refactor

linkml · Jun 21, 2024 · 8d73917 · 8d73917
1 parent 88af46c
commit 8d73917
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Showing 51 changed files with 21,953 additions and 8,922 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
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": "2024-06-13T22:32:40",
+      "generation_date": "2024-06-20T18:35:53",
       "source": "linkml_common.yaml"
    },
    "@context": {
@@ -21,10 +21,14 @@
          "@id": "http://purl.obolibrary.org/obo/OBI_",
          "@prefix": true
       },
+      "OrganizationPersonnelRelationshipEnum": "http://example.org/UNKNOWN/OrganizationPersonnelRelationshipEnum/",
       "PATO": {
          "@id": "http://purl.obolibrary.org/obo/PATO_",
          "@prefix": true
       },
+      "PersonInRole": {
+         "@id": "PersonInRole"
+      },
       "UCUM": "http://unitsofmeasure.org/",
       "UO": {
          "@id": "http://purl.obolibrary.org/obo/UO_",
@@ -84,6 +88,10 @@
          "@type": "@id",
          "@id": "patient"
       },
+      "subject": {
+         "@type": "@id",
+         "@id": "subject"
+      },
       "immediate_preceding_steps": {
          "@type": "@id",
          "@id": "immediate_preceding_steps"
@@ -143,6 +151,10 @@
       "description": {
          "@id": "schema:description"
       },
+      "economy_of_place": {
+         "@type": "@id",
+         "@id": "economy_of_place"
+      },
       "plants": {
          "@type": "@id",
          "@id": "plants"
@@ -306,9 +318,21 @@
          "@id": "dam"
       },
       "id": "@id",
+      "design": {
+         "@type": "@id",
+         "@id": "design"
+      },
+      "hypothesis": {
+         "@type": "@id",
+         "@id": "hypothesis"
+      },
       "objectives": {
          "@id": "objectives"
       },
+      "results": {
+         "@type": "@id",
+         "@id": "results"
+      },
       "variables": {
          "@type": "@id",
          "@id": "variables"
@@ -350,6 +374,10 @@
          },
          "@id": "mining_method"
       },
+      "models": {
+         "@type": "@id",
+         "@id": "models"
+      },
       "unit": {
          "@type": "@id",
          "@id": "unit"
@@ -363,7 +391,7 @@
       },
       "object": {
          "@type": "@id",
-         "@id": "rdf:object"
+         "@id": "object"
       },
       "measured_using": {
          "@type": "@id",
@@ -381,6 +409,27 @@
          "@type": "@id",
          "@id": "ontology_types"
       },
+      "has_person_roles": {
+         "@type": "@id",
+         "@id": "has_person_roles"
+      },
+      "predicate": {
+         "@context": {
+            "@vocab": "@null",
+            "text": "skos:notation",
+            "description": "skos:prefLabel",
+            "meaning": "@id"
+         },
+         "@id": "predicate"
+      },
+      "for_organization": {
+         "@type": "@id",
+         "@id": "for_organization"
+      },
+      "relationships": {
+         "@type": "@id",
+         "@id": "relationships"
+      },
       "accuracy": {
          "@type": "xsd:float",
          "@id": "accuracy"
@@ -413,6 +462,22 @@
          "@type": "xsd:integer",
          "@id": "true_positive_count"
       },
+      "person_role": {
+         "@type": "@id",
+         "@id": "person_role"
+      },
+      "subject_person": {
+         "@type": "@id",
+         "@id": "subject_person"
+      },
+      "components": {
+         "@type": "@id",
+         "@id": "components"
+      },
+      "events": {
+         "@type": "@id",
+         "@id": "events"
+      },
       "uses_configuration": {
          "@type": "@id",
          "@id": "uses_configuration"
@@ -521,6 +586,10 @@
          "@type": "@id",
          "@id": "material_collected"
       },
+      "observations": {
+         "@type": "@id",
+         "@id": "observations"
+      },
       "outcome": {
          "@context": {
             "@vocab": "@null",
@@ -534,18 +603,20 @@
          "@type": "@id",
          "@id": "starts_at"
       },
-      "subject": {
+      "result": {
+         "@id": "result"
+      },
+      "over_interval": {
          "@type": "@id",
-         "@id": "rdf:subject"
+         "@id": "over_interval"
       },
-      "predicate": {
-         "@context": {
-            "@vocab": "@null",
-            "text": "skos:notation",
-            "description": "skos:prefLabel",
-            "meaning": "@id"
-         },
-         "@id": "predicate"
+      "interpretations": {
+         "@type": "@id",
+         "@id": "interpretations"
+      },
+      "measurements": {
+         "@type": "@id",
+         "@id": "measurements"
       },
       "relative_to": {
          "@type": "@id",
@@ -593,6 +664,9 @@
       "Any": {
          "@id": "linkml:Any"
       },
+      "AstronomicalBody": {
+         "@id": "AstronomicalBody"
+      },
       "AutomatedAgent": {
          "@id": "AutomatedAgent"
       },
@@ -608,6 +682,12 @@
       "BuiltSystem": {
          "@id": "BuiltSystem"
       },
+      "Climate": {
+         "@id": "Climate"
+      },
+      "ClimateModel": {
+         "@id": "ClimateModel"
+      },
       "ClinicalCohort": {
          "@id": "ClinicalCohort"
       },
@@ -617,9 +697,15 @@
       "ClinicalCohortEnrollment": {
          "@id": "ClinicalCohortEnrollment"
       },
+      "ClinicalHistory": {
+         "@id": "ClinicalHistory"
+      },
       "CompositeFoodType": {
          "@id": "CompositeFoodType"
       },
+      "ComputationalModel": {
+         "@id": "ComputationalModel"
+      },
       "ComputationalPlannedProcess": {
          "@id": "ComputationalPlannedProcess"
       },
@@ -644,9 +730,15 @@
       "DataStructure": {
          "@id": "DataStructure"
       },
+      "DigitalTwin": {
+         "@id": "DigitalTwin"
+      },
       "Duration": {
          "@id": "Duration"
       },
+      "EconomicSystem": {
+         "@id": "EconomicSystem"
+      },
       "ElectricalGrid": {
          "@id": "ElectricalGrid"
       },
@@ -668,6 +760,9 @@
       "EnvironmentalSite": {
          "@id": "EnvironmentalSite"
       },
+      "EnvironmentalSystem": {
+         "@id": "EnvironmentalSystem"
+      },
       "Equipment": {
          "@id": "Equipment"
       },
@@ -704,6 +799,9 @@
       "FoodIngredient": {
          "@id": "FoodIngredient"
       },
+      "FoodPreparation": {
+         "@id": "FoodPreparation"
+      },
       "FoodProcessing": {
          "@id": "FoodProcessing"
       },
@@ -746,6 +844,9 @@
       "Identified": {
          "@id": "Identified"
       },
+      "IndividualOrganism": {
+         "@id": "organisms/IndividualOrganism"
+      },
       "InformationEntity": {
          "@id": "InformationEntity"
       },
@@ -782,21 +883,33 @@
       "MiningFacility": {
          "@id": "MiningFacility"
       },
+      "Model": {
+         "@id": "Model"
+      },
       "MoneyQuantity": {
          "@id": "fhir:MoneyQuantity"
       },
-      "NamedThing": {
-         "@id": "NamedThing"
-      },
       "NuclearPlant": {
          "@id": "NuclearPlant"
       },
       "Observation": {
          "@id": "Observation"
       },
+      "OrganismalRelationship": {
+         "@id": "organisms/OrganismalRelationship"
+      },
       "Organization": {
          "@id": "Organization"
       },
+      "OrganizationalRole": {
+         "@id": "OrganizationalRole"
+      },
+      "OrganizationPersonnelRelationship": {
+         "@id": "OrganizationPersonnelRelationship"
+      },
+      "OrgChart": {
+         "@id": "OrgChart"
+      },
       "OutcomeStatistics": {
          "@id": "OutcomeStatistics"
       },
@@ -809,6 +922,12 @@
       "PhysicalDevice": {
          "@id": "PhysicalDevice"
       },
+      "PhysicalEntity": {
+         "@id": "PhysicalEntity"
+      },
+      "PhysicalSystem": {
+         "@id": "PhysicalSystem"
+      },
       "Place": {
          "@id": "schema:Place"
       },
@@ -884,12 +1003,18 @@
       "Service": {
          "@id": "Service"
       },
+      "SetOfObservations": {
+         "@id": "SetOfObservations"
+      },
       "SimplePrediction": {
          "@id": "SimplePrediction"
       },
       "SimpleQuantity": {
          "@id": "fhir:SimpleQuantity"
       },
+      "Simulation": {
+         "@id": "Simulation"
+      },
       "SolarPlant": {
          "@id": "SolarPlant"
       },
@@ -902,6 +1027,18 @@
       "StudyDesign": {
          "@id": "StudyDesign"
       },
+      "StudyHypothesis": {
+         "@id": "StudyHypothesis"
+      },
+      "StudyResult": {
+         "@id": "StudyResult"
+      },
+      "SubjectHistory": {
+         "@id": "SubjectHistory"
+      },
+      "SubjectObservationHistory": {
+         "@id": "SubjectObservationHistory"
+      },
       "TemporalInterval": {
          "@id": "TemporalInterval"
       },
@@ -923,6 +1060,9 @@
       "Variable": {
          "@id": "Variable"
       },
+      "VeterinaryAnimal": {
+         "@id": "VeterinaryAnimal"
+      },
       "WellFacility": {
          "@id": "WellFacility"
       },