         "@id": "variable_measured"
-      },
       "area": {
          "@type": "@id",
          "@id": "area"
@@ -369,6 +365,18 @@
          "@type": "@id",
          "@id": "rdf:object"
       },
+      "measured_using": {
+         "@type": "@id",
+         "@id": "measured_using"
+      },
+      "observation_subject": {
+         "@type": "@id",
+         "@id": "observation_subject"
+      },
+      "variable_measured": {
+         "@type": "@id",
+         "@id": "variable_measured"
+      },
       "ontology_types": {
          "@type": "@id",
          "@id": "ontology_types"
@@ -834,6 +842,9 @@
       "Publication": {
          "@id": "Publication"
       },
+      "QualitativeObservation": {
+         "@id": "QualitativeObservation"
+      },
       "Quantity": {
          "@id": "fhir:Quantity"
       },

diff --git a/project/jsonld/linkml_common.jsonld b/project/jsonld/linkml_common.jsonld
@@ -1957,30 +1957,55 @@
       "@type": "SlotDefinition"
     },
     {
-      "name": "measurement__quantity_measured",
-      "description": "The quantity being measured",
+      "name": "observation__observation_subject",
       "from_schema": "https://w3id.org/linkml-common/meaurements",
-      "slot_uri": "https://w3id.org/linkml-common/quantity_measured",
-      "alias": "quantity_measured",
-      "owner": "Measurement",
+      "slot_uri": "https://w3id.org/linkml-common/observation_subject",
+      "alias": "observation_subject",
+      "owner": "Observation",
       "domain_of": [
-        "Measurement"
+        "Observation"
       ],
-      "range": "Quantity",
+      "range": "Entity",
       "inlined": true,
       "@type": "SlotDefinition"
     },
     {
-      "name": "measurement__variable_measured",
+      "name": "observation__variable_measured",
       "description": "The variable being measured",
       "from_schema": "https://w3id.org/linkml-common/meaurements",
       "slot_uri": "https://w3id.org/linkml-common/variable_measured",
       "alias": "variable_measured",
+      "owner": "Observation",
+      "domain_of": [
+        "Observation"
+      ],
+      "range": "Variable",
+      "inlined": true,
+      "@type": "SlotDefinition"
+    },
+    {
+      "name": "observation__measured_using",
+      "from_schema": "https://w3id.org/linkml-common/meaurements",
+      "slot_uri": "https://w3id.org/linkml-common/measured_using",
+      "alias": "measured_using",
+      "owner": "Observation",
+      "domain_of": [
+        "Observation"
+      ],
+      "range": "PhysicalDevice",
+      "@type": "SlotDefinition"
+    },
+    {
+      "name": "measurement__quantity_measured",
+      "description": "The quantity being measured",
+      "from_schema": "https://w3id.org/linkml-common/meaurements",
+      "slot_uri": "https://w3id.org/linkml-common/quantity_measured",
+      "alias": "quantity_measured",
       "owner": "Measurement",
       "domain_of": [
         "Measurement"
       ],
-      "range": "Variable",
+      "range": "Quantity",
       "inlined": true,
       "@type": "SlotDefinition"
     },
@@ -4766,10 +4791,11 @@
       "@type": "ClassDefinition"
     },
     {
-      "name": "Measurement",
-      "definition_uri": "https://w3id.org/linkml-common/Measurement",
+      "name": "Observation",
+      "definition_uri": "https://w3id.org/linkml-common/Observation",
+      "description": "A statement about the state of something",
       "from_schema": "https://w3id.org/linkml-common/meaurements",
-      "is_a": "Observation",
+      "is_a": "Event",
       "slots": [
         "type",
         "starts_at",
@@ -4780,55 +4806,69 @@
         "is_ongoing_as_of",
         "id",
         "name",
-        "measurement__quantity_measured",
-        "measurement__variable_measured"
+        "observation__observation_subject",
+        "observation__variable_measured",
+        "observation__measured_using"
       ],
       "slot_usage": {},
       "attributes": [
         {
-          "name": "quantity_measured",
-          "description": "The quantity being measured",
-          "range": "Quantity",
+          "name": "observation_subject",
+          "range": "Entity",
           "@type": "SlotDefinition"
         },
         {
           "name": "variable_measured",
           "description": "The variable being measured",
           "range": "Variable",
           "@type": "SlotDefinition"
+        },
+        {
+          "name": "measured_using",
+          "range": "PhysicalDevice",
+          "@type": "SlotDefinition"
         }
       ],
-      "class_uri": "https://w3id.org/linkml-common/Measurement",
+      "class_uri": "https://w3id.org/linkml-common/Observation",
       "@type": "ClassDefinition"
     },
     {
-      "name": "Variable",
-      "definition_uri": "https://w3id.org/linkml-common/Variable",
+      "name": "Measurement",
+      "definition_uri": "https://w3id.org/linkml-common/Measurement",
       "from_schema": "https://w3id.org/linkml-common/meaurements",
-      "is_a": "Intangible",
+      "is_a": "Observation",
       "slots": [
         "type",
-        "variable__allowed_units"
+        "starts_at",
+        "ends_at",
+        "happens_at",
+        "has_interval",
+        "has_duration",
+        "is_ongoing_as_of",
+        "id",
+        "name",
+        "observation__observation_subject",
+        "observation__variable_measured",
+        "observation__measured_using",
+        "measurement__quantity_measured"
       ],
       "slot_usage": {},
       "attributes": [
         {
-          "name": "allowed_units",
-          "description": "The units that are allowed for this variable",
-          "multivalued": true,
-          "range": "UnitConcept",
+          "name": "quantity_measured",
+          "description": "The quantity being measured",
+          "range": "Quantity",
           "@type": "SlotDefinition"
         }
       ],
-      "class_uri": "https://w3id.org/linkml-common/Variable",
+      "class_uri": "https://w3id.org/linkml-common/Measurement",
       "@type": "ClassDefinition"
     },
     {
-      "name": "Observation",
-      "definition_uri": "https://w3id.org/linkml-common/Observation",
-      "description": "A statement about the state of something",
-      "from_schema": "https://w3id.org/linkml-common/quantities",
-      "is_a": "Event",
+      "name": "QualitativeObservation",
+      "definition_uri": "https://w3id.org/linkml-common/QualitativeObservation",
+      "from_schema": "https://w3id.org/linkml-common/meaurements",
+      "is_a": "Observation",
       "slots": [
         "type",
         "starts_at",
@@ -4838,10 +4878,35 @@
         "has_duration",
         "is_ongoing_as_of",
         "id",
-        "name"
+        "name",
+        "observation__observation_subject",
+        "observation__variable_measured",
+        "observation__measured_using"
       ],
       "slot_usage": {},
-      "class_uri": "https://w3id.org/linkml-common/Observation",
+      "class_uri": "https://w3id.org/linkml-common/QualitativeObservation",
+      "@type": "ClassDefinition"
+    },
+    {
+      "name": "Variable",
+      "definition_uri": "https://w3id.org/linkml-common/Variable",
+      "from_schema": "https://w3id.org/linkml-common/meaurements",
+      "is_a": "Intangible",
+      "slots": [
+        "type",
+        "variable__allowed_units"
+      ],
+      "slot_usage": {},
+      "attributes": [
+        {
+          "name": "allowed_units",
+          "description": "The units that are allowed for this variable",
+          "multivalued": true,
+          "range": "UnitConcept",
+          "@type": "SlotDefinition"
+        }
+      ],
+      "class_uri": "https://w3id.org/linkml-common/Variable",
       "@type": "ClassDefinition"
     },
     {
@@ -5830,7 +5895,7 @@
   "source_file": "linkml_common.yaml",
   "source_file_date": "2024-06-13T21:47:13",
   "source_file_size": 830,
-  "generation_date": "2024-06-13T22:19:59",
+  "generation_date": "2024-06-13T22:32:40",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/linkml_common.context.jsonld",