From ac86255d13cfa75c86e13f34090f3bebd64a5c10 Mon Sep 17 00:00:00 2001 From: linkmluser Date: Fri, 2 Feb 2024 17:35:11 -0800 Subject: [PATCH] examples --- README.md | 39 +- poetry.lock | 2629 +++++++++++---- project/excel/linkml_common.xlsx | Bin 37406 -> 45894 bytes project/graphql/linkml_common.graphql | 208 +- project/jsonld/linkml_common.context.jsonld | 75 +- project/jsonld/linkml_common.jsonld | 827 ++++- project/jsonschema/linkml_common.schema.json | 998 +++++- project/owl/linkml_common.owl.ttl | 1486 ++++++--- project/prefixmap/linkml_common.yaml | 17 +- project/protobuf/linkml_common.proto | 199 +- project/shacl/linkml_common.shacl.ttl | 2946 +++++++++++------ project/shex/linkml_common.shex | 288 +- project/sqlschema/linkml_common.sql | 249 +- pyproject.toml | 3 +- src/data/examples/valid/Dataset-001.yaml | 11 + src/data/examples/valid/Event-001.yaml | 6 + src/linkml_common/datamodel/linkml_common.py | 616 +++- src/linkml_common/schema/bibliographic.yaml | 4 +- .../schema/clinicalresearch.yaml | 7 +- src/linkml_common/schema/computational.yaml | 1 - src/linkml_common/schema/core.yaml | 28 +- src/linkml_common/schema/datasets.yaml | 33 + src/linkml_common/schema/environmental.yaml | 7 + src/linkml_common/schema/financial.yaml | 24 +- src/linkml_common/schema/foods.yaml | 2 + src/linkml_common/schema/healthcare.yaml | 1 + src/linkml_common/schema/investigations.yaml | 25 + src/linkml_common/schema/linkml_common.yaml | 1 + src/linkml_common/schema/plannedprocess.yaml | 3 + src/linkml_common/schema/quantities.yaml | 20 + src/linkml_common/schema/social.yaml | 76 +- src/linkml_common/schema/time.yaml | 68 +- 32 files changed, 8488 insertions(+), 2409 deletions(-) create mode 100644 src/data/examples/valid/Dataset-001.yaml create mode 100644 src/data/examples/valid/Event-001.yaml create mode 100644 src/linkml_common/schema/datasets.yaml diff --git a/README.md b/README.md index 21f46eb..2660a97 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,46 @@ # linkml-common -Common Data Model Elements +LinkML Common Modeling Elements and Types (COMET) -## Website +## Web Index of Elements [https://linkml.github.io/linkml-common](https://linkml.github.io/linkml-common) +## Why not schema.org? + +The [schema.org](https://schema.org) project is a great resource for high level annotation of web pages and other +resources. LinkML-Common differs from schema.org in a number of ways + +* Opinionated + - schema.org is great for annotating data with minimum fuss + - LinkML-Common enforces a more constrained data model, and is a *validation-first* framework +* Focused on Science, Technology, Engineering, Mathematics, and Scholarly Communication + - schema.org has excellent broad coverage of a number of domains + - LinkML-Common has a focus on science and adjacent domains. There is more emphasis on modeling investigations, + and adhering to ontologies such as the [Ontology for Biomedical Investigations](https://obofoundry.org/ontology/obi.html) + +## How does it compare to FHIR/OMOP/CDISC + +LinkML-Common has a broader remit than healthcare or clinical research data models. However, it is intended +to give broad coverage in these domains, and to be extensible. We aim to provide rigorous computable transformations +between COMET and these models + +## How does it compare to Biolink? + +Biolink is a Knowledge Graph model that emphasizes shared knowledge entities such as genes, diseases, drugs. +These are largely not modeled to any great extent in COMET, and the idea is that these models can be combined. + +## Can I adapt it? + +Yes! If you don't like our modeling, the idea is to use [LinkML-Transformer](https://github.com/linkml/linkml-transformer) +to profile, extend, and adapt the modeling elements here. + +Note that like COMET, LinkML-Transformer is not yet mature and is under active development. + +## Do I have to use LinkML? + +We also provide Pydantic, OWL, JSON-Schema, and many other representations. + ## Repository Structure * [examples/](examples/) - example data diff --git a/poetry.lock b/poetry.lock index 9f42805..f13d247 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,5 +1,21 @@ # This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +[[package]] +name = "airium" +version = "0.2.6" +description = "Easy and quick html builder with natural syntax correspondence (python->html). No templates needed. 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b/project/graphql/linkml_common.graphql index 1c823c3..b5f590a 100644 --- a/project/graphql/linkml_common.graphql +++ b/project/graphql/linkml_common.graphql @@ -1,7 +1,27 @@ +type Agent + { + id: Uriorcurie! + name: String + type: String + subtype: String + ontologyTypes: [Concept] + description: String + } + type Any { } +type AutomatedAgent + { + id: Uriorcurie! + name: String + type: String + subtype: String + ontologyTypes: [Concept] + description: String + } + type BasicFoodType { id: Uriorcurie! @@ -43,6 +63,9 @@ type ClinicalCohortEnrollment description: String startsAt: TimePoint endsAt: TimePoint + happensAt: TimePoint + hasInterval: TemporalInterval + hasDuration: Duration patient: Patient cohort: ClinicalCohort } @@ -73,6 +96,23 @@ type Concept description: String } +type CreativeWork + { + id: Uriorcurie! + name: String + type: String + subtype: String + ontologyTypes: [Concept] + description: String + title: String + abstract: String + rights: String + creators: [Agent] + contributors: [Agent] + contacts: [Agent] + keywords: [String] + } + type DataGenerationFromSample { id: Uriorcurie! @@ -83,16 +123,43 @@ type DataGenerationFromSample description: String startsAt: TimePoint endsAt: TimePoint + happensAt: TimePoint + hasInterval: TemporalInterval + hasDuration: Duration usesPhysicalDevice: PhysicalDevice followsProcedure: InvestigativeProtocol partOf: Investigation } +type Dataset + { + id: Uriorcurie! + name: String + type: String + subtype: String + ontologyTypes: [Concept] + description: String + title: String + abstract: String + rights: String + creators: [Agent] + contributors: [Agent] + contacts: [Agent] + keywords: [String] + collectedAsPartOf: [Investigation] + } + type DataStructure { type: String } +type Duration + { + type: String + hasQuantityKind: QuantityKind + } + type EngineeringMaterialProcessing { id: Uriorcurie! @@ -103,6 +170,9 @@ type EngineeringMaterialProcessing description: String startsAt: TimePoint endsAt: TimePoint + happensAt: TimePoint + hasInterval: TemporalInterval + hasDuration: Duration followsProcedure: Procedure usesPhysicalDevice: PhysicalDevice } @@ -117,6 +187,9 @@ type EngineeringProcess description: String startsAt: TimePoint endsAt: TimePoint + happensAt: TimePoint + hasInterval: TemporalInterval + hasDuration: Duration followsProcedure: EngineeringSpecification partOf: EngineeringProcess } @@ -136,10 +209,26 @@ interface Entity type: String } +type EnvironmentalMonitoring + { + } + type EnvironmentalProcess { } +type EnvironmentalSite + { + id: Uriorcurie! + name: String + type: String + subtype: String + ontologyTypes: [Concept] + description: String + address: PostalAddress + geolocation: GeoPointLocation + } + type Event { id: Uriorcurie! @@ -150,11 +239,15 @@ type Event description: String startsAt: TimePoint endsAt: TimePoint + happensAt: TimePoint + hasInterval: TemporalInterval + hasDuration: Duration } type FoodIngredient { type: String + hasQuantityKind: QuantityKind } type FoodProcessing @@ -167,6 +260,9 @@ type FoodProcessing description: String startsAt: TimePoint endsAt: TimePoint + happensAt: TimePoint + hasInterval: TemporalInterval + hasDuration: Duration followsProcedure: Procedure usesPhysicalDevice: PhysicalDevice } @@ -210,6 +306,9 @@ type HealthcareConditionOccurrence description: String startsAt: TimePoint endsAt: TimePoint + happensAt: TimePoint + hasInterval: TemporalInterval + hasDuration: Duration patient: Patient observedDuring: HealthcareEncounter } @@ -223,6 +322,9 @@ type HealthcareEncounter description: String startsAt: TimePoint endsAt: TimePoint + happensAt: TimePoint + hasInterval: TemporalInterval + hasDuration: Duration patient: Patient provider: HealthcareProvider subtype: HealthcareEncounterClassification @@ -240,6 +342,7 @@ type HealthcareOrganization type HealthcareProvider { + type: String isPerson: Person speciality: Concept careSite: HealthcareSite @@ -247,6 +350,7 @@ type HealthcareProvider type HealthcareRole { + type: String isPerson: Person } @@ -287,6 +391,7 @@ type Investigation ontologyTypes: [Concept] description: String objectives: String + variables: [Variable] } type InvestigativeProcess @@ -299,6 +404,9 @@ type InvestigativeProcess description: String startsAt: TimePoint endsAt: TimePoint + happensAt: TimePoint + hasInterval: TemporalInterval + hasDuration: Duration usesPhysicalDevice: PhysicalDevice followsProcedure: InvestigativeProtocol partOf: Investigation @@ -336,6 +444,9 @@ type LifeEvent description: String startsAt: TimePoint endsAt: TimePoint + happensAt: TimePoint + hasInterval: TemporalInterval + hasDuration: Duration } interface Location @@ -352,6 +463,9 @@ type MaterialCollection description: String startsAt: TimePoint endsAt: TimePoint + happensAt: TimePoint + hasInterval: TemporalInterval + hasDuration: Duration followsProcedure: Procedure usesPhysicalDevice: PhysicalDevice } @@ -366,6 +480,9 @@ type MaterialProcessing description: String startsAt: TimePoint endsAt: TimePoint + happensAt: TimePoint + hasInterval: TemporalInterval + hasDuration: Duration followsProcedure: Procedure usesPhysicalDevice: PhysicalDevice } @@ -412,6 +529,7 @@ type Organization type Patient { + type: String isPerson: Person } @@ -461,6 +579,9 @@ type PlannedProcess description: String startsAt: TimePoint endsAt: TimePoint + happensAt: TimePoint + hasInterval: TemporalInterval + hasDuration: Duration followsProcedure: Procedure usesPhysicalDevice: PhysicalDevice } @@ -498,11 +619,29 @@ type Publication subtype: String ontologyTypes: [Concept] description: String + title: String + abstract: String + rights: String + creators: [Agent] + contributors: [Agent] + contacts: [Agent] + keywords: [String] } type Quantity { type: String + hasQuantityKind: QuantityKind + } + +type QuantityKind + { + id: Uriorcurie! + name: String + type: String + subtype: String + ontologyTypes: [Concept] + description: String } type QuantityRange @@ -515,6 +654,7 @@ type QuantityRange type Ratio { type: String + hasQuantityKind: QuantityKind numerator: Quantity denominator: Quantity } @@ -531,6 +671,12 @@ type RawMaterial interface Relationship { + type: String + } + +interface Role + { + type: String } type SampleCollectionProcess @@ -543,6 +689,9 @@ type SampleCollectionProcess description: String startsAt: TimePoint endsAt: TimePoint + happensAt: TimePoint + hasInterval: TemporalInterval + hasDuration: Duration usesPhysicalDevice: PhysicalDevice followsProcedure: InvestigativeProtocol partOf: Investigation @@ -570,19 +719,66 @@ type SampleProcessing description: String startsAt: TimePoint endsAt: TimePoint + happensAt: TimePoint + hasInterval: TemporalInterval + hasDuration: Duration followsProcedure: Procedure usesPhysicalDevice: PhysicalDevice } +type Service + { + type: String + } + type SimpleQuantity { type: String + hasQuantityKind: QuantityKind value: Float unit: UnitConcept } +type Specification + { + id: Uriorcurie! + name: String + type: String + subtype: String + ontologyTypes: [Concept] + description: String + } + +type StudyDesign + { + id: Uriorcurie! + name: String + type: String + subtype: String + ontologyTypes: [Concept] + description: String + } + +type TemporalInterval + { + type: String + startsAt: TimePoint + endsAt: TimePoint + } + +type TemporalRelationship + { + type: String + predicate: RelativeTimeEnum + relativeTo: Entity + } + type TimePoint { + type: String + startsAt: TimePoint + endsAt: TimePoint + yearValue: Integer dateValue: Date timeValue: Time datetimeValue: Datetime @@ -590,6 +786,13 @@ type TimePoint description: String } +type TimePointOrTemporalInterval + { + type: String + startsAt: TimePoint + endsAt: TimePoint + } + type UnitConcept { id: Uriorcurie! @@ -614,8 +817,3 @@ type Variable allowedUnits: [UnitConcept] } -type XProcess - { - type: String - } - diff --git a/project/jsonld/linkml_common.context.jsonld b/project/jsonld/linkml_common.context.jsonld index 411473d..d8c8e61 100644 --- a/project/jsonld/linkml_common.context.jsonld +++ b/project/jsonld/linkml_common.context.jsonld @@ -1,14 +1,26 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2024-01-13T18:02:29", + "generation_date": "2024-02-02T17:33:00", "source": "linkml_common.yaml" }, "@context": { + "BFO": { + "@id": "http://purl.obolibrary.org/obo/BFO_", + "@prefix": true + }, "ENVO": { "@id": "http://purl.obolibrary.org/obo/ENVO_", "@prefix": true }, + "IAO": { + "@id": "http://purl.obolibrary.org/obo/IAO_", + "@prefix": true + }, + "OBI": { + "@id": "http://purl.obolibrary.org/obo/OBI_", + "@prefix": true + }, "PATO": { "@id": "http://purl.obolibrary.org/obo/PATO_", "@prefix": true @@ -16,14 +28,21 @@ "UCUM": "http://example.org/UNKNOWN/UCUM/", "UO": "http://example.org/UNKNOWN/UO/", "biolink": "https://w3id.org/biolink/", + "dcterms": "http://purl.org/dc/terms/", "example": "https://example.org/", "fhir": "http://hl7.org/fhir/", + "fibo": "http://example.org/UNKNOWN/fibo/", + "fibo.DatesAndTimes": "https://www.omg.org/spec/Commons/DatesAndTimes/", + "fibo.QuantitiesAndUnits": "https://www.omg.org/spec/Commons/QuantitiesAndUnits/", + "fibo.commons.PartiesAndSituations": "https://spec.edmcouncil.org/fibo/ontology/FBC/ommons/PartiesAndSituations/", "linkml": "https://w3id.org/linkml/", "linkml_common": "https://w3id.org/linkml-common/", "nmdcschema": "http://example.org/UNKNOWN/nmdcschema/", "omopschema": "http://example.org/omop/", - "qudt": "http://example.org/UNKNOWN/qudt/", - "rdf": "http://example.org/UNKNOWN/rdf/", + "prov": "http://www.w3.org/ns/prov#", + "qudt": "http://qudt.org/vocab/unit/", + "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", "schema": "http://schema.org/", "skos": "http://www.w3.org/2004/02/skos/core#", "@vocab": "https://w3id.org/linkml-common/", @@ -49,6 +68,24 @@ "members": { "@type": "@id" }, + "contacts": { + "@type": "@id", + "@id": "schema:contactPoint" + }, + "contributors": { + "@type": "@id", + "@id": "dcterms:contributor" + }, + "creators": { + "@type": "@id", + "@id": "dcterms:creator" + }, + "keywords": { + "@id": "schema:keywords" + }, + "collected_as_part_of": { + "@type": "@id" + }, "date_value": { "@type": "xsd:date" }, @@ -89,6 +126,15 @@ "longitude": { "@type": "xsd:decimal" }, + "happens_at": { + "@type": "@id" + }, + "has_duration": { + "@type": "@id" + }, + "has_interval": { + "@type": "@id" + }, "observed_during": { "@type": "@id" }, @@ -105,6 +151,9 @@ "@type": "@id" }, "id": "@id", + "variables": { + "@type": "@id" + }, "marker_event": { "@type": "@id" }, @@ -142,6 +191,9 @@ "primary_email": { "@id": "schema:email" }, + "has_quantity_kind": { + "@type": "@id" + }, "lower_bound": { "@type": "@id" }, @@ -173,6 +225,17 @@ "@type": "@id", "@id": "rdf:subject" }, + "predicate": { + "@context": { + "@vocab": "@null", + "text": "skos:notation", + "description": "skos:prefLabel", + "meaning": "@id" + } + }, + "relative_to": { + "@type": "@id" + }, "time_value": { "@type": "xsd:time" }, @@ -187,6 +250,9 @@ "meaning": "@id" } }, + "year_value": { + "@type": "xsd:integer" + }, "Any": { "@id": "linkml:Any" }, @@ -211,6 +277,9 @@ "Ratio": { "@id": "fhir:Ratio" }, + "Role": { + "@id": "schema:Role" + }, "SimpleQuantity": { "@id": "fhir:SimpleQuantity" } diff --git a/project/jsonld/linkml_common.jsonld b/project/jsonld/linkml_common.jsonld index 6f08aa8..57cf697 100644 --- a/project/jsonld/linkml_common.jsonld +++ b/project/jsonld/linkml_common.jsonld @@ -10,6 +10,7 @@ "linkml:types", "core", "bibliographic", + "datasets", "clinicalresearch", "computational", "engineering", @@ -416,6 +417,42 @@ } ] }, + { + "name": "CaseOrControlEnum", + "definition_uri": "https://w3id.org/linkml-common/CaseOrControlEnum", + "from_schema": "https://w3id.org/linkml-common/investigations", + "permissible_values": [ + { + "text": "CASE", + "meaning": "OBI:0002492", + "title": "case role in case-control study" + }, + { + "text": "CONTROL", + "meaning": "OBI:0002493", + "title": "control role in case-control study" + } + ] + }, + { + "name": "StudyDesignEnum", + "definition_uri": "https://w3id.org/linkml-common/StudyDesignEnum", + "from_schema": "https://w3id.org/linkml-common/investigations", + "reachable_from": { + "source_nodes": [ + "OBI:0500000" + ], + "relationship_types": [ + "rdfs:subClassOf" + ] + } + }, + { + "name": "HumanLanguageCodeEnum", + "definition_uri": "https://w3id.org/linkml-common/HumanLanguageCodeEnum", + "description": "An enumeration of languages", + "from_schema": "https://w3id.org/linkml-common/social" + }, { "name": "PersonStatus", "definition_uri": "https://w3id.org/linkml-common/PersonStatus", @@ -439,6 +476,22 @@ ] } ] + }, + { + "name": "RelativeTimeEnum", + "definition_uri": "https://w3id.org/linkml-common/RelativeTimeEnum", + "from_schema": "https://w3id.org/linkml-common/time", + "permissible_values": [ + { + "text": "BEFORE" + }, + { + "text": "AFTER" + }, + { + "text": "AT_SAME_TIME_AS" + } + ] } ], "slots": [ @@ -557,9 +610,9 @@ "description": "The subject of a relationship", "from_schema": "https://w3id.org/linkml-common/core", "mappings": [ - "http://example.org/UNKNOWN/rdf/subject" + "http://www.w3.org/1999/02/22-rdf-syntax-ns#subject" ], - "slot_uri": "http://example.org/UNKNOWN/rdf/subject", + "slot_uri": "http://www.w3.org/1999/02/22-rdf-syntax-ns#subject", "range": "Any", "inlined": true, "@type": "SlotDefinition" @@ -570,9 +623,9 @@ "description": "The object of a relationship", "from_schema": "https://w3id.org/linkml-common/core", "mappings": [ - "http://example.org/UNKNOWN/rdf/object" + "http://www.w3.org/1999/02/22-rdf-syntax-ns#object" ], - "slot_uri": "http://example.org/UNKNOWN/rdf/object", + "slot_uri": "http://www.w3.org/1999/02/22-rdf-syntax-ns#object", "range": "Any", "inlined": true, "@type": "SlotDefinition" @@ -667,9 +720,11 @@ "definition_uri": "https://w3id.org/linkml-common/starts_at", "from_schema": "https://w3id.org/linkml-common/time", "slot_uri": "https://w3id.org/linkml-common/starts_at", - "owner": "Event", + "owner": "TemporalInterval", "domain_of": [ - "Event" + "Event", + "TimePointOrTemporalInterval", + "TemporalInterval" ], "range": "TimePoint", "inlined": true, @@ -680,6 +735,21 @@ "definition_uri": "https://w3id.org/linkml-common/ends_at", "from_schema": "https://w3id.org/linkml-common/time", "slot_uri": "https://w3id.org/linkml-common/ends_at", + "owner": "TemporalInterval", + "domain_of": [ + "Event", + "TimePointOrTemporalInterval", + "TemporalInterval" + ], + "range": "TimePoint", + "inlined": true, + "@type": "SlotDefinition" + }, + { + "name": "happens_at", + "definition_uri": "https://w3id.org/linkml-common/happens_at", + "from_schema": "https://w3id.org/linkml-common/time", + "slot_uri": "https://w3id.org/linkml-common/happens_at", "owner": "Event", "domain_of": [ "Event" @@ -688,6 +758,18 @@ "inlined": true, "@type": "SlotDefinition" }, + { + "name": "year_value", + "definition_uri": "https://w3id.org/linkml-common/year_value", + "from_schema": "https://w3id.org/linkml-common/time", + "slot_uri": "https://w3id.org/linkml-common/year_value", + "owner": "TimePoint", + "domain_of": [ + "TimePoint" + ], + "range": "integer", + "@type": "SlotDefinition" + }, { "name": "date_value", "definition_uri": "https://w3id.org/linkml-common/date_value", @@ -736,6 +818,32 @@ "range": "Event", "@type": "SlotDefinition" }, + { + "name": "has_interval", + "definition_uri": "https://w3id.org/linkml-common/has_interval", + "from_schema": "https://w3id.org/linkml-common/time", + "slot_uri": "https://w3id.org/linkml-common/has_interval", + "owner": "Event", + "domain_of": [ + "Event" + ], + "range": "TemporalInterval", + "inlined": true, + "@type": "SlotDefinition" + }, + { + "name": "has_duration", + "definition_uri": "https://w3id.org/linkml-common/has_duration", + "from_schema": "https://w3id.org/linkml-common/time", + "slot_uri": "https://w3id.org/linkml-common/has_duration", + "owner": "Event", + "domain_of": [ + "Event" + ], + "range": "Duration", + "inlined": true, + "@type": "SlotDefinition" + }, { "name": "mathematicalOperation__inputs", "description": "The inputs to the operation", @@ -812,6 +920,19 @@ "inlined_as_list": true, "@type": "SlotDefinition" }, + { + "name": "dataset__collected_as_part_of", + "from_schema": "https://w3id.org/linkml-common/datasets", + "slot_uri": "https://w3id.org/linkml-common/collected_as_part_of", + "multivalued": true, + "alias": "collected_as_part_of", + "owner": "Dataset", + "domain_of": [ + "Dataset" + ], + "range": "Investigation", + "@type": "SlotDefinition" + }, { "name": "clinicalCohort__definition", "from_schema": "https://w3id.org/linkml-common/clinicalresearch", @@ -1128,6 +1249,20 @@ "range": "string", "@type": "SlotDefinition" }, + { + "name": "investigation__variables", + "from_schema": "https://w3id.org/linkml-common/investigations", + "slot_uri": "https://w3id.org/linkml-common/variables", + "multivalued": true, + "alias": "variables", + "owner": "Investigation", + "domain_of": [ + "Investigation" + ], + "range": "Variable", + "inlined": true, + "@type": "SlotDefinition" + }, { "name": "investigativeProcess__follows_procedure", "from_schema": "https://w3id.org/linkml-common/investigations", @@ -1218,6 +1353,19 @@ "range": "UnitConcept", "@type": "SlotDefinition" }, + { + "name": "quantity__has_quantity_kind", + "description": "The kind of quantity", + "from_schema": "https://w3id.org/linkml-common/quantities", + "slot_uri": "https://w3id.org/linkml-common/has_quantity_kind", + "alias": "has_quantity_kind", + "owner": "Quantity", + "domain_of": [ + "Quantity" + ], + "range": "QuantityKind", + "@type": "SlotDefinition" + }, { "name": "simpleQuantity__value", "description": "The value of the quantity", @@ -1234,6 +1382,10 @@ { "name": "simpleQuantity__unit", "from_schema": "https://w3id.org/linkml-common/quantities", + "exact_mappings": [ + "http://schema.org/unitCode", + "http://qudt.org/vocab/unit/unit" + ], "slot_uri": "https://w3id.org/linkml-common/unit", "alias": "unit", "owner": "SimpleQuantity", @@ -1299,6 +1451,156 @@ "inlined": true, "@type": "SlotDefinition" }, + { + "name": "creativeWork__title", + "description": "The title of the item", + "from_schema": "https://w3id.org/linkml-common/social", + "exact_mappings": [ + "http://purl.org/dc/terms/title" + ], + "slot_uri": "https://w3id.org/linkml-common/title", + "alias": "title", + "owner": "CreativeWork", + "domain_of": [ + "CreativeWork" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "creativeWork__abstract", + "description": "A summary of the item", + "from_schema": "https://w3id.org/linkml-common/social", + "slot_uri": "https://w3id.org/linkml-common/abstract", + "alias": "abstract", + "owner": "CreativeWork", + "domain_of": [ + "CreativeWork" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "creativeWork__rights", + "description": "Information about rights held in and over the item", + "from_schema": "https://w3id.org/linkml-common/social", + "slot_uri": "https://w3id.org/linkml-common/rights", + "alias": "rights", + "owner": "CreativeWork", + "domain_of": [ + "CreativeWork" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "creativeWork__creators", + "description": "The person or organization who created the work", + "from_schema": "https://w3id.org/linkml-common/social", + "mappings": [ + "http://purl.org/dc/terms/creator" + ], + "slot_uri": "http://purl.org/dc/terms/creator", + "multivalued": true, + "alias": "creators", + "owner": "CreativeWork", + "domain_of": [ + "CreativeWork" + ], + "range": "Agent", + "@type": "SlotDefinition" + }, + { + "name": "creativeWork__contributors", + "description": "A person or organization that contributed to the creation of the work", + "from_schema": "https://w3id.org/linkml-common/social", + "mappings": [ + "http://purl.org/dc/terms/contributor" + ], + "slot_uri": "http://purl.org/dc/terms/contributor", + "multivalued": true, + "alias": "contributors", + "owner": "CreativeWork", + "domain_of": [ + "CreativeWork" + ], + "range": "Agent", + "@type": "SlotDefinition" + }, + { + "name": "creativeWork__contacts", + "description": "A contact point for a person or organization", + "from_schema": "https://w3id.org/linkml-common/social", + "mappings": [ + "http://schema.org/contactPoint" + ], + "slot_uri": "http://schema.org/contactPoint", + "multivalued": true, + "alias": "contacts", + "owner": "CreativeWork", + "domain_of": [ + "CreativeWork" + ], + "range": "Agent", + "@type": "SlotDefinition" + }, + { + "name": "creativeWork__keywords", + "description": "Keywords or tags used to describe this item", + "from_schema": "https://w3id.org/linkml-common/social", + "mappings": [ + "http://schema.org/keywords" + ], + "slot_uri": "http://schema.org/keywords", + "multivalued": true, + "alias": "keywords", + "owner": "CreativeWork", + "domain_of": [ + "CreativeWork" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "temporalRelationship__predicate", + "description": "The relationship between the two time points", + "from_schema": "https://w3id.org/linkml-common/time", + "slot_uri": "https://w3id.org/linkml-common/predicate", + "alias": "predicate", + "owner": "TemporalRelationship", + "domain_of": [ + "TemporalRelationship" + ], + "range": "RelativeTimeEnum", + "@type": "SlotDefinition" + }, + { + "name": "temporalRelationship__relative_to", + "from_schema": "https://w3id.org/linkml-common/time", + "slot_uri": "https://w3id.org/linkml-common/relative_to", + "alias": "relative_to", + "owner": "TemporalRelationship", + "domain_of": [ + "TemporalRelationship" + ], + "range": "Entity", + "inlined": true, + "any_of": [ + { + "range": "TimePoint", + "@type": "AnonymousSlotExpression" + }, + { + "range": "TemporalInterval", + "@type": "AnonymousSlotExpression" + }, + { + "range": "Event", + "@type": "AnonymousSlotExpression" + } + ], + "@type": "SlotDefinition" + }, { "name": "plannedProcess__follows_procedure", "from_schema": "https://w3id.org/linkml-common/plannedprocess", @@ -1531,11 +1833,37 @@ "class_uri": "http://schema.org/Intangible", "@type": "ClassDefinition" }, + { + "name": "Role", + "definition_uri": "https://w3id.org/linkml-common/Role", + "from_schema": "https://w3id.org/linkml-common/core", + "mappings": [ + "schema:Role" + ], + "close_mappings": [ + "BFO:0000023" + ], + "is_a": "Intangible", + "abstract": true, + "slots": [ + "type" + ], + "slot_usage": {}, + "class_uri": "http://schema.org/Role", + "@type": "ClassDefinition" + }, { "name": "Relationship", "definition_uri": "https://w3id.org/linkml-common/Relationship", "from_schema": "https://w3id.org/linkml-common/core", + "close_mappings": [ + "rdfs:Statement" + ], + "is_a": "Intangible", "abstract": true, + "slots": [ + "type" + ], "slot_usage": {}, "class_uri": "https://w3id.org/linkml-common/Relationship", "@type": "ClassDefinition" @@ -1572,10 +1900,13 @@ "@type": "ClassDefinition" }, { - "name": "Procedure", - "definition_uri": "https://w3id.org/linkml-common/Procedure", - "description": "A canonical series of actions conducted in a certain order or manner", + "name": "Specification", + "definition_uri": "https://w3id.org/linkml-common/Specification", + "description": "A specification of a thing", "from_schema": "https://w3id.org/linkml-common/core", + "exact_mappings": [ + "IAO:0000104" + ], "is_a": "NamedThing", "slots": [ "id", @@ -1586,20 +1917,25 @@ "description" ], "slot_usage": {}, - "class_uri": "https://w3id.org/linkml-common/Procedure", + "class_uri": "https://w3id.org/linkml-common/Specification", "@type": "ClassDefinition" }, { - "name": "XProcess", - "definition_uri": "https://w3id.org/linkml-common/XProcess", - "description": "A series of actions or steps taken in order to achieve a particular end", + "name": "Procedure", + "definition_uri": "https://w3id.org/linkml-common/Procedure", + "description": "A canonical series of actions conducted in a certain order or manner", "from_schema": "https://w3id.org/linkml-common/core", - "is_a": "Entity", + "is_a": "Specification", "slots": [ - "type" + "id", + "name", + "type", + "subtype", + "ontology_types", + "description" ], "slot_usage": {}, - "class_uri": "https://w3id.org/linkml-common/XProcess", + "class_uri": "https://w3id.org/linkml-common/Procedure", "@type": "ClassDefinition" }, { @@ -1686,22 +2022,63 @@ "name": "Publication", "definition_uri": "https://w3id.org/linkml-common/Publication", "from_schema": "https://w3id.org/linkml-common/financial", - "is_a": "NamedThing", + "is_a": "CreativeWork", "slots": [ "id", "name", "type", "subtype", "ontology_types", - "description" + "description", + "creativeWork__title", + "creativeWork__abstract", + "creativeWork__rights", + "creativeWork__creators", + "creativeWork__contributors", + "creativeWork__contacts", + "creativeWork__keywords" ], "slot_usage": {}, "class_uri": "https://w3id.org/linkml-common/Publication", "@type": "ClassDefinition" }, + { + "name": "Dataset", + "definition_uri": "https://w3id.org/linkml-common/Dataset", + "from_schema": "https://w3id.org/linkml-common/datasets", + "is_a": "CreativeWork", + "slots": [ + "id", + "name", + "type", + "subtype", + "ontology_types", + "description", + "creativeWork__title", + "creativeWork__abstract", + "creativeWork__rights", + "creativeWork__creators", + "creativeWork__contributors", + "creativeWork__contacts", + "creativeWork__keywords", + "dataset__collected_as_part_of" + ], + "slot_usage": {}, + "attributes": [ + { + "name": "collected_as_part_of", + "multivalued": true, + "range": "Investigation", + "@type": "SlotDefinition" + } + ], + "class_uri": "https://w3id.org/linkml-common/Dataset", + "@type": "ClassDefinition" + }, { "name": "ClinicalCohort", "definition_uri": "https://w3id.org/linkml-common/ClinicalCohort", + "description": "A group of patients who share a common set of characteristics", "from_schema": "https://w3id.org/linkml-common/clinicalresearch", "is_a": "NamedThing", "slots": [ @@ -1727,6 +2104,7 @@ { "name": "ClinicalCohortDefinition", "definition_uri": "https://w3id.org/linkml-common/ClinicalCohortDefinition", + "description": "A definition of a clinical cohort", "from_schema": "https://w3id.org/linkml-common/clinicalresearch", "exact_mappings": [ "omopschema:COHORT_DEFINITION" @@ -1747,6 +2125,7 @@ { "name": "ClinicalCohortEnrollment", "definition_uri": "https://w3id.org/linkml-common/ClinicalCohortEnrollment", + "description": "An event relating a patient to a clinical cohort", "from_schema": "https://w3id.org/linkml-common/clinicalresearch", "exact_mappings": [ "omopschema:COHORT" @@ -1761,6 +2140,9 @@ "description", "starts_at", "ends_at", + "happens_at", + "has_interval", + "has_duration", "clinicalCohortEnrollment__patient", "clinicalCohortEnrollment__cohort" ], @@ -1840,6 +2222,9 @@ "description", "starts_at", "ends_at", + "happens_at", + "has_interval", + "has_duration", "engineeringProcess__follows_procedure", "engineeringProcess__part_of" ], @@ -1873,6 +2258,9 @@ "description", "starts_at", "ends_at", + "happens_at", + "has_interval", + "has_duration", "plannedProcess__follows_procedure", "plannedProcess__uses_physical_device" ], @@ -1880,6 +2268,26 @@ "class_uri": "https://w3id.org/linkml-common/EngineeringMaterialProcessing", "@type": "ClassDefinition" }, + { + "name": "EnvironmentalSite", + "definition_uri": "https://w3id.org/linkml-common/EnvironmentalSite", + "description": "A location or site that is the subject of environmental monitoring", + "from_schema": "https://w3id.org/linkml-common/environmental", + "is_a": "Place", + "slots": [ + "id", + "name", + "type", + "subtype", + "ontology_types", + "description", + "address", + "geolocation" + ], + "slot_usage": {}, + "class_uri": "https://w3id.org/linkml-common/EnvironmentalSite", + "@type": "ClassDefinition" + }, { "name": "EnvironmentalProcess", "definition_uri": "https://w3id.org/linkml-common/EnvironmentalProcess", @@ -1891,6 +2299,15 @@ "class_uri": "https://w3id.org/linkml-common/EnvironmentalProcess", "@type": "ClassDefinition" }, + { + "name": "EnvironmentalMonitoring", + "definition_uri": "https://w3id.org/linkml-common/EnvironmentalMonitoring", + "from_schema": "https://w3id.org/linkml-common/environmental", + "is_a": "EnvironmentalProcess", + "slot_usage": {}, + "class_uri": "https://w3id.org/linkml-common/EnvironmentalMonitoring", + "@type": "ClassDefinition" + }, { "name": "FoodRecipe", "definition_uri": "https://w3id.org/linkml-common/FoodRecipe", @@ -1930,7 +2347,8 @@ "from_schema": "https://w3id.org/linkml-common/foods", "is_a": "Quantity", "slots": [ - "type" + "type", + "quantity__has_quantity_kind" ], "slot_usage": {}, "class_uri": "https://w3id.org/linkml-common/FoodIngredient", @@ -1950,6 +2368,9 @@ "description", "starts_at", "ends_at", + "happens_at", + "has_interval", + "has_duration", "plannedProcess__follows_procedure", "plannedProcess__uses_physical_device" ], @@ -1994,6 +2415,9 @@ { "name": "CompositeFoodType", "definition_uri": "https://w3id.org/linkml-common/CompositeFoodType", + "implements": [ + "linkml_common:Composable" + ], "from_schema": "https://w3id.org/linkml-common/foods", "is_a": "FoodTypeConcept", "slots": [ @@ -2193,6 +2617,9 @@ "description", "starts_at", "ends_at", + "happens_at", + "has_interval", + "has_duration", "healthcareEncounter__patient", "healthcareEncounter__provider", "HealthcareEncounter_subtype" @@ -2234,7 +2661,9 @@ "name": "HealthcareRole", "definition_uri": "https://w3id.org/linkml-common/HealthcareRole", "from_schema": "https://w3id.org/linkml-common/healthcare", + "is_a": "Role", "slots": [ + "type", "healthcareRole__is_person" ], "slot_usage": {}, @@ -2254,6 +2683,7 @@ "from_schema": "https://w3id.org/linkml-common/healthcare", "is_a": "HealthcareRole", "slots": [ + "type", "healthcareRole__is_person", "healthcareProvider__speciality", "healthcareProvider__care_site" @@ -2291,6 +2721,9 @@ "description", "starts_at", "ends_at", + "happens_at", + "has_interval", + "has_duration", "healthcareConditionOccurrence__patient", "healthcareConditionOccurrence__observed_during" ], @@ -2319,6 +2752,7 @@ "from_schema": "https://w3id.org/linkml-common/healthcare", "is_a": "HealthcareRole", "slots": [ + "type", "healthcareRole__is_person" ], "slot_usage": {}, @@ -2340,7 +2774,8 @@ "subtype", "ontology_types", "description", - "investigation__objectives" + "investigation__objectives", + "investigation__variables" ], "slot_usage": {}, "attributes": [ @@ -2348,6 +2783,12 @@ "name": "objectives", "range": "string", "@type": "SlotDefinition" + }, + { + "name": "variables", + "multivalued": true, + "range": "Variable", + "@type": "SlotDefinition" } ], "class_uri": "https://w3id.org/linkml-common/Investigation", @@ -2370,6 +2811,23 @@ "class_uri": "https://w3id.org/linkml-common/InvestigativeProtocol", "@type": "ClassDefinition" }, + { + "name": "StudyDesign", + "definition_uri": "https://w3id.org/linkml-common/StudyDesign", + "from_schema": "https://w3id.org/linkml-common/investigations", + "is_a": "Procedure", + "slots": [ + "id", + "name", + "type", + "subtype", + "ontology_types", + "description" + ], + "slot_usage": {}, + "class_uri": "https://w3id.org/linkml-common/StudyDesign", + "@type": "ClassDefinition" + }, { "name": "SampleMaterial", "definition_uri": "https://w3id.org/linkml-common/SampleMaterial", @@ -2401,6 +2859,9 @@ "description", "starts_at", "ends_at", + "happens_at", + "has_interval", + "has_duration", "plannedProcess__uses_physical_device", "investigativeProcess__follows_procedure", "investigativeProcess__part_of" @@ -2438,6 +2899,9 @@ "description", "starts_at", "ends_at", + "happens_at", + "has_interval", + "has_duration", "plannedProcess__uses_physical_device", "investigativeProcess__follows_procedure", "investigativeProcess__part_of", @@ -2474,6 +2938,9 @@ "description", "starts_at", "ends_at", + "happens_at", + "has_interval", + "has_duration", "plannedProcess__follows_procedure", "plannedProcess__uses_physical_device" ], @@ -2495,6 +2962,9 @@ "description", "starts_at", "ends_at", + "happens_at", + "has_interval", + "has_duration", "plannedProcess__uses_physical_device", "investigativeProcess__follows_procedure", "investigativeProcess__part_of" @@ -2553,6 +3023,27 @@ "class_uri": "https://w3id.org/linkml-common/Variable", "@type": "ClassDefinition" }, + { + "name": "QuantityKind", + "definition_uri": "https://w3id.org/linkml-common/QuantityKind", + "from_schema": "https://w3id.org/linkml-common/quantities", + "exact_mappings": [ + "qudt:QuantityKind", + "fibo.QuantitiesAndUnits:ScalarQuantity" + ], + "is_a": "Concept", + "slots": [ + "id", + "name", + "type", + "subtype", + "ontology_types", + "description" + ], + "slot_usage": {}, + "class_uri": "https://w3id.org/linkml-common/QuantityKind", + "@type": "ClassDefinition" + }, { "name": "Quantity", "definition_uri": "https://w3id.org/linkml-common/Quantity", @@ -2560,11 +3051,23 @@ "mappings": [ "fhir:Quantity" ], + "exact_mappings": [ + "schema:Quantity" + ], "is_a": "Intangible", "slots": [ - "type" + "type", + "quantity__has_quantity_kind" ], "slot_usage": {}, + "attributes": [ + { + "name": "has_quantity_kind", + "description": "The kind of quantity", + "range": "QuantityKind", + "@type": "SlotDefinition" + } + ], "class_uri": "http://hl7.org/fhir/Quantity", "union_of": [ "Quantity", @@ -2581,9 +3084,13 @@ "mappings": [ "fhir:SimpleQuantity" ], + "exact_mappings": [ + "fibo:ScalarQuantityValue" + ], "is_a": "Quantity", "slots": [ "type", + "quantity__has_quantity_kind", "simpleQuantity__value", "simpleQuantity__unit" ], @@ -2597,6 +3104,10 @@ }, { "name": "unit", + "exact_mappings": [ + "schema:unitCode", + "qudt:unit" + ], "range": "UnitConcept", "@type": "SlotDefinition" } @@ -2615,6 +3126,7 @@ "is_a": "Quantity", "slots": [ "type", + "quantity__has_quantity_kind", "ratio__numerator", "ratio__denominator" ], @@ -2706,12 +3218,37 @@ "class_uri": "https://w3id.org/linkml-common/UnitConcept", "@type": "ClassDefinition" }, + { + "name": "Agent", + "definition_uri": "https://w3id.org/linkml-common/Agent", + "description": "Represents an Agent", + "from_schema": "https://w3id.org/linkml-common/social", + "exact_mappings": [ + "prov:Agent", + "fibo.commons.PartiesAndSituations:Agent" + ], + "is_a": "NamedThing", + "slots": [ + "id", + "name", + "type", + "subtype", + "ontology_types", + "description" + ], + "slot_usage": {}, + "class_uri": "https://w3id.org/linkml-common/Agent", + "@type": "ClassDefinition" + }, { "name": "Person", "definition_uri": "https://w3id.org/linkml-common/Person", "description": "Represents a Person", "from_schema": "https://w3id.org/linkml-common/social", - "is_a": "NamedThing", + "exact_mappings": [ + "schema:Person" + ], + "is_a": "Agent", "slots": [ "id", "name", @@ -2733,7 +3270,10 @@ "definition_uri": "https://w3id.org/linkml-common/Organization", "description": "Represents an Organization", "from_schema": "https://w3id.org/linkml-common/social", - "is_a": "NamedThing", + "exact_mappings": [ + "schema:Organization" + ], + "is_a": "Agent", "slots": [ "id", "name", @@ -2746,6 +3286,24 @@ "class_uri": "https://w3id.org/linkml-common/Organization", "@type": "ClassDefinition" }, + { + "name": "AutomatedAgent", + "definition_uri": "https://w3id.org/linkml-common/AutomatedAgent", + "description": "Represents an Automated Agent", + "from_schema": "https://w3id.org/linkml-common/social", + "is_a": "Agent", + "slots": [ + "id", + "name", + "type", + "subtype", + "ontology_types", + "description" + ], + "slot_usage": {}, + "class_uri": "https://w3id.org/linkml-common/AutomatedAgent", + "@type": "ClassDefinition" + }, { "name": "LifeEvent", "definition_uri": "https://w3id.org/linkml-common/LifeEvent", @@ -2759,12 +3317,114 @@ "ontology_types", "description", "starts_at", - "ends_at" + "ends_at", + "happens_at", + "has_interval", + "has_duration" ], "slot_usage": {}, "class_uri": "https://w3id.org/linkml-common/LifeEvent", "@type": "ClassDefinition" }, + { + "name": "CreativeWork", + "definition_uri": "https://w3id.org/linkml-common/CreativeWork", + "description": "The most generic kind of creative work, including books, movies, photographs, software programs, etc.", + "from_schema": "https://w3id.org/linkml-common/social", + "exact_mappings": [ + "schema:CreativeWork" + ], + "is_a": "NamedThing", + "slots": [ + "id", + "name", + "type", + "subtype", + "ontology_types", + "description", + "creativeWork__title", + "creativeWork__abstract", + "creativeWork__rights", + "creativeWork__creators", + "creativeWork__contributors", + "creativeWork__contacts", + "creativeWork__keywords" + ], + "slot_usage": {}, + "attributes": [ + { + "name": "title", + "description": "The title of the item", + "exact_mappings": [ + "dcterms:title" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "abstract", + "description": "A summary of the item", + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "rights", + "description": "Information about rights held in and over the item", + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "creators", + "description": "The person or organization who created the work", + "slot_uri": "dcterms:creator", + "multivalued": true, + "range": "Agent", + "@type": "SlotDefinition" + }, + { + "name": "contributors", + "description": "A person or organization that contributed to the creation of the work", + "slot_uri": "dcterms:contributor", + "multivalued": true, + "range": "Agent", + "@type": "SlotDefinition" + }, + { + "name": "contacts", + "description": "A contact point for a person or organization", + "slot_uri": "schema:contactPoint", + "multivalued": true, + "range": "Agent", + "@type": "SlotDefinition" + }, + { + "name": "keywords", + "description": "Keywords or tags used to describe this item", + "slot_uri": "schema:keywords", + "multivalued": true, + "range": "string", + "@type": "SlotDefinition" + } + ], + "class_uri": "https://w3id.org/linkml-common/CreativeWork", + "@type": "ClassDefinition" + }, + { + "name": "Service", + "definition_uri": "https://w3id.org/linkml-common/Service", + "description": "A service provided by an organization", + "from_schema": "https://w3id.org/linkml-common/social", + "exact_mappings": [ + "schema:Service" + ], + "is_a": "Intangible", + "slots": [ + "type" + ], + "slot_usage": {}, + "class_uri": "https://w3id.org/linkml-common/Service", + "@type": "ClassDefinition" + }, { "name": "Event", "definition_uri": "https://w3id.org/linkml-common/Event", @@ -2779,17 +3439,58 @@ "ontology_types", "description", "starts_at", - "ends_at" + "ends_at", + "happens_at", + "has_interval", + "has_duration" ], "slot_usage": {}, "class_uri": "https://w3id.org/linkml-common/Event", "@type": "ClassDefinition" }, + { + "name": "TimePointOrTemporalInterval", + "definition_uri": "https://w3id.org/linkml-common/TimePointOrTemporalInterval", + "from_schema": "https://w3id.org/linkml-common/time", + "is_a": "Intangible", + "slots": [ + "type", + "starts_at", + "ends_at" + ], + "slot_usage": {}, + "class_uri": "https://w3id.org/linkml-common/TimePointOrTemporalInterval", + "@type": "ClassDefinition" + }, + { + "name": "TemporalInterval", + "definition_uri": "https://w3id.org/linkml-common/TemporalInterval", + "description": "A period of time", + "from_schema": "https://w3id.org/linkml-common/time", + "is_a": "TimePointOrTemporalInterval", + "slots": [ + "type", + "starts_at", + "ends_at" + ], + "slot_usage": {}, + "class_uri": "https://w3id.org/linkml-common/TemporalInterval", + "@type": "ClassDefinition" + }, { "name": "TimePoint", "definition_uri": "https://w3id.org/linkml-common/TimePoint", + "description": "A point in time. Can be fully specified, or specified in relative terms.", "from_schema": "https://w3id.org/linkml-common/time", + "exact_mappings": [ + "fibo.DatesAndTimes:TimeInstant" + ], + "is_a": "TimePointOrTemporalInterval", "slots": [ + "type", + "starts_at", + "ends_at", + "year_value", "date_value", "time_value", "datetime_value", @@ -2800,10 +3501,70 @@ "class_uri": "https://w3id.org/linkml-common/TimePoint", "@type": "ClassDefinition" }, + { + "name": "Duration", + "definition_uri": "https://w3id.org/linkml-common/Duration", + "description": "A length of time", + "from_schema": "https://w3id.org/linkml-common/time", + "is_a": "Quantity", + "slots": [ + "type", + "quantity__has_quantity_kind" + ], + "slot_usage": {}, + "class_uri": "https://w3id.org/linkml-common/Duration", + "@type": "ClassDefinition" + }, + { + "name": "TemporalRelationship", + "definition_uri": "https://w3id.org/linkml-common/TemporalRelationship", + "description": "A relationship to another time point", + "from_schema": "https://w3id.org/linkml-common/time", + "is_a": "Relationship", + "slots": [ + "type", + "temporalRelationship__predicate", + "temporalRelationship__relative_to" + ], + "slot_usage": {}, + "attributes": [ + { + "name": "predicate", + "description": "The relationship between the two time points", + "range": "RelativeTimeEnum", + "@type": "SlotDefinition" + }, + { + "name": "relative_to", + "range": "Entity", + "any_of": [ + { + "range": "TimePoint", + "@type": "AnonymousSlotExpression" + }, + { + "range": "TemporalInterval", + "@type": "AnonymousSlotExpression" + }, + { + "range": "Event", + "@type": "AnonymousSlotExpression" + } + ], + "@type": "SlotDefinition" + } + ], + "class_uri": "https://w3id.org/linkml-common/TemporalRelationship", + "@type": "ClassDefinition" + }, { "name": "PlannedProcess", "definition_uri": "https://w3id.org/linkml-common/PlannedProcess", + "description": "A process that follows a defined procedure or plan", "from_schema": "https://w3id.org/linkml-common/plannedprocess", + "exact_mappings": [ + "OBI:0000011" + ], "is_a": "Event", "slots": [ "id", @@ -2814,6 +3575,9 @@ "description", "starts_at", "ends_at", + "happens_at", + "has_interval", + "has_duration", "plannedProcess__follows_procedure", "plannedProcess__uses_physical_device" ], @@ -2847,6 +3611,9 @@ "description", "starts_at", "ends_at", + "happens_at", + "has_interval", + "has_duration", "plannedProcess__follows_procedure", "plannedProcess__uses_physical_device" ], @@ -2868,6 +3635,9 @@ "description", "starts_at", "ends_at", + "happens_at", + "has_interval", + "has_duration", "plannedProcess__follows_procedure", "plannedProcess__uses_physical_device" ], @@ -2878,15 +3648,16 @@ ], "metamodel_version": "1.7.0", "source_file": "linkml_common.yaml", - "source_file_date": "2024-01-11T17:31:02", - "source_file_size": 736, - "generation_date": "2024-01-13T18:02:36", + "source_file_date": "2024-02-02T15:51:52", + "source_file_size": 749, + "generation_date": "2024-02-02T17:33:01", "@type": "SchemaDefinition", "@context": [ "project/jsonld/linkml_common.context.jsonld", "https://w3id.org/linkml/types.context.jsonld", "core.context.jsonld", "bibliographic.context.jsonld", + "datasets.context.jsonld", "clinicalresearch.context.jsonld", "computational.context.jsonld", "engineering.context.jsonld", diff --git a/project/jsonschema/linkml_common.schema.json b/project/jsonschema/linkml_common.schema.json index 3797c36..9ff7379 100644 --- a/project/jsonschema/linkml_common.schema.json +++ b/project/jsonschema/linkml_common.schema.json @@ -1,5 +1,45 @@ { "$defs": { + "Agent": { + "additionalProperties": false, + "description": "Represents an Agent", + "properties": { + "description": { + "description": "A human-readable description for a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing", + "type": "string" + }, + "name": { + "description": "A human-readable name for a thing", + "type": "string" + }, + "ontology_types": { + "items": { + "type": "string" + }, + "type": "array" + }, + "subtype": { + "description": "An enum with a more specific type", + "type": "string" + }, + "type": { + "description": "A type for a thing", + "enum": [ + "Agent" + ], + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "Agent", + "type": "object" + }, "Any": { "additionalProperties": true, "description": "", @@ -12,6 +52,46 @@ "string" ] }, + "AutomatedAgent": { + "additionalProperties": false, + "description": "Represents an Automated Agent", + "properties": { + "description": { + "description": "A human-readable description for a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing", + "type": "string" + }, + "name": { + "description": "A human-readable name for a thing", + "type": "string" + }, + "ontology_types": { + "items": { + "type": "string" + }, + "type": "array" + }, + "subtype": { + "description": "An enum with a more specific type", + "type": "string" + }, + "type": { + "description": "A type for a thing", + "enum": [ + "AutomatedAgent" + ], + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "AutomatedAgent", + "type": "object" + }, "BasicFoodType": { "additionalProperties": false, "description": "", @@ -52,9 +132,18 @@ "title": "BasicFoodType", "type": "object" }, + "CaseOrControlEnum": { + "description": "", + "enum": [ + "CASE", + "CONTROL" + ], + "title": "CaseOrControlEnum", + "type": "string" + }, "ClinicalCohort": { "additionalProperties": false, - "description": "", + "description": "A group of patients who share a common set of characteristics", "properties": { "definition": { "type": "string" @@ -97,7 +186,7 @@ }, "ClinicalCohortDefinition": { "additionalProperties": false, - "description": "", + "description": "A definition of a clinical cohort", "properties": { "description": { "description": "A human-readable description for a thing", @@ -137,7 +226,7 @@ }, "ClinicalCohortEnrollment": { "additionalProperties": false, - "description": "", + "description": "An event relating a patient to a clinical cohort", "properties": { "cohort": { "type": "string" @@ -149,6 +238,15 @@ "ends_at": { "$ref": "#/$defs/TimePoint" }, + "happens_at": { + "$ref": "#/$defs/TimePoint" + }, + "has_duration": { + "$ref": "#/$defs/Duration" + }, + "has_interval": { + "$ref": "#/$defs/TemporalInterval" + }, "id": { "description": "A unique identifier for a thing", "type": "string" @@ -204,9 +302,6 @@ { "$ref": "#/$defs/Observation" }, - { - "$ref": "#/$defs/XProcess" - }, { "$ref": "#/$defs/Variable" }, @@ -216,6 +311,9 @@ { "$ref": "#/$defs/Measurement" }, + { + "$ref": "#/$defs/TimePointOrTemporalInterval" + }, { "$ref": "#/$defs/Quantity" }, @@ -225,9 +323,33 @@ { "$ref": "#/$defs/Collection" }, + { + "$ref": "#/$defs/Service" + }, { "$ref": "#/$defs/DataStructure" }, + { + "$ref": "#/$defs/FinancialProduct" + }, + { + "$ref": "#/$defs/FinancialAccount" + }, + { + "$ref": "#/$defs/TemporalRelationship" + }, + { + "$ref": "#/$defs/HealthcareRole" + }, + { + "$ref": "#/$defs/HealthcareProvider" + }, + { + "$ref": "#/$defs/Patient" + }, + { + "$ref": "#/$defs/Duration" + }, { "$ref": "#/$defs/SimpleQuantity" }, @@ -240,6 +362,12 @@ { "$ref": "#/$defs/MoneyQuantity" }, + { + "$ref": "#/$defs/TemporalInterval" + }, + { + "$ref": "#/$defs/TimePoint" + }, { "$ref": "#/$defs/Event" }, @@ -253,13 +381,13 @@ "$ref": "#/$defs/PhysicalDevice" }, { - "$ref": "#/$defs/Procedure" + "$ref": "#/$defs/Specification" }, { - "$ref": "#/$defs/Person" + "$ref": "#/$defs/Agent" }, { - "$ref": "#/$defs/Organization" + "$ref": "#/$defs/CreativeWork" }, { "$ref": "#/$defs/Investigation" @@ -279,27 +407,51 @@ { "$ref": "#/$defs/ClinicalCohortDefinition" }, + { + "$ref": "#/$defs/HealthcareSite" + }, + { + "$ref": "#/$defs/Landform" + }, + { + "$ref": "#/$defs/EnvironmentalSite" + }, + { + "$ref": "#/$defs/Dataset" + }, { "$ref": "#/$defs/Publication" }, { - "$ref": "#/$defs/HealthcareSite" + "$ref": "#/$defs/Person" }, { - "$ref": "#/$defs/Landform" + "$ref": "#/$defs/Organization" + }, + { + "$ref": "#/$defs/AutomatedAgent" }, { "$ref": "#/$defs/HealthcareOrganization" }, + { + "$ref": "#/$defs/Procedure" + }, { "$ref": "#/$defs/InvestigativeProtocol" }, + { + "$ref": "#/$defs/StudyDesign" + }, { "$ref": "#/$defs/FoodRecipe" }, { "$ref": "#/$defs/EngineeringSpecification" }, + { + "$ref": "#/$defs/QuantityKind" + }, { "$ref": "#/$defs/UnitConcept" }, @@ -452,6 +604,86 @@ "title": "Concept", "type": "object" }, + "CreativeWork": { + "additionalProperties": false, + "description": "The most generic kind of creative work, including books, movies, photographs, software programs, etc.", + "properties": { + "abstract": { + "description": "A summary of the item", + "type": "string" + }, + "contacts": { + "description": "A contact point for a person or organization", + "items": { + "type": "string" + }, + "type": "array" + }, + "contributors": { + "description": "A person or organization that contributed to the creation of the work", + "items": { + "type": "string" + }, + "type": "array" + }, + "creators": { + "description": "The person or organization who created the work", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "A human-readable description for a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing", + "type": "string" + }, + "keywords": { + "description": "Keywords or tags used to describe this item", + "items": { + "type": "string" + }, + "type": "array" + }, + "name": { + "description": "A human-readable name for a thing", + "type": "string" + }, + "ontology_types": { + "items": { + "type": "string" + }, + "type": "array" + }, + "rights": { + "description": "Information about rights held in and over the item", + "type": "string" + }, + "subtype": { + "description": "An enum with a more specific type", + "type": "string" + }, + "title": { + "description": "The title of the item", + "type": "string" + }, + "type": { + "description": "A type for a thing", + "enum": [ + "CreativeWork" + ], + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "CreativeWork", + "type": "object" + }, "CurrencyConcept": { "additionalProperties": false, "description": "A currency", @@ -506,6 +738,15 @@ "follows_procedure": { "type": "string" }, + "happens_at": { + "$ref": "#/$defs/TimePoint" + }, + "has_duration": { + "$ref": "#/$defs/Duration" + }, + "has_interval": { + "$ref": "#/$defs/TemporalInterval" + }, "id": { "description": "A unique identifier for a thing", "type": "string" @@ -562,24 +803,56 @@ "title": "DataStructure", "type": "object" }, - "EngineeringMaterialProcessing": { + "Dataset": { "additionalProperties": false, "description": "", "properties": { - "description": { - "description": "A human-readable description for a thing", + "abstract": { + "description": "A summary of the item", "type": "string" }, - "ends_at": { - "$ref": "#/$defs/TimePoint" + "collected_as_part_of": { + "items": { + "type": "string" + }, + "type": "array" }, - "follows_procedure": { + "contacts": { + "description": "A contact point for a person or organization", + "items": { + "type": "string" + }, + "type": "array" + }, + "contributors": { + "description": "A person or organization that contributed to the creation of the work", + "items": { + "type": "string" + }, + "type": "array" + }, + "creators": { + "description": "The person or organization who created the work", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "A human-readable description for a thing", "type": "string" }, "id": { "description": "A unique identifier for a thing", "type": "string" }, + "keywords": { + "description": "Keywords or tags used to describe this item", + "items": { + "type": "string" + }, + "type": "array" + }, "name": { "description": "A human-readable name for a thing", "type": "string" @@ -590,45 +863,136 @@ }, "type": "array" }, - "starts_at": { - "$ref": "#/$defs/TimePoint" + "rights": { + "description": "Information about rights held in and over the item", + "type": "string" }, "subtype": { "description": "An enum with a more specific type", "type": "string" }, + "title": { + "description": "The title of the item", + "type": "string" + }, "type": { "description": "A type for a thing", "enum": [ - "EngineeringMaterialProcessing" + "Dataset" ], "type": "string" - }, - "uses_physical_device": { - "type": "string" } }, "required": [ "id" ], - "title": "EngineeringMaterialProcessing", + "title": "Dataset", "type": "object" }, - "EngineeringProcess": { + "Duration": { "additionalProperties": false, - "description": "", + "description": "A length of time", "properties": { - "description": { - "description": "A human-readable description for a thing", + "has_quantity_kind": { + "description": "The kind of quantity", "type": "string" }, - "ends_at": { - "$ref": "#/$defs/TimePoint" - }, - "follows_procedure": { + "type": { + "description": "A type for a thing", + "enum": [ + "Duration" + ], "type": "string" - }, - "id": { + } + }, + "title": "Duration", + "type": "object" + }, + "EngineeringMaterialProcessing": { + "additionalProperties": false, + "description": "", + "properties": { + "description": { + "description": "A human-readable description for a thing", + "type": "string" + }, + "ends_at": { + "$ref": "#/$defs/TimePoint" + }, + "follows_procedure": { + "type": "string" + }, + "happens_at": { + "$ref": "#/$defs/TimePoint" + }, + "has_duration": { + "$ref": "#/$defs/Duration" + }, + "has_interval": { + "$ref": "#/$defs/TemporalInterval" + }, + "id": { + "description": "A unique identifier for a thing", + "type": "string" + }, + "name": { + "description": "A human-readable name for a thing", + "type": "string" + }, + "ontology_types": { + "items": { + "type": "string" + }, + "type": "array" + }, + "starts_at": { + "$ref": "#/$defs/TimePoint" + }, + "subtype": { + "description": "An enum with a more specific type", + "type": "string" + }, + "type": { + "description": "A type for a thing", + "enum": [ + "EngineeringMaterialProcessing" + ], + "type": "string" + }, + "uses_physical_device": { + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "EngineeringMaterialProcessing", + "type": "object" + }, + "EngineeringProcess": { + "additionalProperties": false, + "description": "", + "properties": { + "description": { + "description": "A human-readable description for a thing", + "type": "string" + }, + "ends_at": { + "$ref": "#/$defs/TimePoint" + }, + "follows_procedure": { + "type": "string" + }, + "happens_at": { + "$ref": "#/$defs/TimePoint" + }, + "has_duration": { + "$ref": "#/$defs/Duration" + }, + "has_interval": { + "$ref": "#/$defs/TemporalInterval" + }, + "id": { "description": "A unique identifier for a thing", "type": "string" }, @@ -706,12 +1070,65 @@ "title": "EngineeringSpecification", "type": "object" }, + "EnvironmentalMonitoring": { + "additionalProperties": false, + "description": "", + "title": "EnvironmentalMonitoring", + "type": "object" + }, "EnvironmentalProcess": { "additionalProperties": false, "description": "", "title": "EnvironmentalProcess", "type": "object" }, + "EnvironmentalSite": { + "additionalProperties": false, + "description": "A location or site that is the subject of environmental monitoring", + "properties": { + "address": { + "$ref": "#/$defs/PostalAddress" + }, + "description": { + "description": "A human-readable description for a thing", + "type": "string" + }, + "geolocation": { + "$ref": "#/$defs/GeoPointLocation", + "description": "The geolocation of the place" + }, + "id": { + "description": "A unique identifier for a thing", + "type": "string" + }, + "name": { + "description": "A human-readable name for a thing", + "type": "string" + }, + "ontology_types": { + "items": { + "type": "string" + }, + "type": "array" + }, + "subtype": { + "description": "An enum with a more specific type", + "type": "string" + }, + "type": { + "description": "A type for a thing", + "enum": [ + "EnvironmentalSite" + ], + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "EnvironmentalSite", + "type": "object" + }, "Event": { "additionalProperties": false, "description": "A thing that happens", @@ -723,6 +1140,15 @@ "ends_at": { "$ref": "#/$defs/TimePoint" }, + "happens_at": { + "$ref": "#/$defs/TimePoint" + }, + "has_duration": { + "$ref": "#/$defs/Duration" + }, + "has_interval": { + "$ref": "#/$defs/TemporalInterval" + }, "id": { "description": "A unique identifier for a thing", "type": "string" @@ -758,10 +1184,56 @@ "title": "Event", "type": "object" }, + "FinancialAccount": { + "additionalProperties": false, + "description": "A bank account", + "properties": { + "account_holder": { + "description": "The person or organization that holds the account", + "type": "string" + }, + "account_number": { + "description": "The account number", + "type": "string" + }, + "bank": { + "description": "The bank that holds the account", + "type": "string" + }, + "type": { + "description": "A type for a thing", + "enum": [ + "FinancialAccount" + ], + "type": "string" + } + }, + "title": "FinancialAccount", + "type": "object" + }, + "FinancialProduct": { + "additionalProperties": false, + "description": "A product or service offered by a bank whereby one may deposit, withdraw or transfer money and in some cases be paid interest.", + "properties": { + "type": { + "description": "A type for a thing", + "enum": [ + "FinancialProduct" + ], + "type": "string" + } + }, + "title": "FinancialProduct", + "type": "object" + }, "FoodIngredient": { "additionalProperties": false, "description": "", "properties": { + "has_quantity_kind": { + "description": "The kind of quantity", + "type": "string" + }, "type": { "description": "A type for a thing", "enum": [ @@ -787,6 +1259,15 @@ "follows_procedure": { "type": "string" }, + "happens_at": { + "$ref": "#/$defs/TimePoint" + }, + "has_duration": { + "$ref": "#/$defs/Duration" + }, + "has_interval": { + "$ref": "#/$defs/TemporalInterval" + }, "id": { "description": "A unique identifier for a thing", "type": "string" @@ -948,6 +1429,15 @@ "ends_at": { "$ref": "#/$defs/TimePoint" }, + "happens_at": { + "$ref": "#/$defs/TimePoint" + }, + "has_duration": { + "$ref": "#/$defs/Duration" + }, + "has_interval": { + "$ref": "#/$defs/TemporalInterval" + }, "id": { "description": "A unique identifier for a thing", "type": "string" @@ -1000,6 +1490,15 @@ "ends_at": { "$ref": "#/$defs/TimePoint" }, + "happens_at": { + "$ref": "#/$defs/TimePoint" + }, + "has_duration": { + "$ref": "#/$defs/Duration" + }, + "has_interval": { + "$ref": "#/$defs/TemporalInterval" + }, "id": { "description": "A unique identifier for a thing", "type": "string" @@ -1111,6 +1610,13 @@ }, "speciality": { "type": "string" + }, + "type": { + "description": "A type for a thing", + "enum": [ + "HealthcareProvider" + ], + "type": "string" } }, "title": "HealthcareProvider", @@ -1122,6 +1628,13 @@ "properties": { "is_person": { "type": "string" + }, + "type": { + "description": "A type for a thing", + "enum": [ + "HealthcareRole" + ], + "type": "string" } }, "title": "HealthcareRole", @@ -1174,6 +1687,11 @@ "title": "HealthcareSite", "type": "object" }, + "HumanLanguageCodeEnum": { + "description": "An enumeration of languages", + "title": "HumanLanguageCodeEnum", + "type": "string" + }, "InformationEntity": { "additionalProperties": false, "description": "An entity that describes some information", @@ -1268,6 +1786,12 @@ "Investigation" ], "type": "string" + }, + "variables": { + "items": { + "$ref": "#/$defs/Variable" + }, + "type": "array" } }, "required": [ @@ -1290,6 +1814,15 @@ "follows_procedure": { "type": "string" }, + "happens_at": { + "$ref": "#/$defs/TimePoint" + }, + "has_duration": { + "$ref": "#/$defs/Duration" + }, + "has_interval": { + "$ref": "#/$defs/TemporalInterval" + }, "id": { "description": "A unique identifier for a thing", "type": "string" @@ -1430,6 +1963,15 @@ "ends_at": { "$ref": "#/$defs/TimePoint" }, + "happens_at": { + "$ref": "#/$defs/TimePoint" + }, + "has_duration": { + "$ref": "#/$defs/Duration" + }, + "has_interval": { + "$ref": "#/$defs/TemporalInterval" + }, "id": { "description": "A unique identifier for a thing", "type": "string" @@ -1479,6 +2021,15 @@ "follows_procedure": { "type": "string" }, + "happens_at": { + "$ref": "#/$defs/TimePoint" + }, + "has_duration": { + "$ref": "#/$defs/Duration" + }, + "has_interval": { + "$ref": "#/$defs/TemporalInterval" + }, "id": { "description": "A unique identifier for a thing", "type": "string" @@ -1531,6 +2082,15 @@ "follows_procedure": { "type": "string" }, + "happens_at": { + "$ref": "#/$defs/TimePoint" + }, + "has_duration": { + "$ref": "#/$defs/Duration" + }, + "has_interval": { + "$ref": "#/$defs/TemporalInterval" + }, "id": { "description": "A unique identifier for a thing", "type": "string" @@ -1614,6 +2174,9 @@ { "$ref": "#/$defs/Quantity" }, + { + "$ref": "#/$defs/Duration" + }, { "$ref": "#/$defs/SimpleQuantity" }, @@ -1648,6 +2211,10 @@ "additionalProperties": false, "description": "A quantity of money", "properties": { + "has_quantity_kind": { + "description": "The kind of quantity", + "type": "string" + }, "type": { "description": "A type for a thing", "enum": [ @@ -1768,6 +2335,13 @@ "properties": { "is_person": { "type": "string" + }, + "type": { + "description": "A type for a thing", + "enum": [ + "Patient" + ], + "type": "string" } }, "title": "Patient", @@ -1930,7 +2504,7 @@ }, "PlannedProcess": { "additionalProperties": false, - "description": "", + "description": "A process that follows a defined procedure or plan", "properties": { "description": { "description": "A human-readable description for a thing", @@ -1942,6 +2516,15 @@ "follows_procedure": { "type": "string" }, + "happens_at": { + "$ref": "#/$defs/TimePoint" + }, + "has_duration": { + "$ref": "#/$defs/Duration" + }, + "has_interval": { + "$ref": "#/$defs/TemporalInterval" + }, "id": { "description": "A unique identifier for a thing", "type": "string" @@ -2068,6 +2651,31 @@ "additionalProperties": false, "description": "", "properties": { + "abstract": { + "description": "A summary of the item", + "type": "string" + }, + "contacts": { + "description": "A contact point for a person or organization", + "items": { + "type": "string" + }, + "type": "array" + }, + "contributors": { + "description": "A person or organization that contributed to the creation of the work", + "items": { + "type": "string" + }, + "type": "array" + }, + "creators": { + "description": "The person or organization who created the work", + "items": { + "type": "string" + }, + "type": "array" + }, "description": { "description": "A human-readable description for a thing", "type": "string" @@ -2076,6 +2684,13 @@ "description": "A unique identifier for a thing", "type": "string" }, + "keywords": { + "description": "Keywords or tags used to describe this item", + "items": { + "type": "string" + }, + "type": "array" + }, "name": { "description": "A human-readable name for a thing", "type": "string" @@ -2086,10 +2701,18 @@ }, "type": "array" }, + "rights": { + "description": "Information about rights held in and over the item", + "type": "string" + }, "subtype": { "description": "An enum with a more specific type", "type": "string" }, + "title": { + "description": "The title of the item", + "type": "string" + }, "type": { "description": "A type for a thing", "enum": [ @@ -2108,6 +2731,10 @@ "additionalProperties": false, "description": "", "properties": { + "has_quantity_kind": { + "description": "The kind of quantity", + "type": "string" + }, "type": { "description": "A type for a thing", "enum": [ @@ -2119,6 +2746,46 @@ "title": "Quantity", "type": "object" }, + "QuantityKind": { + "additionalProperties": false, + "description": "", + "properties": { + "description": { + "description": "A human-readable description for a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing", + "type": "string" + }, + "name": { + "description": "A human-readable name for a thing", + "type": "string" + }, + "ontology_types": { + "items": { + "type": "string" + }, + "type": "array" + }, + "subtype": { + "description": "An enum with a more specific type", + "type": "string" + }, + "type": { + "description": "A type for a thing", + "enum": [ + "QuantityKind" + ], + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "QuantityKind", + "type": "object" + }, "QuantityRange": { "additionalProperties": false, "description": "A quantity range is a property that can be measured or counted", @@ -2128,6 +2795,9 @@ { "$ref": "#/$defs/Quantity" }, + { + "$ref": "#/$defs/Duration" + }, { "$ref": "#/$defs/SimpleQuantity" }, @@ -2155,6 +2825,9 @@ { "$ref": "#/$defs/Quantity" }, + { + "$ref": "#/$defs/Duration" + }, { "$ref": "#/$defs/SimpleQuantity" }, @@ -2183,6 +2856,9 @@ { "$ref": "#/$defs/Quantity" }, + { + "$ref": "#/$defs/Duration" + }, { "$ref": "#/$defs/SimpleQuantity" }, @@ -2198,11 +2874,18 @@ ], "description": "The denominator of the ratio" }, + "has_quantity_kind": { + "description": "The kind of quantity", + "type": "string" + }, "numerator": { "anyOf": [ { "$ref": "#/$defs/Quantity" }, + { + "$ref": "#/$defs/Duration" + }, { "$ref": "#/$defs/SimpleQuantity" }, @@ -2269,6 +2952,16 @@ "title": "RawMaterial", "type": "object" }, + "RelativeTimeEnum": { + "description": "", + "enum": [ + "BEFORE", + "AFTER", + "AT_SAME_TIME_AS" + ], + "title": "RelativeTimeEnum", + "type": "string" + }, "SampleCollectionProcess": { "additionalProperties": false, "description": "", @@ -2286,6 +2979,15 @@ "follows_procedure": { "type": "string" }, + "happens_at": { + "$ref": "#/$defs/TimePoint" + }, + "has_duration": { + "$ref": "#/$defs/Duration" + }, + "has_interval": { + "$ref": "#/$defs/TemporalInterval" + }, "id": { "description": "A unique identifier for a thing", "type": "string" @@ -2384,6 +3086,15 @@ "follows_procedure": { "type": "string" }, + "happens_at": { + "$ref": "#/$defs/TimePoint" + }, + "has_duration": { + "$ref": "#/$defs/Duration" + }, + "has_interval": { + "$ref": "#/$defs/TemporalInterval" + }, "id": { "description": "A unique identifier for a thing", "type": "string" @@ -2422,10 +3133,29 @@ "title": "SampleProcessing", "type": "object" }, + "Service": { + "additionalProperties": false, + "description": "A service provided by an organization", + "properties": { + "type": { + "description": "A type for a thing", + "enum": [ + "Service" + ], + "type": "string" + } + }, + "title": "Service", + "type": "object" + }, "SimpleQuantity": { "additionalProperties": false, "description": "A quantity is a property that can be measured or counted", "properties": { + "has_quantity_kind": { + "description": "The kind of quantity", + "type": "string" + }, "type": { "description": "A type for a thing", "enum": [ @@ -2444,9 +3174,147 @@ "title": "SimpleQuantity", "type": "object" }, - "TimePoint": { + "Specification": { + "additionalProperties": false, + "description": "A specification of a thing", + "properties": { + "description": { + "description": "A human-readable description for a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing", + "type": "string" + }, + "name": { + "description": "A human-readable name for a thing", + "type": "string" + }, + "ontology_types": { + "items": { + "type": "string" + }, + "type": "array" + }, + "subtype": { + "description": "An enum with a more specific type", + "type": "string" + }, + "type": { + "description": "A type for a thing", + "enum": [ + "Specification" + ], + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "Specification", + "type": "object" + }, + "StudyDesign": { "additionalProperties": false, "description": "", + "properties": { + "description": { + "description": "A human-readable description for a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing", + "type": "string" + }, + "name": { + "description": "A human-readable name for a thing", + "type": "string" + }, + "ontology_types": { + "items": { + "type": "string" + }, + "type": "array" + }, + "subtype": { + "description": "An enum with a more specific type", + "type": "string" + }, + "type": { + "description": "A type for a thing", + "enum": [ + "StudyDesign" + ], + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "StudyDesign", + "type": "object" + }, + "StudyDesignEnum": { + "description": "", + "title": "StudyDesignEnum", + "type": "string" + }, + "TemporalInterval": { + "additionalProperties": false, + "description": "A period of time", + "properties": { + "ends_at": { + "$ref": "#/$defs/TimePoint" + }, + "starts_at": { + "$ref": "#/$defs/TimePoint" + }, + "type": { + "description": "A type for a thing", + "enum": [ + "TemporalInterval" + ], + "type": "string" + } + }, + "title": "TemporalInterval", + "type": "object" + }, + "TemporalRelationship": { + "additionalProperties": false, + "description": "A relationship to another time point", + "properties": { + "predicate": { + "$ref": "#/$defs/RelativeTimeEnum", + "description": "The relationship between the two time points" + }, + "relative_to": { + "anyOf": [ + { + "$ref": "#/$defs/TimePoint" + }, + { + "$ref": "#/$defs/TemporalInterval" + }, + { + "type": "string" + } + ] + }, + "type": { + "description": "A type for a thing", + "enum": [ + "TemporalRelationship" + ], + "type": "string" + } + }, + "title": "TemporalRelationship", + "type": "object" + }, + "TimePoint": { + "additionalProperties": false, + "description": "A point in time. Can be fully specified, or specified in relative terms.", "properties": { "date_value": { "format": "date", @@ -2460,17 +3328,54 @@ "description": "A human-readable description for a thing", "type": "string" }, + "ends_at": { + "$ref": "#/$defs/TimePoint" + }, "marker_event": { "type": "string" }, + "starts_at": { + "$ref": "#/$defs/TimePoint" + }, "time_value": { "format": "time", "type": "string" + }, + "type": { + "description": "A type for a thing", + "enum": [ + "TimePoint" + ], + "type": "string" + }, + "year_value": { + "type": "integer" } }, "title": "TimePoint", "type": "object" }, + "TimePointOrTemporalInterval": { + "additionalProperties": false, + "description": "", + "properties": { + "ends_at": { + "$ref": "#/$defs/TimePoint" + }, + "starts_at": { + "$ref": "#/$defs/TimePoint" + }, + "type": { + "description": "A type for a thing", + "enum": [ + "TimePointOrTemporalInterval" + ], + "type": "string" + } + }, + "title": "TimePointOrTemporalInterval", + "type": "object" + }, "UnitConcept": { "additionalProperties": false, "description": "", @@ -2529,6 +3434,9 @@ { "$ref": "#/$defs/Quantity" }, + { + "$ref": "#/$defs/Duration" + }, { "$ref": "#/$defs/SimpleQuantity" }, @@ -2553,6 +3461,9 @@ { "$ref": "#/$defs/Quantity" }, + { + "$ref": "#/$defs/Duration" + }, { "$ref": "#/$defs/SimpleQuantity" }, @@ -2602,21 +3513,6 @@ }, "title": "Variable", "type": "object" - }, - "XProcess": { - "additionalProperties": false, - "description": "A series of actions or steps taken in order to achieve a particular end", - "properties": { - "type": { - "description": "A type for a thing", - "enum": [ - "XProcess" - ], - "type": "string" - } - }, - "title": "XProcess", - "type": "object" } }, "$id": "https://w3id.org/linkml/linkml-common", diff --git a/project/owl/linkml_common.owl.ttl b/project/owl/linkml_common.owl.ttl index 2e3ebab..20912c8 100644 --- a/project/owl/linkml_common.owl.ttl +++ b/project/owl/linkml_common.owl.ttl @@ -1,3 +1,4 @@ +@prefix IAO: . @prefix PATO: . @prefix biolink: . @prefix dcterms: . @@ -6,35 +7,35 @@ @prefix owl: . @prefix rdf: . @prefix rdfs: . -@prefix schema1: . +@prefix schema: . @prefix skos: . @prefix xsd: . -linkml_common:EnvironmentalProcess a owl:Class ; - rdfs:label "EnvironmentalProcess" ; - rdfs:subClassOf linkml:ClassDefinition ; - skos:inScheme linkml_common:environmental ; - skos:note "TODO" . +linkml_common:EnvironmentalMonitoring a owl:Class ; + rdfs:label "EnvironmentalMonitoring" ; + rdfs:subClassOf linkml_common:EnvironmentalProcess ; + skos:inScheme linkml_common:environmental . -linkml_common:Relationship a owl:Class ; - rdfs:label "Relationship" ; - rdfs:subClassOf linkml:ClassDefinition ; - skos:inScheme linkml_common:core . +linkml_common:HumanLanguageCodeEnum a owl:Class ; + rdfs:subClassOf linkml:EnumDefinition . + +linkml_common:StudyDesignEnum a owl:Class ; + rdfs:subClassOf linkml:EnumDefinition . linkml_common:UnitConversionOperation a owl:Class ; rdfs:label "UnitConversionOperation" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom linkml_common:Quantity ; owl:onProperty linkml_common:inputs ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty linkml_common:inputs ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty linkml_common:outputs ], [ a owl:Restriction ; owl:allValuesFrom linkml_common:Quantity ; owl:onProperty linkml_common:outputs ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:inputs ], linkml_common:MathematicalOperation ; skos:definition "A unit conversion operation" ; skos:inScheme linkml_common:quantities . @@ -58,28 +59,11 @@ linkml:linkml-common a owl:Ontology ; rdfs:seeAlso ; skos:definition "Common Data Model Elements" . -linkml_common:HealthcareProvider a owl:Class ; - rdfs:label "HealthcareProvider" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty linkml_common:speciality ], - [ a owl:Restriction ; - owl:allValuesFrom linkml_common:Concept ; - owl:onProperty linkml_common:speciality ], - [ a owl:Restriction ; - owl:allValuesFrom linkml_common:HealthcareSite ; - owl:onProperty linkml_common:care_site ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty linkml_common:care_site ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty linkml_common:speciality ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty linkml_common:care_site ], - linkml_common:HealthcareRole ; - skos:inScheme linkml_common:healthcare . +linkml_common:EnvironmentalProcess a owl:Class ; + rdfs:label "EnvironmentalProcess" ; + rdfs:subClassOf linkml:ClassDefinition ; + skos:inScheme linkml_common:environmental ; + skos:note "TODO" . linkml_common:Location a owl:Class ; rdfs:label "Location" ; @@ -91,6 +75,16 @@ linkml_common:PointLocation a owl:Class ; rdfs:subClassOf linkml_common:Location ; skos:inScheme linkml_common:core . + a owl:Class ; + rdfs:label "CASE" ; + rdfs:subClassOf linkml_common:CaseOrControlEnum, + linkml:PermissibleValue . + + a owl:Class ; + rdfs:label "CONTROL" ; + rdfs:subClassOf linkml_common:CaseOrControlEnum, + linkml:PermissibleValue . + PATO:0001421 a owl:Class ; rdfs:label "ALIVE" ; rdfs:subClassOf linkml_common:PersonStatus, @@ -101,42 +95,55 @@ PATO:0001422 a owl:Class ; rdfs:subClassOf linkml_common:PersonStatus, linkml:PermissibleValue . +linkml_common:AutomatedAgent a owl:Class ; + rdfs:label "AutomatedAgent" ; + rdfs:subClassOf linkml_common:Agent ; + skos:definition "Represents an Automated Agent" ; + skos:inScheme linkml_common:social . + linkml_common:BasicFoodType a owl:Class ; rdfs:label "BasicFoodType" ; rdfs:subClassOf linkml_common:FoodTypeConcept ; skos:inScheme linkml_common:foods . +linkml_common:CaseOrControlEnum a owl:Class ; + rdfs:subClassOf linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + . + linkml_common:ClinicalCohortEnrollment a owl:Class ; rdfs:label "ClinicalCohortEnrollment" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom linkml_common:ClinicalCohort ; owl:onProperty linkml_common:cohort ], [ a owl:Restriction ; - owl:allValuesFrom linkml_common:Patient ; - owl:onProperty linkml_common:patient ], - [ a owl:Restriction ; - owl:allValuesFrom linkml_common:ClinicalCohort ; + owl:maxCardinality 1 ; owl:onProperty linkml_common:cohort ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty linkml_common:patient ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:cohort ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty linkml_common:patient ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty linkml_common:cohort ], + owl:allValuesFrom linkml_common:Patient ; + owl:onProperty linkml_common:patient ], linkml_common:Event ; + skos:definition "An event relating a patient to a clinical cohort" ; skos:exactMatch ; skos:inScheme linkml_common:clinicalresearch . linkml_common:Collection a owl:Class ; rdfs:label "Collection" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml_common:Entity ; + owl:minCardinality 0 ; owl:onProperty linkml_common:members ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom linkml_common:Entity ; owl:onProperty linkml_common:members ], linkml_common:Intangible ; skos:definition "A group of things. The collection may be heterogeneous or homogeneous." ; @@ -157,25 +164,77 @@ linkml_common:DataStructure a owl:Class ; rdfs:subClassOf linkml_common:Intangible ; skos:inScheme linkml_common:computational . +linkml_common:Dataset a owl:Class ; + rdfs:label "Dataset" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:collected_as_part_of ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:Investigation ; + owl:onProperty linkml_common:collected_as_part_of ], + linkml_common:CreativeWork ; + skos:inScheme linkml_common:datasets . + linkml_common:EngineeringMaterialProcessing a owl:Class ; rdfs:label "EngineeringMaterialProcessing" ; rdfs:subClassOf linkml_common:MaterialProcessing ; skos:inScheme linkml_common:engineering . +linkml_common:EnvironmentalSite a owl:Class ; + rdfs:label "EnvironmentalSite" ; + rdfs:subClassOf linkml_common:Place ; + skos:definition "A location or site that is the subject of environmental monitoring" ; + skos:inScheme linkml_common:environmental . + +linkml_common:FinancialAccount a owl:Class ; + rdfs:label "FinancialAccount" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:account_number ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty linkml_common:account_number ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:account_holder ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:Person ; + owl:onProperty linkml_common:account_holder ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:Organization ; + owl:onProperty linkml_common:bank ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:account_number ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:bank ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:account_holder ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:bank ], + linkml_common:FinancialProduct ; + skos:definition "A bank account" ; + skos:exactMatch schema:BankAccount, + ; + skos:inScheme linkml_common:financial . + linkml_common:FoodRecipe a owl:Class ; rdfs:label "FoodRecipe" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml_common:FoodProcessing ; - owl:onProperty linkml_common:steps ], - [ a owl:Restriction ; owl:allValuesFrom linkml_common:FoodIngredient ; owl:onProperty linkml_common:ingredients ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty linkml_common:ingredients ], + owl:allValuesFrom linkml_common:FoodProcessing ; + owl:onProperty linkml_common:steps ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty linkml_common:steps ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:ingredients ], linkml_common:Procedure ; skos:inScheme linkml_common:foods . @@ -183,27 +242,27 @@ linkml_common:GeoPointLocation a owl:Class ; rdfs:label "GeoPointLocation" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty linkml_common:longitude ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:decimal ; owl:onProperty linkml_common:altitude ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty linkml_common:longitude ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:longitude ], + owl:onProperty linkml_common:altitude ], [ a owl:Restriction ; owl:allValuesFrom xsd:decimal ; owl:onProperty linkml_common:latitude ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:altitude ], + owl:onProperty linkml_common:latitude ], [ a owl:Restriction ; owl:allValuesFrom xsd:decimal ; owl:onProperty linkml_common:longitude ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:latitude ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:decimal ; owl:onProperty linkml_common:altitude ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -217,8 +276,8 @@ linkml_common:HealthcareConditionOccurrence a owl:Class ; owl:allValuesFrom linkml_common:Patient ; owl:onProperty linkml_common:patient ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty linkml_common:patient ], + owl:minCardinality 0 ; + owl:onProperty linkml_common:observed_during ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty linkml_common:observed_during ], @@ -227,9 +286,9 @@ linkml_common:HealthcareConditionOccurrence a owl:Class ; owl:onProperty linkml_common:observed_during ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:observed_during ], + owl:onProperty linkml_common:patient ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty linkml_common:patient ], linkml_common:Event ; skos:exactMatch ; @@ -295,30 +354,16 @@ linkml_common:HealthcareOrganization a owl:Class ; rdfs:subClassOf linkml_common:Organization ; skos:inScheme linkml_common:healthcare . -linkml_common:HealthcareRole a owl:Class ; - rdfs:label "HealthcareRole" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml_common:Person ; - owl:onProperty linkml_common:is_person ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty linkml_common:is_person ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty linkml_common:is_person ], - linkml:ClassDefinition ; - skos:inScheme linkml_common:healthcare . - linkml_common:InformationEntity a owl:Class ; rdfs:label "InformationEntity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml_common:Any ; owl:onProperty linkml_common:describes ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty linkml_common:describes ], [ a owl:Restriction ; - owl:allValuesFrom linkml_common:Any ; + owl:maxCardinality 1 ; owl:onProperty linkml_common:describes ], linkml_common:NamedThing ; skos:definition "An entity that describes some information" ; @@ -327,13 +372,13 @@ linkml_common:InformationEntity a owl:Class ; linkml_common:Landform a owl:Class ; rdfs:label "Landform" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty linkml_common:geolocation ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:minCardinality 1 ; owl:onProperty linkml_common:geolocation ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty linkml_common:geolocation ], linkml_common:Place ; skos:definition "A natural feature of the solid surface of the Earth or other planetary body" ; @@ -356,37 +401,34 @@ linkml_common:Measurement a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom linkml_common:Quantity ; owl:onProperty linkml_common:quantity_measured ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:quantity_measured ], [ a owl:Restriction ; owl:allValuesFrom linkml_common:Variable ; owl:onProperty linkml_common:variable_measured ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty linkml_common:variable_measured ], + owl:maxCardinality 1 ; + owl:onProperty linkml_common:quantity_measured ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty linkml_common:variable_measured ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:quantity_measured ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty linkml_common:quantity_measured ], + owl:onProperty linkml_common:variable_measured ], linkml_common:Observation ; skos:inScheme linkml_common:meaurements . linkml_common:MoneyQuantity a owl:Class ; rdfs:label "MoneyQuantity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty linkml_common:unit ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:float ; owl:onProperty linkml_common:value ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:unit ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; owl:onProperty linkml_common:value ], [ a owl:Restriction ; owl:allValuesFrom linkml_common:CurrencyConcept ; @@ -394,6 +436,9 @@ linkml_common:MoneyQuantity a owl:Class ; [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty linkml_common:value ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:unit ], linkml_common:Quantity ; skos:definition "A quantity of money" ; skos:exactMatch ; @@ -406,29 +451,29 @@ linkml_common:MoneyQuantity a owl:Class ; linkml_common:Publication a owl:Class ; rdfs:label "Publication" ; - rdfs:subClassOf linkml_common:NamedThing ; + rdfs:subClassOf linkml_common:CreativeWork ; skos:inScheme linkml_common:financial . linkml_common:QuantityRange a owl:Class ; rdfs:label "QuantityRange" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml_common:Quantity ; + owl:maxCardinality 1 ; owl:onProperty linkml_common:upper_bound ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty linkml_common:lower_bound ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:lower_bound ], + owl:onProperty linkml_common:upper_bound ], [ a owl:Restriction ; - owl:allValuesFrom linkml_common:Quantity ; + owl:minCardinality 0 ; owl:onProperty linkml_common:lower_bound ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom linkml_common:Quantity ; owl:onProperty linkml_common:upper_bound ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty linkml_common:upper_bound ], + owl:allValuesFrom linkml_common:Quantity ; + owl:onProperty linkml_common:lower_bound ], linkml_common:Intangible ; skos:definition "A quantity range is a property that can be measured or counted" ; skos:exactMatch ; @@ -437,23 +482,23 @@ linkml_common:QuantityRange a owl:Class ; linkml_common:Ratio a owl:Class ; rdfs:label "Ratio" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty linkml_common:numerator ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml_common:Quantity ; owl:onProperty linkml_common:denominator ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml_common:Quantity ; owl:onProperty linkml_common:numerator ], [ a owl:Restriction ; - owl:allValuesFrom linkml_common:Quantity ; + owl:minCardinality 0 ; owl:onProperty linkml_common:numerator ], [ a owl:Restriction ; - owl:allValuesFrom linkml_common:Quantity ; - owl:onProperty linkml_common:denominator ], + owl:maxCardinality 1 ; + owl:onProperty linkml_common:numerator ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty linkml_common:denominator ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:denominator ], linkml_common:Quantity ; skos:definition "A tuple of two quantities" ; skos:exactMatch ; @@ -464,26 +509,41 @@ linkml_common:RawMaterial a owl:Class ; rdfs:subClassOf linkml_common:NamedThing ; skos:inScheme linkml_common:engineering . + a owl:Class ; + rdfs:label "AFTER" ; + rdfs:subClassOf linkml_common:RelativeTimeEnum, + linkml:PermissibleValue . + + a owl:Class ; + rdfs:label "AT_SAME_TIME_AS" ; + rdfs:subClassOf linkml_common:RelativeTimeEnum, + linkml:PermissibleValue . + + a owl:Class ; + rdfs:label "BEFORE" ; + rdfs:subClassOf linkml_common:RelativeTimeEnum, + linkml:PermissibleValue . + linkml_common:SampleCollectionProcess a owl:Class ; rdfs:label "SampleCollectionProcess" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:material_collected ], + owl:onProperty linkml_common:collected_from ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:material_collected ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty linkml_common:collected_from ], [ a owl:Restriction ; - owl:allValuesFrom linkml_common:SampleMaterial ; + owl:maxCardinality 1 ; owl:onProperty linkml_common:material_collected ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty linkml_common:collected_from ], [ a owl:Restriction ; owl:allValuesFrom linkml_common:NamedThing ; owl:onProperty linkml_common:collected_from ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:material_collected ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:SampleMaterial ; + owl:onProperty linkml_common:material_collected ], linkml_common:InvestigativeProcess ; skos:exactMatch ; skos:inScheme linkml_common:investigations . @@ -496,48 +556,96 @@ linkml_common:SampleProcessing a owl:Class ; linkml_common:SimpleQuantity a owl:Class ; rdfs:label "SimpleQuantity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty linkml_common:value ], - [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty linkml_common:unit ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty linkml_common:value ], + owl:allValuesFrom linkml_common:UnitConcept ; + owl:onProperty linkml_common:unit ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty linkml_common:value ], [ a owl:Restriction ; - owl:allValuesFrom linkml_common:UnitConcept ; + owl:maxCardinality 1 ; owl:onProperty linkml_common:unit ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:float ; + owl:onProperty linkml_common:value ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:unit ], + owl:onProperty linkml_common:value ], linkml_common:Quantity ; skos:definition "A quantity is a property that can be measured or counted" ; - skos:exactMatch ; + skos:exactMatch , + ; skos:inScheme linkml_common:quantities . -linkml_common:XProcess a owl:Class ; - rdfs:label "XProcess" ; - rdfs:subClassOf linkml_common:Entity ; - skos:definition "A series of actions or steps taken in order to achieve a particular end" ; - skos:inScheme linkml_common:core . +linkml_common:StudyDesign a owl:Class ; + rdfs:label "StudyDesign" ; + rdfs:subClassOf linkml_common:Procedure ; + skos:inScheme linkml_common:investigations . + +linkml_common:TemporalRelationship a owl:Class ; + rdfs:label "TemporalRelationship" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom [ owl:intersectionOf ( [ owl:unionOf ( linkml_common:TimePoint linkml_common:TemporalInterval linkml_common:Event ) ] linkml_common:Entity ) ] ; + owl:onProperty linkml_common:relative_to ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:relative_to ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:relative_to ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:RelativeTimeEnum ; + owl:onProperty linkml_common:predicate ], + linkml_common:Relationship ; + skos:definition "A relationship to another time point" ; + skos:inScheme linkml_common:time . linkml_common:allowed_units a owl:ObjectProperty ; rdfs:label "allowed_units" ; skos:definition "The units that are allowed for this variable" ; skos:inScheme linkml_common:meaurements . -linkml_common:immediate_preceding_steps a owl:ObjectProperty ; - rdfs:label "immediate_preceding_steps" ; - skos:definition "The steps that immediately precede this step" ; - skos:inScheme linkml_common:core . +linkml_common:collected_as_part_of a owl:ObjectProperty ; + rdfs:label "collected_as_part_of" ; + skos:inScheme linkml_common:datasets . -linkml_common:ingredients a owl:ObjectProperty ; - rdfs:label "ingredients" ; +linkml_common:contacts a owl:ObjectProperty ; + rdfs:label "contacts" ; + skos:definition "A contact point for a person or organization" ; + skos:inScheme linkml_common:social . + +linkml_common:contributors a owl:ObjectProperty ; + rdfs:label "contributors" ; + skos:definition "A person or organization that contributed to the creation of the work" ; + skos:inScheme linkml_common:social . + +linkml_common:creators a owl:ObjectProperty ; + rdfs:label "creators" ; + skos:definition "The person or organization who created the work" ; + skos:inScheme linkml_common:social . + +linkml_common:immediate_preceding_steps a owl:ObjectProperty ; + rdfs:label "immediate_preceding_steps" ; + skos:definition "The steps that immediately precede this step" ; + skos:inScheme linkml_common:core . + +linkml_common:ingredients a owl:ObjectProperty ; + rdfs:label "ingredients" ; skos:inScheme linkml_common:foods . +linkml_common:keywords a owl:DatatypeProperty ; + rdfs:label "keywords" ; + skos:definition "Keywords or tags used to describe this item" ; + skos:inScheme linkml_common:social . + linkml_common:members a owl:ObjectProperty ; rdfs:label "members" ; skos:definition "The members of the collection" ; @@ -557,23 +665,29 @@ linkml_common:steps a owl:ObjectProperty ; rdfs:label "steps" ; skos:inScheme linkml_common:foods . +linkml_common:variables a owl:ObjectProperty ; + rdfs:label "variables" ; + skos:inScheme linkml_common:investigations . + linkml_common:ClinicalCohort a owl:Class ; rdfs:label "ClinicalCohort" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml_common:ClinicalCohortDefinition ; owl:onProperty linkml_common:definition ], [ a owl:Restriction ; - owl:allValuesFrom linkml_common:ClinicalCohortDefinition ; + owl:maxCardinality 1 ; owl:onProperty linkml_common:definition ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty linkml_common:definition ], linkml_common:NamedThing ; + skos:definition "A group of patients who share a common set of characteristics" ; skos:inScheme linkml_common:clinicalresearch . linkml_common:ClinicalCohortDefinition a owl:Class ; rdfs:label "ClinicalCohortDefinition" ; rdfs:subClassOf linkml_common:NamedThing ; + skos:definition "A definition of a clinical cohort" ; skos:exactMatch ; skos:inScheme linkml_common:clinicalresearch . @@ -586,22 +700,22 @@ linkml_common:CurrencyConcept a owl:Class ; linkml_common:EngineeringProcess a owl:Class ; rdfs:label "EngineeringProcess" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty linkml_common:part_of ], + owl:allValuesFrom linkml_common:EngineeringSpecification ; + owl:onProperty linkml_common:follows_procedure ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty linkml_common:part_of ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty linkml_common:follows_procedure ], [ a owl:Restriction ; - owl:allValuesFrom linkml_common:EngineeringSpecification ; - owl:onProperty linkml_common:follows_procedure ], + owl:allValuesFrom linkml_common:EngineeringProcess ; + owl:onProperty linkml_common:part_of ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty linkml_common:follows_procedure ], [ a owl:Restriction ; - owl:allValuesFrom linkml_common:EngineeringProcess ; + owl:maxCardinality 1 ; owl:onProperty linkml_common:part_of ], linkml_common:Event ; skos:inScheme linkml_common:engineering . @@ -611,6 +725,12 @@ linkml_common:EngineeringSpecification a owl:Class ; rdfs:subClassOf linkml_common:Procedure ; skos:inScheme linkml_common:engineering . +linkml_common:FinancialProduct a owl:Class ; + rdfs:label "FinancialProduct" ; + rdfs:subClassOf linkml_common:Service ; + skos:definition "A product or service offered by a bank whereby one may deposit, withdraw or transfer money and in some cases be paid interest." ; + skos:inScheme linkml_common:financial . + linkml_common:FoodIngredient a owl:Class ; rdfs:label "FoodIngredient" ; rdfs:subClassOf linkml_common:Quantity ; @@ -624,55 +744,64 @@ linkml_common:FoodProcessing a owl:Class ; linkml_common:HealthcareEncounter a owl:Class ; rdfs:label "HealthcareEncounter" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml_common:HealthcareProvider ; + owl:maxCardinality 1 ; owl:onProperty linkml_common:provider ], [ a owl:Restriction ; - owl:allValuesFrom linkml_common:HealthcareEncounterClassification ; + owl:minCardinality 0 ; owl:onProperty linkml_common:subtype ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:provider ], + owl:onProperty linkml_common:patient ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty linkml_common:patient ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:provider ], + owl:onProperty linkml_common:subtype ], [ a owl:Restriction ; - owl:allValuesFrom linkml_common:Patient ; - owl:onProperty linkml_common:patient ], + owl:allValuesFrom linkml_common:HealthcareProvider ; + owl:onProperty linkml_common:provider ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:subtype ], + owl:onProperty linkml_common:provider ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml_common:HealthcareEncounterClassification ; owl:onProperty linkml_common:subtype ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom linkml_common:Patient ; owl:onProperty linkml_common:patient ], linkml_common:Event ; skos:exactMatch ; skos:inScheme linkml_common:healthcare . -linkml_common:HealthcareSite a owl:Class ; - rdfs:label "HealthcareSite" ; - rdfs:subClassOf linkml_common:Place ; - skos:exactMatch ; - skos:inScheme linkml_common:healthcare . - -linkml_common:Investigation a owl:Class ; - rdfs:label "Investigation" ; +linkml_common:HealthcareProvider a owl:Class ; + rdfs:label "HealthcareProvider" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:objectives ], + owl:onProperty linkml_common:speciality ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty linkml_common:objectives ], + owl:maxCardinality 1 ; + owl:onProperty linkml_common:care_site ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:Concept ; + owl:onProperty linkml_common:speciality ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:HealthcareSite ; + owl:onProperty linkml_common:care_site ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:objectives ], - linkml_common:NamedThing ; - skos:inScheme linkml_common:investigations . + owl:onProperty linkml_common:care_site ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:speciality ], + linkml_common:HealthcareRole ; + skos:inScheme linkml_common:healthcare . + +linkml_common:HealthcareSite a owl:Class ; + rdfs:label "HealthcareSite" ; + rdfs:subClassOf linkml_common:Place ; + skos:exactMatch ; + skos:inScheme linkml_common:healthcare . linkml_common:InvestigativeProtocol a owl:Class ; rdfs:label "InvestigativeProtocol" ; @@ -682,6 +811,9 @@ linkml_common:InvestigativeProtocol a owl:Class ; linkml_common:MathematicalOperation a owl:Class ; rdfs:label "MathematicalOperation" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:outputs ], + [ a owl:Restriction ; owl:allValuesFrom linkml_common:MathematicalOperation ; owl:onProperty linkml_common:immediate_preceding_steps ], [ a owl:Restriction ; @@ -689,22 +821,19 @@ linkml_common:MathematicalOperation a owl:Class ; owl:onProperty linkml_common:parts ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:parts ], + owl:onProperty linkml_common:inputs ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:Any ; + owl:onProperty linkml_common:outputs ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty linkml_common:immediate_preceding_steps ], - [ a owl:Restriction ; - owl:allValuesFrom linkml_common:Any ; - owl:onProperty linkml_common:inputs ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:inputs ], + owl:onProperty linkml_common:parts ], [ a owl:Restriction ; owl:allValuesFrom linkml_common:Any ; - owl:onProperty linkml_common:outputs ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty linkml_common:outputs ], + owl:onProperty linkml_common:inputs ], linkml:ClassDefinition ; skos:definition "Application of a mathematical operation to one or more inputs to produce one or more outputs" ; skos:inScheme linkml_common:core . @@ -715,64 +844,29 @@ linkml_common:Observation a owl:Class ; skos:definition "A statement about the state of something" ; skos:inScheme linkml_common:core . -linkml_common:Organization a owl:Class ; - rdfs:label "Organization" ; +linkml_common:PhysicalDevice a owl:Class ; + rdfs:label "PhysicalDevice" ; rdfs:subClassOf linkml_common:NamedThing ; - skos:definition "Represents an Organization" ; - skos:inScheme linkml_common:social . + skos:inScheme linkml_common:core . -linkml_common:Patient a owl:Class ; - rdfs:label "Patient" ; - rdfs:subClassOf linkml_common:HealthcareRole ; - skos:inScheme linkml_common:healthcare . +linkml_common:QuantityKind a owl:Class ; + rdfs:label "QuantityKind" ; + rdfs:subClassOf linkml_common:Concept ; + skos:exactMatch , + ; + skos:inScheme linkml_common:quantities . -linkml_common:Person a owl:Class ; - rdfs:label "Person" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty linkml_common:birth_date ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty linkml_common:age_in_years ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty linkml_common:primary_email ], - [ a owl:Restriction ; - owl:allValuesFrom linkml_common:PersonStatus ; - owl:onProperty linkml_common:vital_status ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty linkml_common:birth_date ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty linkml_common:age_in_years ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty linkml_common:primary_email ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:date ; - owl:onProperty linkml_common:birth_date ], - [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^\\S+@[\\S+\\.]+\\S+" ] ) ] ; - owl:onProperty linkml_common:primary_email ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty linkml_common:age_in_years ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty linkml_common:vital_status ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty linkml_common:vital_status ], - linkml_common:NamedThing ; - skos:definition "Represents a Person" ; - skos:inScheme linkml_common:social . +linkml_common:Relationship a owl:Class ; + rdfs:label "Relationship" ; + rdfs:subClassOf linkml_common:Intangible ; + skos:closeMatch rdfs:Statement ; + skos:inScheme linkml_common:core . -linkml_common:PhysicalDevice a owl:Class ; - rdfs:label "PhysicalDevice" ; - rdfs:subClassOf linkml_common:NamedThing ; +linkml_common:Role a owl:Class ; + rdfs:label "Role" ; + rdfs:subClassOf linkml_common:Intangible ; + skos:closeMatch ; + skos:exactMatch schema:Role ; skos:inScheme linkml_common:core . linkml_common:SampleMaterial a owl:Class ; @@ -780,16 +874,34 @@ linkml_common:SampleMaterial a owl:Class ; rdfs:subClassOf linkml_common:NamedThing ; skos:inScheme linkml_common:investigations . -linkml_common:Variable a owl:Class ; - rdfs:label "Variable" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty linkml_common:allowed_units ], - [ a owl:Restriction ; - owl:allValuesFrom linkml_common:UnitConcept ; - owl:onProperty linkml_common:allowed_units ], - linkml_common:Entity ; - skos:inScheme linkml_common:meaurements . +linkml_common:Service a owl:Class ; + rdfs:label "Service" ; + rdfs:subClassOf linkml_common:Intangible ; + skos:definition "A service provided by an organization" ; + skos:exactMatch schema:Service ; + skos:inScheme linkml_common:social . + +linkml_common:Specification a owl:Class ; + rdfs:label "Specification" ; + rdfs:subClassOf linkml_common:NamedThing ; + skos:definition "A specification of a thing" ; + skos:exactMatch IAO:0000104 ; + skos:inScheme linkml_common:core . + +linkml_common:abstract a owl:DatatypeProperty ; + rdfs:label "abstract" ; + skos:definition "A summary of the item" ; + skos:inScheme linkml_common:social . + +linkml_common:account_holder a owl:ObjectProperty ; + rdfs:label "account_holder" ; + skos:definition "The person or organization that holds the account" ; + skos:inScheme linkml_common:financial . + +linkml_common:account_number a owl:DatatypeProperty ; + rdfs:label "account_number" ; + skos:definition "The account number" ; + skos:inScheme linkml_common:financial . linkml_common:address a owl:ObjectProperty ; rdfs:label "address" ; @@ -807,6 +919,11 @@ linkml_common:altitude a owl:DatatypeProperty ; skos:definition "The altitude of the location" ; skos:inScheme linkml_common:geography . +linkml_common:bank a owl:ObjectProperty ; + rdfs:label "bank" ; + skos:definition "The bank that holds the account" ; + skos:inScheme linkml_common:financial . + linkml_common:birth_date a owl:DatatypeProperty ; rdfs:label "birth_date" ; rdfs:range xsd:date ; @@ -860,11 +977,26 @@ linkml_common:describes a owl:ObjectProperty ; skos:definition "The thing that is being described" ; skos:inScheme linkml_common:core . -linkml_common:ends_at a owl:ObjectProperty ; - rdfs:label "ends_at" ; +linkml_common:happens_at a owl:ObjectProperty ; + rdfs:label "happens_at" ; rdfs:range linkml_common:TimePoint ; skos:inScheme linkml_common:time . +linkml_common:has_duration a owl:ObjectProperty ; + rdfs:label "has_duration" ; + rdfs:range linkml_common:Duration ; + skos:inScheme linkml_common:time . + +linkml_common:has_interval a owl:ObjectProperty ; + rdfs:label "has_interval" ; + rdfs:range linkml_common:TemporalInterval ; + skos:inScheme linkml_common:time . + +linkml_common:has_quantity_kind a owl:ObjectProperty ; + rdfs:label "has_quantity_kind" ; + skos:definition "The kind of quantity" ; + skos:inScheme linkml_common:quantities . + linkml_common:id a owl:DatatypeProperty ; rdfs:label "id" ; rdfs:range xsd:anyURI ; @@ -923,6 +1055,11 @@ linkml_common:postal_code a owl:DatatypeProperty ; skos:definition "The postal code or zip code" ; skos:inScheme linkml_common:geography . +linkml_common:predicate a owl:ObjectProperty ; + rdfs:label "predicate" ; + skos:definition "The relationship between the two time points" ; + skos:inScheme linkml_common:time . + linkml_common:primary_email a owl:DatatypeProperty ; rdfs:label "primary_email" ; skos:definition "The main email address of a person" ; @@ -937,15 +1074,19 @@ linkml_common:quantity_measured a owl:ObjectProperty ; skos:definition "The quantity being measured" ; skos:inScheme linkml_common:meaurements . +linkml_common:relative_to a owl:ObjectProperty ; + rdfs:label "relative_to" ; + skos:inScheme linkml_common:time . + +linkml_common:rights a owl:DatatypeProperty ; + rdfs:label "rights" ; + skos:definition "Information about rights held in and over the item" ; + skos:inScheme linkml_common:social . + linkml_common:speciality a owl:ObjectProperty ; rdfs:label "speciality" ; skos:inScheme linkml_common:healthcare . -linkml_common:starts_at a owl:ObjectProperty ; - rdfs:label "starts_at" ; - rdfs:range linkml_common:TimePoint ; - skos:inScheme linkml_common:time . - linkml_common:state a owl:DatatypeProperty ; rdfs:label "state" ; skos:definition "The state" ; @@ -967,6 +1108,12 @@ linkml_common:time_value a owl:DatatypeProperty ; rdfs:range xsd:time ; skos:inScheme linkml_common:time . +linkml_common:title a owl:DatatypeProperty ; + rdfs:label "title" ; + skos:definition "The title of the item" ; + skos:exactMatch dcterms:title ; + skos:inScheme linkml_common:social . + linkml_common:upper_bound a owl:ObjectProperty ; rdfs:label "upper_bound" ; skos:definition "The upper bound of the range" ; @@ -987,169 +1134,279 @@ linkml_common:vital_status a owl:ObjectProperty ; skos:definition "living or dead status" ; skos:inScheme linkml_common:social . -linkml_common:FoodTypeConcept a owl:Class ; - rdfs:label "FoodTypeConcept" ; - rdfs:subClassOf linkml_common:Concept ; - skos:inScheme linkml_common:foods . +linkml_common:year_value a owl:DatatypeProperty ; + rdfs:label "year_value" ; + rdfs:range xsd:integer ; + skos:inScheme linkml_common:time . -linkml_common:InvestigativeProcess a owl:Class ; - rdfs:label "InvestigativeProcess" ; +linkml_common:CreativeWork a owl:Class ; + rdfs:label "CreativeWork" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:part_of ], - [ a owl:Restriction ; - owl:allValuesFrom linkml_common:InvestigativeProtocol ; - owl:onProperty linkml_common:follows_procedure ], + owl:onProperty linkml_common:rights ], [ a owl:Restriction ; - owl:allValuesFrom linkml_common:Investigation ; - owl:onProperty linkml_common:part_of ], + owl:minCardinality 0 ; + owl:onProperty linkml_common:abstract ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:follows_procedure ], + owl:onProperty linkml_common:rights ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:follows_procedure ], + owl:onProperty linkml_common:title ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:part_of ], - linkml_common:PlannedProcess ; - skos:inScheme linkml_common:investigations . - -linkml_common:Place a owl:Class ; - rdfs:label "Place" ; - rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty linkml_common:abstract ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty linkml_common:abstract ], + [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:address ], + owl:onProperty linkml_common:contacts ], [ a owl:Restriction ; - owl:allValuesFrom linkml_common:PostalAddress ; - owl:onProperty linkml_common:address ], + owl:allValuesFrom xsd:string ; + owl:onProperty linkml_common:rights ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:Agent ; + owl:onProperty linkml_common:contacts ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:address ], + owl:onProperty linkml_common:title ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:geolocation ], + owl:onProperty linkml_common:contributors ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty linkml_common:geolocation ], + owl:minCardinality 0 ; + owl:onProperty linkml_common:creators ], [ a owl:Restriction ; - owl:allValuesFrom linkml_common:GeoPointLocation ; - owl:onProperty linkml_common:geolocation ], + owl:allValuesFrom xsd:string ; + owl:onProperty linkml_common:title ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty linkml_common:keywords ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:Agent ; + owl:onProperty linkml_common:contributors ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:Agent ; + owl:onProperty linkml_common:creators ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:keywords ], linkml_common:NamedThing ; - skos:definition "Entities that have a somewhat fixed, physical extension." ; - skos:exactMatch schema1:Place ; - skos:inScheme linkml_common:geography . + skos:definition "The most generic kind of creative work, including books, movies, photographs, software programs, etc." ; + skos:exactMatch schema:CreativeWork ; + skos:inScheme linkml_common:social . -linkml_common:PostalAddress a owl:Class ; - rdfs:label "PostalAddress" ; +linkml_common:Duration a owl:Class ; + rdfs:label "Duration" ; + rdfs:subClassOf linkml_common:Quantity ; + skos:definition "A length of time" ; + skos:inScheme linkml_common:time . + +linkml_common:FoodTypeConcept a owl:Class ; + rdfs:label "FoodTypeConcept" ; + rdfs:subClassOf linkml_common:Concept ; + skos:inScheme linkml_common:foods . + +linkml_common:HealthcareRole a owl:Class ; + rdfs:label "HealthcareRole" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:is_person ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:state ], + owl:onProperty linkml_common:is_person ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty linkml_common:country ], + owl:allValuesFrom linkml_common:Person ; + owl:onProperty linkml_common:is_person ], + linkml_common:Role ; + skos:inScheme linkml_common:healthcare . + +linkml_common:Investigation a owl:Class ; + rdfs:label "Investigation" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:variables ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:objectives ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:street_address_additional ], + owl:onProperty linkml_common:objectives ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty linkml_common:street_address_additional ], + owl:onProperty linkml_common:objectives ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:Variable ; + owl:onProperty linkml_common:variables ], + linkml_common:NamedThing ; + skos:inScheme linkml_common:investigations . + +linkml_common:InvestigativeProcess a owl:Class ; + rdfs:label "InvestigativeProcess" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:follows_procedure ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:street_address ], + owl:onProperty linkml_common:part_of ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty linkml_common:postal_code ], + owl:allValuesFrom linkml_common:Investigation ; + owl:onProperty linkml_common:part_of ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:city ], + owl:onProperty linkml_common:part_of ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty linkml_common:city ], + owl:allValuesFrom linkml_common:InvestigativeProtocol ; + owl:onProperty linkml_common:follows_procedure ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty linkml_common:street_address ], + owl:minCardinality 0 ; + owl:onProperty linkml_common:follows_procedure ], + linkml_common:PlannedProcess ; + skos:inScheme linkml_common:investigations . + +linkml_common:Organization a owl:Class ; + rdfs:label "Organization" ; + rdfs:subClassOf linkml_common:Agent ; + skos:definition "Represents an Organization" ; + skos:exactMatch schema:Organization ; + skos:inScheme linkml_common:social . + +linkml_common:Person a owl:Class ; + rdfs:label "Person" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml_common:PersonStatus ; + owl:onProperty linkml_common:vital_status ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:integer ; + owl:onProperty linkml_common:age_in_years ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:postal_code ], + owl:onProperty linkml_common:age_in_years ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:birth_date ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:date ; + owl:onProperty linkml_common:birth_date ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:country ], + owl:onProperty linkml_common:vital_status ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:primary_email ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:street_address_additional ], + owl:onProperty linkml_common:birth_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:country ], + owl:onProperty linkml_common:vital_status ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:age_in_years ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:street_address ], + owl:onProperty linkml_common:primary_email ], [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^\\S+@[\\S+\\.]+\\S+" ] ) ] ; + owl:onProperty linkml_common:primary_email ], + linkml_common:Agent ; + skos:definition "Represents a Person" ; + skos:exactMatch schema:Person ; + skos:inScheme linkml_common:social . + +linkml_common:PostalAddress a owl:Class ; + rdfs:label "PostalAddress" ; + rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty linkml_common:city ], + owl:onProperty linkml_common:country ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:state ], + owl:onProperty linkml_common:country ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:postal_code ], + owl:onProperty linkml_common:country ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty linkml_common:state ], - linkml_common:Entity ; - skos:definition "Represents an Address" ; - skos:exactMatch , - schema1:PostalAddress ; - skos:inScheme linkml_common:geography . - -linkml_common:TimePoint a owl:Class ; - rdfs:label "TimePoint" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty linkml_common:time_value ], + owl:onProperty linkml_common:street_address_additional ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty linkml_common:marker_event ], + owl:allValuesFrom xsd:string ; + owl:onProperty linkml_common:city ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:description ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:dateTime ; - owl:onProperty linkml_common:datetime_value ], + owl:onProperty linkml_common:state ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:time_value ], + owl:onProperty linkml_common:city ], [ a owl:Restriction ; - owl:allValuesFrom linkml_common:Event ; - owl:onProperty linkml_common:marker_event ], + owl:minCardinality 0 ; + owl:onProperty linkml_common:postal_code ], [ a owl:Restriction ; - owl:allValuesFrom xsd:date ; - owl:onProperty linkml_common:date_value ], + owl:maxCardinality 1 ; + owl:onProperty linkml_common:postal_code ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:datetime_value ], + owl:onProperty linkml_common:street_address_additional ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty linkml_common:date_value ], + owl:minCardinality 0 ; + owl:onProperty linkml_common:street_address ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:marker_event ], + owl:onProperty linkml_common:state ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty linkml_common:description ], + owl:onProperty linkml_common:state ], [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; - owl:onProperty linkml_common:time_value ], + owl:maxCardinality 1 ; + owl:onProperty linkml_common:city ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:datetime_value ], + owl:onProperty linkml_common:street_address ], [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:street_address_additional ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty linkml_common:postal_code ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty linkml_common:street_address ], + linkml_common:Entity ; + skos:definition "Represents an Address" ; + skos:exactMatch , + schema:PostalAddress ; + skos:inScheme linkml_common:geography . + +linkml_common:RelativeTimeEnum a owl:Class ; + rdfs:subClassOf linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + . + +linkml_common:TimePointOrTemporalInterval a owl:Class ; + rdfs:label "TimePointOrTemporalInterval" ; + rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:date_value ], + owl:onProperty linkml_common:ends_at ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:ends_at ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:TimePoint ; + owl:onProperty linkml_common:starts_at ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:description ], - linkml:ClassDefinition ; + owl:onProperty linkml_common:starts_at ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:starts_at ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:TimePoint ; + owl:onProperty linkml_common:ends_at ], + linkml_common:Intangible ; skos:inScheme linkml_common:time . linkml_common:UnitConcept a owl:Class ; @@ -1157,6 +1414,17 @@ linkml_common:UnitConcept a owl:Class ; rdfs:subClassOf linkml_common:Concept ; skos:inScheme linkml_common:quantities . +linkml_common:Variable a owl:Class ; + rdfs:label "Variable" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml_common:UnitConcept ; + owl:onProperty linkml_common:allowed_units ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:allowed_units ], + linkml_common:Entity ; + skos:inScheme linkml_common:meaurements . + linkml_common:inputs a owl:ObjectProperty ; rdfs:label "inputs" ; skos:definition "The inputs to the operation" ; @@ -1172,6 +1440,11 @@ linkml_common:MaterialProcessing a owl:Class ; rdfs:subClassOf linkml_common:PlannedProcess ; skos:inScheme linkml_common:plannedprocess . +linkml_common:Patient a owl:Class ; + rdfs:label "Patient" ; + rdfs:subClassOf linkml_common:HealthcareRole ; + skos:inScheme linkml_common:healthcare . + linkml_common:PersonStatus a owl:Class ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( PATO:0001421 PATO:0001422 ) ; @@ -1179,48 +1452,86 @@ linkml_common:PersonStatus a owl:Class ; PATO:0001422, . +linkml_common:Place a owl:Class ; + rdfs:label "Place" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:address ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:GeoPointLocation ; + owl:onProperty linkml_common:geolocation ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:geolocation ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:geolocation ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:PostalAddress ; + owl:onProperty linkml_common:address ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:address ], + linkml_common:NamedThing ; + skos:definition "Entities that have a somewhat fixed, physical extension." ; + skos:exactMatch schema:Place ; + skos:inScheme linkml_common:geography . + linkml_common:PlannedProcess a owl:Class ; rdfs:label "PlannedProcess" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom linkml_common:Procedure ; owl:onProperty linkml_common:follows_procedure ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty linkml_common:uses_physical_device ], [ a owl:Restriction ; owl:allValuesFrom linkml_common:PhysicalDevice ; owl:onProperty linkml_common:uses_physical_device ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty linkml_common:uses_physical_device ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty linkml_common:follows_procedure ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty linkml_common:follows_procedure ], linkml_common:Event ; + skos:definition "A process that follows a defined procedure or plan" ; + skos:exactMatch ; skos:inScheme linkml_common:plannedprocess . +linkml_common:TemporalInterval a owl:Class ; + rdfs:label "TemporalInterval" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml_common:TimePoint ; + owl:onProperty linkml_common:ends_at ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:starts_at ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:ends_at ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:starts_at ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:TimePoint ; + owl:onProperty linkml_common:starts_at ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:ends_at ], + linkml_common:TimePointOrTemporalInterval ; + skos:definition "A period of time" ; + skos:inScheme linkml_common:time . + linkml_common:Any a owl:Class ; rdfs:label "Any" ; rdfs:subClassOf linkml:ClassDefinition ; skos:exactMatch linkml:Any ; skos:inScheme linkml_common:core . -linkml_common:Intangible a owl:Class ; - rdfs:label "Intangible" ; - rdfs:subClassOf linkml_common:Entity ; - skos:definition "An entity that is not a physical object, process, or information" ; - skos:exactMatch schema1:Intangible ; - skos:inScheme linkml_common:core . - -linkml_common:Procedure a owl:Class ; - rdfs:label "Procedure" ; - rdfs:subClassOf linkml_common:NamedThing ; - skos:definition "A canonical series of actions conducted in a certain order or manner" ; - skos:inScheme linkml_common:core . - linkml_common:description a owl:DatatypeProperty ; rdfs:label "description" ; skos:definition "A human-readable description for a thing" ; @@ -1244,6 +1555,20 @@ linkml_common:unit a owl:ObjectProperty . linkml_common:value a owl:DatatypeProperty . +linkml_common:Procedure a owl:Class ; + rdfs:label "Procedure" ; + rdfs:subClassOf linkml_common:Specification ; + skos:definition "A canonical series of actions conducted in a certain order or manner" ; + skos:inScheme linkml_common:core . + +linkml_common:Agent a owl:Class ; + rdfs:label "Agent" ; + rdfs:subClassOf linkml_common:NamedThing ; + skos:definition "Represents an Agent" ; + skos:exactMatch , + ; + skos:inScheme linkml_common:social . + linkml_common:Concept a owl:Class ; rdfs:label "Concept" ; rdfs:subClassOf linkml_common:NamedThing ; @@ -1264,32 +1589,76 @@ linkml_common:Entity a owl:Class ; owl:onProperty linkml_common:type ], linkml:ClassDefinition ; skos:definition "A physical, digital, conceptual, or other kind of thing with some common characteristics" ; - skos:exactMatch schema1:Thing ; + skos:exactMatch schema:Thing ; skos:inScheme linkml_common:core . +linkml_common:ends_at a owl:ObjectProperty ; + rdfs:label "ends_at" ; + rdfs:range linkml_common:TimePoint ; + skos:inScheme linkml_common:time . + linkml_common:follows_procedure a owl:ObjectProperty . linkml_common:patient a owl:ObjectProperty . +linkml_common:starts_at a owl:ObjectProperty ; + rdfs:label "starts_at" ; + rdfs:range linkml_common:TimePoint ; + skos:inScheme linkml_common:time . + +linkml_common:Intangible a owl:Class ; + rdfs:label "Intangible" ; + rdfs:subClassOf linkml_common:Entity ; + skos:definition "An entity that is not a physical object, process, or information" ; + skos:exactMatch schema:Intangible ; + skos:inScheme linkml_common:core . + linkml_common:Event a owl:Class ; rdfs:label "Event" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:starts_at ], + owl:onProperty linkml_common:happens_at ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty linkml_common:has_duration ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:TimePoint ; owl:onProperty linkml_common:ends_at ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty linkml_common:ends_at ], [ a owl:Restriction ; - owl:allValuesFrom linkml_common:TimePoint ; + owl:minCardinality 0 ; owl:onProperty linkml_common:ends_at ], [ a owl:Restriction ; - owl:allValuesFrom linkml_common:TimePoint ; + owl:maxCardinality 1 ; owl:onProperty linkml_common:starts_at ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty linkml_common:has_interval ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:TemporalInterval ; + owl:onProperty linkml_common:has_interval ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:has_duration ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:starts_at ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:has_interval ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:TimePoint ; + owl:onProperty linkml_common:happens_at ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:Duration ; + owl:onProperty linkml_common:has_duration ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:happens_at ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:TimePoint ; owl:onProperty linkml_common:starts_at ], linkml_common:NamedThing ; skos:definition "A thing that happens" ; @@ -1310,62 +1679,133 @@ linkml_common:HealthcareEncounterClassification a owl:Class ; , . +linkml_common:TimePoint a owl:Class ; + rdfs:label "TimePoint" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:datetime_value ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:marker_event ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:time_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:description ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty linkml_common:description ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:date_value ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:dateTime ; + owl:onProperty linkml_common:datetime_value ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:time ; + owl:onProperty linkml_common:time_value ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:description ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:datetime_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:marker_event ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:Event ; + owl:onProperty linkml_common:marker_event ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:year_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:date_value ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:date ; + owl:onProperty linkml_common:date_value ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:integer ; + owl:onProperty linkml_common:year_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:year_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:time_value ], + linkml_common:TimePointOrTemporalInterval ; + skos:definition "A point in time. Can be fully specified, or specified in relative terms." ; + skos:exactMatch ; + skos:inScheme linkml_common:time . + linkml_common:Quantity a owl:Class ; rdfs:label "Quantity" ; - rdfs:subClassOf linkml_common:Intangible ; - skos:exactMatch ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty linkml_common:has_quantity_kind ], + [ a owl:Restriction ; + owl:allValuesFrom linkml_common:QuantityKind ; + owl:onProperty linkml_common:has_quantity_kind ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty linkml_common:has_quantity_kind ], + linkml_common:Intangible ; + skos:exactMatch , + schema:Quantity ; skos:inScheme linkml_common:quantities . linkml_common:NamedThing a owl:Class ; rdfs:label "NamedThing" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml_common:Concept ; - owl:onProperty linkml_common:ontology_types ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty linkml_common:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:type ], + owl:onProperty linkml_common:subtype ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:name ], + owl:onProperty linkml_common:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:description ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty linkml_common:id ], + owl:onProperty linkml_common:name ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty linkml_common:id ], + owl:minCardinality 0 ; + owl:onProperty linkml_common:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:id ], + owl:onProperty linkml_common:description ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty linkml_common:ontology_types ], + owl:allValuesFrom xsd:string ; + owl:onProperty linkml_common:type ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty linkml_common:name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:description ], + owl:onProperty linkml_common:ontology_types ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty linkml_common:subtype ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty linkml_common:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty linkml_common:subtype ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty linkml_common:name ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty linkml_common:type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty linkml_common:type ], + owl:onProperty linkml_common:description ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty linkml_common:subtype ], + owl:allValuesFrom linkml_common:Concept ; + owl:onProperty linkml_common:ontology_types ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty linkml_common:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty linkml_common:description ], @@ -1379,49 +1819,69 @@ linkml_common:type a owl:DatatypeProperty ; skos:inScheme linkml_common:core . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:CompositeFoodType ; + rdfs:subClassOf linkml_common:Measurement ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:CompositeFoodType . + owl:someValuesFrom linkml_common:Measurement . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:Ratio ; + rdfs:subClassOf linkml_common:MaterialProcessing ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:Ratio . + owl:someValuesFrom linkml_common:MaterialProcessing . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:LifeEvent ; + rdfs:subClassOf linkml_common:Specification ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:LifeEvent . + owl:someValuesFrom linkml_common:Specification . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:EngineeringProcess ; + rdfs:subClassOf linkml_common:Publication ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:EngineeringProcess . + owl:someValuesFrom linkml_common:Publication . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:MoneyQuantity ; + rdfs:subClassOf linkml_common:InvestigativeProcess ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:MoneyQuantity . + owl:someValuesFrom linkml_common:InvestigativeProcess . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:Organization ; + rdfs:subClassOf linkml_common:UnitConcept ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:Organization . + owl:someValuesFrom linkml_common:UnitConcept . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:ClinicalCohort ; + rdfs:subClassOf linkml_common:Relationship ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:ClinicalCohort . + owl:someValuesFrom linkml_common:Relationship . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:Landform ; + rdfs:subClassOf linkml_common:Collection ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:Landform . + owl:someValuesFrom linkml_common:Collection . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:EngineeringMaterialProcessing ; + rdfs:subClassOf linkml_common:HealthcareSite ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:EngineeringMaterialProcessing . + owl:someValuesFrom linkml_common:HealthcareSite . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:FoodTypeConcept ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:FoodTypeConcept . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:SampleCollectionProcess ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:SampleCollectionProcess . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:CreativeWork ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:CreativeWork . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:Service ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:Service . [] a owl:Restriction ; rdfs:subClassOf linkml_common:MaterialCollection ; @@ -1429,55 +1889,75 @@ linkml_common:type a owl:DatatypeProperty ; owl:someValuesFrom linkml_common:MaterialCollection . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:NamedThing ; + rdfs:subClassOf linkml_common:EngineeringMaterialProcessing ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:NamedThing . + owl:someValuesFrom linkml_common:EngineeringMaterialProcessing . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:SampleProcessing ; + rdfs:subClassOf linkml_common:EngineeringSpecification ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:SampleProcessing . + owl:someValuesFrom linkml_common:EngineeringSpecification . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:Event ; + rdfs:subClassOf linkml_common:Patient ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:Event . + owl:someValuesFrom linkml_common:Patient . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:PostalAddress ; + rdfs:subClassOf linkml_common:FinancialProduct ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:PostalAddress . + owl:someValuesFrom linkml_common:FinancialProduct . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:Measurement ; + rdfs:subClassOf linkml_common:HealthcareRole ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:Measurement . + owl:someValuesFrom linkml_common:HealthcareRole . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:QuantityRange ; + rdfs:subClassOf linkml_common:BasicFoodType ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:QuantityRange . + owl:someValuesFrom linkml_common:BasicFoodType . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:FoodRecipe ; + rdfs:subClassOf linkml_common:ClinicalCohortEnrollment ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:FoodRecipe . + owl:someValuesFrom linkml_common:ClinicalCohortEnrollment . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:SampleCollectionProcess ; + rdfs:subClassOf linkml_common:Landform ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:SampleCollectionProcess . + owl:someValuesFrom linkml_common:Landform . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:DataStructure ; + rdfs:subClassOf linkml_common:TimePoint ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:DataStructure . + owl:someValuesFrom linkml_common:TimePoint . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:SimpleQuantity ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:SimpleQuantity . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:FinancialAccount ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:FinancialAccount . [] a owl:Restriction ; rdfs:subClassOf linkml_common:Observation ; owl:onProperty linkml_common:type ; owl:someValuesFrom linkml_common:Observation . +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:SampleProcessing ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:SampleProcessing . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:ClinicalCohort ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:ClinicalCohort . + [] a owl:Restriction ; rdfs:subClassOf linkml_common:SampleMaterial ; owl:onProperty linkml_common:type ; @@ -1489,64 +1969,84 @@ linkml_common:type a owl:DatatypeProperty ; owl:someValuesFrom linkml_common:Quantity . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:InformationEntity ; + rdfs:subClassOf linkml_common:PostalAddress ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:InformationEntity . + owl:someValuesFrom linkml_common:PostalAddress . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:SimpleQuantity ; + rdfs:subClassOf linkml_common:FoodIngredient ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:SimpleQuantity . + owl:someValuesFrom linkml_common:FoodIngredient . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:BasicFoodType ; + rdfs:subClassOf linkml_common:HealthcareOrganization ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:BasicFoodType . + owl:someValuesFrom linkml_common:HealthcareOrganization . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:UnitConcept ; + rdfs:subClassOf linkml_common:HealthcareEncounter ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:UnitConcept . + owl:someValuesFrom linkml_common:HealthcareEncounter . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:RawMaterial ; + rdfs:subClassOf linkml_common:PhysicalDevice ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:RawMaterial . + owl:someValuesFrom linkml_common:PhysicalDevice . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:FoodIngredient ; + rdfs:subClassOf linkml_common:QuantityRange ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:FoodIngredient . + owl:someValuesFrom linkml_common:QuantityRange . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:EngineeringSpecification ; + rdfs:subClassOf linkml_common:TemporalRelationship ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:EngineeringSpecification . + owl:someValuesFrom linkml_common:TemporalRelationship . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:FoodTypeConcept ; + rdfs:subClassOf linkml_common:Organization ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:FoodTypeConcept . + owl:someValuesFrom linkml_common:Organization . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:HealthcareConditionOccurrence ; + rdfs:subClassOf linkml_common:FoodRecipe ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:HealthcareConditionOccurrence . + owl:someValuesFrom linkml_common:FoodRecipe . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:Investigation ; + rdfs:subClassOf linkml_common:AutomatedAgent ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:Investigation . + owl:someValuesFrom linkml_common:AutomatedAgent . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:Person ; + rdfs:subClassOf linkml_common:Place ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:Person . + owl:someValuesFrom linkml_common:Place . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:MaterialProcessing ; + rdfs:subClassOf linkml_common:TemporalInterval ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:MaterialProcessing . + owl:someValuesFrom linkml_common:TemporalInterval . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:Intangible ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:Intangible . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:MoneyQuantity ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:MoneyQuantity . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:Event ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:Event . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:Variable ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:Variable . [] a owl:Restriction ; rdfs:subClassOf linkml_common:Concept ; @@ -1554,69 +2054,69 @@ linkml_common:type a owl:DatatypeProperty ; owl:someValuesFrom linkml_common:Concept . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:Entity ; + rdfs:subClassOf linkml_common:Dataset ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:Entity . + owl:someValuesFrom linkml_common:Dataset . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:Intangible ; + rdfs:subClassOf linkml_common:ClinicalCohortDefinition ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:Intangible . + owl:someValuesFrom linkml_common:ClinicalCohortDefinition . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:Procedure ; + rdfs:subClassOf linkml_common:Entity ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:Procedure . + owl:someValuesFrom linkml_common:Entity . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:Publication ; + rdfs:subClassOf linkml_common:StudyDesign ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:Publication . + owl:someValuesFrom linkml_common:StudyDesign . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:Collection ; + rdfs:subClassOf linkml_common:DataStructure ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:Collection . + owl:someValuesFrom linkml_common:DataStructure . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:ClinicalCohortEnrollment ; + rdfs:subClassOf linkml_common:Duration ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:ClinicalCohortEnrollment . + owl:someValuesFrom linkml_common:Duration . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:CurrencyConcept ; + rdfs:subClassOf linkml_common:Ratio ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:CurrencyConcept . + owl:someValuesFrom linkml_common:Ratio . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:HealthcareSite ; + rdfs:subClassOf linkml_common:CompositeFoodType ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:HealthcareSite . + owl:someValuesFrom linkml_common:CompositeFoodType . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:ClinicalCohortDefinition ; + rdfs:subClassOf linkml_common:Role ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:ClinicalCohortDefinition . + owl:someValuesFrom linkml_common:Role . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:XProcess ; + rdfs:subClassOf linkml_common:HealthcareConditionOccurrence ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:XProcess . + owl:someValuesFrom linkml_common:HealthcareConditionOccurrence . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:InvestigativeProcess ; + rdfs:subClassOf linkml_common:TimePointOrTemporalInterval ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:InvestigativeProcess . + owl:someValuesFrom linkml_common:TimePointOrTemporalInterval . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:Place ; + rdfs:subClassOf linkml_common:EngineeringProcess ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:Place . + owl:someValuesFrom linkml_common:EngineeringProcess . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:Variable ; + rdfs:subClassOf linkml_common:InvestigativeProtocol ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:Variable . + owl:someValuesFrom linkml_common:InvestigativeProtocol . [] a owl:Restriction ; rdfs:subClassOf linkml_common:DataGenerationFromSample ; @@ -1624,24 +2124,24 @@ linkml_common:type a owl:DatatypeProperty ; owl:someValuesFrom linkml_common:DataGenerationFromSample . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:FoodProcessing ; + rdfs:subClassOf linkml_common:QuantityKind ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:FoodProcessing . + owl:someValuesFrom linkml_common:QuantityKind . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:HealthcareOrganization ; + rdfs:subClassOf linkml_common:HealthcareProvider ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:HealthcareOrganization . + owl:someValuesFrom linkml_common:HealthcareProvider . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:PhysicalDevice ; + rdfs:subClassOf linkml_common:NamedThing ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:PhysicalDevice . + owl:someValuesFrom linkml_common:NamedThing . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:InvestigativeProtocol ; + rdfs:subClassOf linkml_common:EnvironmentalSite ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:InvestigativeProtocol . + owl:someValuesFrom linkml_common:EnvironmentalSite . [] a owl:Restriction ; rdfs:subClassOf linkml_common:PlannedProcess ; @@ -1649,7 +2149,47 @@ linkml_common:type a owl:DatatypeProperty ; owl:someValuesFrom linkml_common:PlannedProcess . [] a owl:Restriction ; - rdfs:subClassOf linkml_common:HealthcareEncounter ; + rdfs:subClassOf linkml_common:Person ; owl:onProperty linkml_common:type ; - owl:someValuesFrom linkml_common:HealthcareEncounter . + owl:someValuesFrom linkml_common:Person . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:RawMaterial ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:RawMaterial . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:CurrencyConcept ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:CurrencyConcept . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:Procedure ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:Procedure . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:FoodProcessing ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:FoodProcessing . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:InformationEntity ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:InformationEntity . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:LifeEvent ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:LifeEvent . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:Agent ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:Agent . + +[] a owl:Restriction ; + rdfs:subClassOf linkml_common:Investigation ; + owl:onProperty linkml_common:type ; + owl:someValuesFrom linkml_common:Investigation . diff --git a/project/prefixmap/linkml_common.yaml b/project/prefixmap/linkml_common.yaml index 21ae515..7fb68e5 100644 --- a/project/prefixmap/linkml_common.yaml +++ b/project/prefixmap/linkml_common.yaml @@ -1,17 +1,27 @@ { + "BFO": "http://purl.obolibrary.org/obo/BFO_", "ENVO": "http://purl.obolibrary.org/obo/ENVO_", + "IAO": "http://purl.obolibrary.org/obo/IAO_", + "OBI": "http://purl.obolibrary.org/obo/OBI_", "PATO": "http://purl.obolibrary.org/obo/PATO_", "UCUM": "http://example.org/UNKNOWN/UCUM/", "UO": "http://example.org/UNKNOWN/UO/", "biolink": "https://w3id.org/biolink/", + "dcterms": "http://purl.org/dc/terms/", "example": "https://example.org/", "fhir": "http://hl7.org/fhir/", + "fibo": "http://example.org/UNKNOWN/fibo/", + "fibo.DatesAndTimes": "https://www.omg.org/spec/Commons/DatesAndTimes/", + "fibo.QuantitiesAndUnits": "https://www.omg.org/spec/Commons/QuantitiesAndUnits/", + "fibo.commons.PartiesAndSituations": "https://spec.edmcouncil.org/fibo/ontology/FBC/ommons/PartiesAndSituations/", "linkml": "https://w3id.org/linkml/", "linkml_common": "https://w3id.org/linkml-common/", "nmdcschema": "http://example.org/UNKNOWN/nmdcschema/", "omopschema": "http://example.org/omop/", - "qudt": "http://example.org/UNKNOWN/qudt/", - "rdf": "http://example.org/UNKNOWN/rdf/", + "prov": "http://www.w3.org/ns/prov#", + "qudt": "http://qudt.org/vocab/unit/", + "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", "schema": "http://schema.org/", "Any": { "@id": "linkml:Any" @@ -37,6 +47,9 @@ "Ratio": { "@id": "fhir:Ratio" }, + "Role": { + "@id": "schema:Role" + }, "SimpleQuantity": { "@id": "fhir:SimpleQuantity" } diff --git a/project/protobuf/linkml_common.proto b/project/protobuf/linkml_common.proto index 2058c47..1914513 100644 --- a/project/protobuf/linkml_common.proto +++ b/project/protobuf/linkml_common.proto @@ -1,3 +1,23 @@ +// Represents an Agent +message Agent + { + uriorcurie id = 0 + string name = 0 + string type = 0 + string subtype = 0 + repeated concept ontologyTypes = 0 + string description = 0 + } +// Represents an Automated Agent +message AutomatedAgent + { + uriorcurie id = 0 + string name = 0 + string type = 0 + string subtype = 0 + repeated concept ontologyTypes = 0 + string description = 0 + } message BasicFoodType { uriorcurie id = 0 @@ -7,6 +27,7 @@ message BasicFoodType repeated concept ontologyTypes = 0 string description = 0 } +// A group of patients who share a common set of characteristics message ClinicalCohort { uriorcurie id = 0 @@ -17,6 +38,7 @@ message ClinicalCohort string description = 0 clinicalCohortDefinition definition = 0 } +// A definition of a clinical cohort message ClinicalCohortDefinition { uriorcurie id = 0 @@ -26,6 +48,7 @@ message ClinicalCohortDefinition repeated concept ontologyTypes = 0 string description = 0 } +// An event relating a patient to a clinical cohort message ClinicalCohortEnrollment { uriorcurie id = 0 @@ -36,6 +59,9 @@ message ClinicalCohortEnrollment string description = 0 timePoint startsAt = 0 timePoint endsAt = 0 + timePoint happensAt = 0 + temporalInterval hasInterval = 0 + duration hasDuration = 0 patient patient = 0 clinicalCohort cohort = 0 } @@ -63,6 +89,23 @@ message Concept repeated concept ontologyTypes = 0 string description = 0 } +// The most generic kind of creative work, including books, movies, photographs, software programs, etc. +message CreativeWork + { + uriorcurie id = 0 + string name = 0 + string type = 0 + string subtype = 0 + repeated concept ontologyTypes = 0 + string description = 0 + string title = 0 + string abstract = 0 + string rights = 0 + repeated agent creators = 0 + repeated agent contributors = 0 + repeated agent contacts = 0 + repeated string keywords = 0 + } message DataGenerationFromSample { uriorcurie id = 0 @@ -73,14 +116,40 @@ message DataGenerationFromSample string description = 0 timePoint startsAt = 0 timePoint endsAt = 0 + timePoint happensAt = 0 + temporalInterval hasInterval = 0 + duration hasDuration = 0 physicalDevice usesPhysicalDevice = 0 investigativeProtocol followsProcedure = 0 investigation partOf = 0 } +message Dataset + { + uriorcurie id = 0 + string name = 0 + string type = 0 + string subtype = 0 + repeated concept ontologyTypes = 0 + string description = 0 + string title = 0 + string abstract = 0 + string rights = 0 + repeated agent creators = 0 + repeated agent contributors = 0 + repeated agent contacts = 0 + repeated string keywords = 0 + repeated investigation collectedAsPartOf = 0 + } message DataStructure { string type = 0 } +// A length of time +message Duration + { + string type = 0 + quantityKind hasQuantityKind = 0 + } message EngineeringMaterialProcessing { uriorcurie id = 0 @@ -91,6 +160,9 @@ message EngineeringMaterialProcessing string description = 0 timePoint startsAt = 0 timePoint endsAt = 0 + timePoint happensAt = 0 + temporalInterval hasInterval = 0 + duration hasDuration = 0 procedure followsProcedure = 0 physicalDevice usesPhysicalDevice = 0 } @@ -104,6 +176,9 @@ message EngineeringProcess string description = 0 timePoint startsAt = 0 timePoint endsAt = 0 + timePoint happensAt = 0 + temporalInterval hasInterval = 0 + duration hasDuration = 0 engineeringSpecification followsProcedure = 0 engineeringProcess partOf = 0 } @@ -116,6 +191,18 @@ message EngineeringSpecification repeated concept ontologyTypes = 0 string description = 0 } +// A location or site that is the subject of environmental monitoring +message EnvironmentalSite + { + uriorcurie id = 0 + string name = 0 + string type = 0 + string subtype = 0 + repeated concept ontologyTypes = 0 + string description = 0 + postalAddress address = 0 + geoPointLocation geolocation = 0 + } // A thing that happens message Event { @@ -127,10 +214,14 @@ message Event string description = 0 timePoint startsAt = 0 timePoint endsAt = 0 + timePoint happensAt = 0 + temporalInterval hasInterval = 0 + duration hasDuration = 0 } message FoodIngredient { string type = 0 + quantityKind hasQuantityKind = 0 } message FoodProcessing { @@ -142,6 +233,9 @@ message FoodProcessing string description = 0 timePoint startsAt = 0 timePoint endsAt = 0 + timePoint happensAt = 0 + temporalInterval hasInterval = 0 + duration hasDuration = 0 procedure followsProcedure = 0 physicalDevice usesPhysicalDevice = 0 } @@ -181,6 +275,9 @@ message HealthcareConditionOccurrence string description = 0 timePoint startsAt = 0 timePoint endsAt = 0 + timePoint happensAt = 0 + temporalInterval hasInterval = 0 + duration hasDuration = 0 patient patient = 0 healthcareEncounter observedDuring = 0 } @@ -193,6 +290,9 @@ message HealthcareEncounter string description = 0 timePoint startsAt = 0 timePoint endsAt = 0 + timePoint happensAt = 0 + temporalInterval hasInterval = 0 + duration hasDuration = 0 patient patient = 0 healthcareProvider provider = 0 healthcareEncounterClassification subtype = 0 @@ -208,12 +308,14 @@ message HealthcareOrganization } message HealthcareProvider { + string type = 0 person isPerson = 0 concept speciality = 0 healthcareSite careSite = 0 } message HealthcareRole { + string type = 0 person isPerson = 0 } message HealthcareSite @@ -252,6 +354,7 @@ message Investigation repeated concept ontologyTypes = 0 string description = 0 string objectives = 0 + repeated variable variables = 0 } message InvestigativeProcess { @@ -263,6 +366,9 @@ message InvestigativeProcess string description = 0 timePoint startsAt = 0 timePoint endsAt = 0 + timePoint happensAt = 0 + temporalInterval hasInterval = 0 + duration hasDuration = 0 physicalDevice usesPhysicalDevice = 0 investigativeProtocol followsProcedure = 0 investigation partOf = 0 @@ -298,6 +404,9 @@ message LifeEvent string description = 0 timePoint startsAt = 0 timePoint endsAt = 0 + timePoint happensAt = 0 + temporalInterval hasInterval = 0 + duration hasDuration = 0 } message MaterialCollection { @@ -309,6 +418,9 @@ message MaterialCollection string description = 0 timePoint startsAt = 0 timePoint endsAt = 0 + timePoint happensAt = 0 + temporalInterval hasInterval = 0 + duration hasDuration = 0 procedure followsProcedure = 0 physicalDevice usesPhysicalDevice = 0 } @@ -322,6 +434,9 @@ message MaterialProcessing string description = 0 timePoint startsAt = 0 timePoint endsAt = 0 + timePoint happensAt = 0 + temporalInterval hasInterval = 0 + duration hasDuration = 0 procedure followsProcedure = 0 physicalDevice usesPhysicalDevice = 0 } @@ -365,6 +480,7 @@ message Organization } message Patient { + string type = 0 person isPerson = 0 } // Represents a Person @@ -402,6 +518,7 @@ message Place postalAddress address = 0 geoPointLocation geolocation = 0 } +// A process that follows a defined procedure or plan message PlannedProcess { uriorcurie id = 0 @@ -412,6 +529,9 @@ message PlannedProcess string description = 0 timePoint startsAt = 0 timePoint endsAt = 0 + timePoint happensAt = 0 + temporalInterval hasInterval = 0 + duration hasDuration = 0 procedure followsProcedure = 0 physicalDevice usesPhysicalDevice = 0 } @@ -444,10 +564,27 @@ message Publication string subtype = 0 repeated concept ontologyTypes = 0 string description = 0 + string title = 0 + string abstract = 0 + string rights = 0 + repeated agent creators = 0 + repeated agent contributors = 0 + repeated agent contacts = 0 + repeated string keywords = 0 } message Quantity { string type = 0 + quantityKind hasQuantityKind = 0 + } +message QuantityKind + { + uriorcurie id = 0 + string name = 0 + string type = 0 + string subtype = 0 + repeated concept ontologyTypes = 0 + string description = 0 } // A quantity range is a property that can be measured or counted message QuantityRange @@ -460,6 +597,7 @@ message QuantityRange message Ratio { string type = 0 + quantityKind hasQuantityKind = 0 quantity numerator = 0 quantity denominator = 0 } @@ -482,6 +620,9 @@ message SampleCollectionProcess string description = 0 timePoint startsAt = 0 timePoint endsAt = 0 + timePoint happensAt = 0 + temporalInterval hasInterval = 0 + duration hasDuration = 0 physicalDevice usesPhysicalDevice = 0 investigativeProtocol followsProcedure = 0 investigation partOf = 0 @@ -507,24 +648,77 @@ message SampleProcessing string description = 0 timePoint startsAt = 0 timePoint endsAt = 0 + timePoint happensAt = 0 + temporalInterval hasInterval = 0 + duration hasDuration = 0 procedure followsProcedure = 0 physicalDevice usesPhysicalDevice = 0 } +// A service provided by an organization +message Service + { + string type = 0 + } // A quantity is a property that can be measured or counted message SimpleQuantity { string type = 0 + quantityKind hasQuantityKind = 0 float value = 0 unitConcept unit = 0 } +// A specification of a thing +message Specification + { + uriorcurie id = 0 + string name = 0 + string type = 0 + string subtype = 0 + repeated concept ontologyTypes = 0 + string description = 0 + } +message StudyDesign + { + uriorcurie id = 0 + string name = 0 + string type = 0 + string subtype = 0 + repeated concept ontologyTypes = 0 + string description = 0 + } +// A period of time +message TemporalInterval + { + string type = 0 + timePoint startsAt = 0 + timePoint endsAt = 0 + } +// A relationship to another time point +message TemporalRelationship + { + string type = 0 + relativeTimeEnum predicate = 0 + entity relativeTo = 0 + } +// A point in time. Can be fully specified, or specified in relative terms. message TimePoint { + string type = 0 + timePoint startsAt = 0 + timePoint endsAt = 0 + integer yearValue = 0 date dateValue = 0 time timeValue = 0 datetime datetimeValue = 0 event markerEvent = 0 string description = 0 } +message TimePointOrTemporalInterval + { + string type = 0 + timePoint startsAt = 0 + timePoint endsAt = 0 + } message UnitConcept { uriorcurie id = 0 @@ -547,8 +741,3 @@ message Variable string type = 0 repeated unitConcept allowedUnits = 0 } -// A series of actions or steps taken in order to achieve a particular end -message XProcess - { - string type = 0 - } diff --git a/project/shacl/linkml_common.shacl.ttl b/project/shacl/linkml_common.shacl.ttl index 7c8913a..9cbc671 100644 --- a/project/shacl/linkml_common.shacl.ttl +++ b/project/shacl/linkml_common.shacl.ttl @@ -2,7 +2,7 @@ @prefix linkml: . @prefix linkml_common: . @prefix rdf: . -@prefix schema1: . +@prefix schema: . @prefix sh: . @prefix xsd: . @@ -10,29 +10,41 @@ sh:closed true ; sh:description "A quantity of money" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; + sh:property [ sh:class linkml_common:QuantityKind ; + sh:description "The kind of quantity" ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 2 ; + sh:path linkml_common:has_quantity_kind ], + [ sh:datatype xsd:float ; + sh:description "The value of the quantity" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path linkml_common:value ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 3 ; sh:path linkml_common:type ], [ sh:class linkml_common:CurrencyConcept ; sh:description "The currency of the quantity" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path linkml_common:unit ], - [ sh:datatype xsd:float ; - sh:description "The value of the quantity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path linkml_common:value ] ; + sh:path linkml_common:unit ] ; sh:targetClass . a sh:NodeShape ; sh:closed true ; sh:description "A quantity range is a property that can be measured or counted" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:class ; + sh:description "The lower bound of the range" ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path linkml_common:lower_bound ], + [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; sh:order 2 ; @@ -42,30 +54,30 @@ sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; sh:order 1 ; - sh:path linkml_common:upper_bound ], - [ sh:class ; - sh:description "The lower bound of the range" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path linkml_common:lower_bound ] ; + sh:path linkml_common:upper_bound ] ; sh:targetClass . a sh:NodeShape ; sh:closed true ; sh:description "A tuple of two quantities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ; - sh:description "The denominator of the ratio" ; + sh:property [ sh:class linkml_common:QuantityKind ; + sh:description "The kind of quantity" ; sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path linkml_common:denominator ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path linkml_common:has_quantity_kind ], [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:order 2 ; + sh:order 3 ; sh:path linkml_common:type ], + [ sh:class ; + sh:description "The denominator of the ratio" ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path linkml_common:denominator ], [ sh:class ; sh:description "The numerator of the ratio" ; sh:maxCount 1 ; @@ -83,19 +95,25 @@ sh:maxCount 1 ; sh:order 0 ; sh:path linkml_common:value ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path linkml_common:type ], [ sh:class linkml_common:UnitConcept ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path linkml_common:unit ], - [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; + [ sh:class linkml_common:QuantityKind ; + sh:description "The kind of quantity" ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path linkml_common:type ] ; + sh:path linkml_common:has_quantity_kind ] ; sh:targetClass . -schema1:Intangible a sh:NodeShape ; +schema:Intangible a sh:NodeShape ; sh:closed true ; sh:description "An entity that is not a physical object, process, or information" ; sh:ignoredProperties ( rdf:type ) ; @@ -104,111 +122,138 @@ schema1:Intangible a sh:NodeShape ; sh:maxCount 1 ; sh:order 0 ; sh:path linkml_common:type ] ; - sh:targetClass schema1:Intangible . + sh:targetClass schema:Intangible . -schema1:Place a sh:NodeShape ; +schema:Place a sh:NodeShape ; sh:closed true ; sh:description "Entities that have a somewhat fixed, physical extension." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; + sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path schema1:description ], - [ sh:class linkml_common:GeoPointLocation ; - sh:description "The geolocation of the place" ; + sh:order 4 ; + sh:path linkml_common:type ], + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path linkml_common:ontology_types ], + [ sh:class schema:PostalAddress ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path linkml_common:geolocation ], + sh:order 0 ; + sh:path linkml_common:address ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path schema:identifier ], [ sh:datatype xsd:string ; sh:description "An enum with a more specific type" ; sh:maxCount 1 ; sh:order 5 ; sh:path linkml_common:subtype ], - [ sh:description "A unique identifier for a thing" ; + [ sh:class linkml_common:GeoPointLocation ; + sh:description "The geolocation of the place" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path schema1:identifier ], + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path linkml_common:geolocation ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path schema:description ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; sh:order 3 ; - sh:path schema1:name ], - [ sh:class schema1:PostalAddress ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path linkml_common:address ], - [ sh:class linkml_common:Concept ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path linkml_common:ontology_types ], - [ sh:datatype xsd:string ; + sh:path schema:name ] ; + sh:targetClass schema:Place . + +schema:Role a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:order 4 ; + sh:order 0 ; sh:path linkml_common:type ] ; - sh:targetClass schema1:Place . + sh:targetClass schema:Role . -linkml_common:BasicFoodType a sh:NodeShape ; +linkml_common:AutomatedAgent a sh:NodeShape ; sh:closed true ; + sh:description "Represents an Automated Agent" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path schema1:name ], - [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; sh:order 5 ; - sh:path schema1:description ], - [ sh:class linkml_common:Concept ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path linkml_common:ontology_types ], + sh:path schema:description ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path linkml_common:subtype ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path schema:name ], [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; - sh:path schema1:identifier ], + sh:path schema:identifier ], [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path linkml_common:type ], - [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path linkml_common:subtype ] ; - sh:targetClass linkml_common:BasicFoodType . + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path linkml_common:ontology_types ] ; + sh:targetClass linkml_common:AutomatedAgent . -linkml_common:ClinicalCohortEnrollment a sh:NodeShape ; +linkml_common:BasicFoodType a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml_common:ClinicalCohort ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path schema:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path linkml_common:cohort ], + sh:path schema:name ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path linkml_common:type ], [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 4 ; sh:path linkml_common:ontology_types ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; + sh:description "An enum with a more specific type" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:name ], + sh:order 3 ; + sh:path linkml_common:subtype ], [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ], - [ sh:class linkml_common:Patient ; + sh:order 0 ; + sh:path schema:identifier ] ; + sh:targetClass linkml_common:BasicFoodType . + +linkml_common:ClinicalCohortEnrollment a sh:NodeShape ; + sh:closed true ; + sh:description "An event relating a patient to a clinical cohort" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class linkml_common:Patient ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; sh:order 0 ; @@ -218,42 +263,76 @@ linkml_common:ClinicalCohortEnrollment a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path linkml_common:starts_at ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path linkml_common:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path schema:description ], + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path linkml_common:ontology_types ], + [ sh:class linkml_common:Duration ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 6 ; + sh:path linkml_common:has_duration ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path linkml_common:subtype ], [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; sh:order 3 ; sh:path linkml_common:ends_at ], - [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + sh:path linkml_common:happens_at ], + [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:order 7 ; - sh:path linkml_common:subtype ], - [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; + sh:path schema:identifier ], + [ sh:class linkml_common:TemporalInterval ; sh:maxCount 1 ; - sh:order 6 ; - sh:path linkml_common:type ], + sh:nodeKind sh:BlankNode ; + sh:order 5 ; + sh:path linkml_common:has_interval ], [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; + sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path schema1:description ] ; + sh:order 8 ; + sh:path schema:name ], + [ sh:class linkml_common:ClinicalCohort ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path linkml_common:cohort ] ; sh:targetClass linkml_common:ClinicalCohortEnrollment . linkml_common:Collection a sh:NodeShape ; sh:closed true ; sh:description "A group of things. The collection may be heterogeneous or homogeneous." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path linkml_common:type ], - [ sh:class schema1:Thing ; + sh:property [ sh:class schema:Thing ; sh:description "The members of the collection" ; sh:nodeKind sh:BlankNode ; sh:order 0 ; - sh:path linkml_common:members ] ; + sh:path linkml_common:members ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path linkml_common:type ] ; sh:targetClass linkml_common:Collection . linkml_common:CompositeFoodType a sh:NodeShape ; @@ -263,26 +342,26 @@ linkml_common:CompositeFoodType a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path linkml_common:ontology_types ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path linkml_common:subtype ], [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; - sh:path schema1:identifier ], + sh:path schema:identifier ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; sh:order 5 ; - sh:path schema1:description ], - [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path linkml_common:subtype ], + sh:path schema:description ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; sh:order 1 ; - sh:path schema1:name ], + sh:path schema:name ], [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; @@ -290,63 +369,147 @@ linkml_common:CompositeFoodType a sh:NodeShape ; sh:path linkml_common:type ] ; sh:targetClass linkml_common:CompositeFoodType . -linkml_common:DataGenerationFromSample a sh:NodeShape ; +linkml_common:CreativeWork a sh:NodeShape ; sh:closed true ; + sh:description "The most generic kind of creative work, including books, movies, photographs, software programs, etc." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path schema1:description ], - [ sh:class linkml_common:TimePoint ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path linkml_common:starts_at ], - [ sh:class linkml_common:TimePoint ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; - sh:path linkml_common:ends_at ], - [ sh:class linkml_common:Investigation ; - sh:maxCount 1 ; + sh:property [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path linkml_common:part_of ], - [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; + sh:order 11 ; + sh:path linkml_common:ontology_types ], + [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:order 7 ; - sh:path linkml_common:type ], - [ sh:class linkml_common:Concept ; + sh:path schema:identifier ], + [ sh:class linkml_common:Agent ; + sh:description "A person or organization that contributed to the creation of the work" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path linkml_common:ontology_types ], + sh:order 4 ; + sh:path ], [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; + sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; - sh:path linkml_common:subtype ], + sh:path schema:name ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; + sh:description "Information about rights held in and over the item" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path schema1:name ], - [ sh:class linkml_common:InvestigativeProtocol ; + sh:order 2 ; + sh:path linkml_common:rights ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; sh:maxCount 1 ; + sh:order 9 ; + sh:path linkml_common:type ], + [ sh:class linkml_common:Agent ; + sh:description "The person or organization who created the work" ; sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path ], + [ sh:datatype xsd:string ; + sh:description "The title of the item" ; + sh:maxCount 1 ; sh:order 0 ; - sh:path linkml_common:follows_procedure ], + sh:path linkml_common:title ], + [ sh:datatype xsd:string ; + sh:description "A summary of the item" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path linkml_common:abstract ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path linkml_common:subtype ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path schema:description ], + [ sh:datatype xsd:string ; + sh:description "Keywords or tags used to describe this item" ; + sh:order 6 ; + sh:path schema:keywords ], + [ sh:class linkml_common:Agent ; + sh:description "A contact point for a person or organization" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path schema:contactPoint ] ; + sh:targetClass linkml_common:CreativeWork . + +linkml_common:DataGenerationFromSample a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path schema:description ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + sh:path linkml_common:ends_at ], + [ sh:class linkml_common:Duration ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 7 ; + sh:path linkml_common:has_duration ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path linkml_common:subtype ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path schema:name ], + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path linkml_common:ontology_types ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path linkml_common:type ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 8 ; + sh:path schema:identifier ], [ sh:class linkml_common:PhysicalDevice ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path linkml_common:uses_physical_device ], - [ sh:description "A unique identifier for a thing" ; + [ sh:class linkml_common:TemporalInterval ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 6 ; + sh:path linkml_common:has_interval ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; sh:order 5 ; - sh:path schema1:identifier ] ; + sh:path linkml_common:happens_at ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path linkml_common:starts_at ], + [ sh:class linkml_common:Investigation ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path linkml_common:part_of ], + [ sh:class linkml_common:InvestigativeProtocol ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path linkml_common:follows_procedure ] ; sh:targetClass linkml_common:DataGenerationFromSample . linkml_common:DataStructure a sh:NodeShape ; @@ -359,227 +522,419 @@ linkml_common:DataStructure a sh:NodeShape ; sh:path linkml_common:type ] ; sh:targetClass linkml_common:DataStructure . -linkml_common:EngineeringMaterialProcessing a sh:NodeShape ; +linkml_common:Dataset a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path linkml_common:ontology_types ], + [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path schema1:description ], - [ sh:class linkml_common:TimePoint ; + sh:order 13 ; + sh:path schema:description ], + [ sh:datatype xsd:string ; + sh:description "Information about rights held in and over the item" ; sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; sh:order 3 ; - sh:path linkml_common:ends_at ], + sh:path linkml_common:rights ], + [ sh:class linkml_common:Agent ; + sh:description "The person or organization who created the work" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path ], [ sh:datatype xsd:string ; sh:description "An enum with a more specific type" ; sh:maxCount 1 ; - sh:order 7 ; + sh:order 11 ; sh:path linkml_common:subtype ], - [ sh:class linkml_common:TimePoint ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path linkml_common:starts_at ], - [ sh:description "A unique identifier for a thing" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ], [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:order 6 ; + sh:order 10 ; sh:path linkml_common:type ], + [ sh:datatype xsd:string ; + sh:description "A summary of the item" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path linkml_common:abstract ], + [ sh:class linkml_common:Agent ; + sh:description "A contact point for a person or organization" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path schema:contactPoint ], + [ sh:datatype xsd:string ; + sh:description "The title of the item" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path linkml_common:title ], + [ sh:class linkml_common:Investigation ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path linkml_common:collected_as_part_of ], + [ sh:datatype xsd:string ; + sh:description "Keywords or tags used to describe this item" ; + sh:order 7 ; + sh:path schema:keywords ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; + sh:order 9 ; + sh:path schema:name ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 8 ; + sh:path schema:identifier ], + [ sh:class linkml_common:Agent ; + sh:description "A person or organization that contributed to the creation of the work" ; + sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path schema1:name ], + sh:path ] ; + sh:targetClass linkml_common:Dataset . + +linkml_common:EngineeringMaterialProcessing a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path schema:name ], + [ sh:class linkml_common:PhysicalDevice ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path linkml_common:uses_physical_device ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path schema:description ], + [ sh:class linkml_common:Duration ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 6 ; + sh:path linkml_common:has_duration ], [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 11 ; sh:path linkml_common:ontology_types ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path linkml_common:type ], [ sh:class linkml_common:Procedure ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path linkml_common:follows_procedure ], - [ sh:class linkml_common:PhysicalDevice ; + [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path linkml_common:uses_physical_device ] ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path linkml_common:starts_at ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path linkml_common:subtype ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path linkml_common:ends_at ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + sh:path linkml_common:happens_at ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path schema:identifier ], + [ sh:class linkml_common:TemporalInterval ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 5 ; + sh:path linkml_common:has_interval ] ; sh:targetClass linkml_common:EngineeringMaterialProcessing . +linkml_common:EnvironmentalMonitoring a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass linkml_common:EnvironmentalMonitoring . + linkml_common:EnvironmentalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass linkml_common:EnvironmentalProcess . -linkml_common:FoodRecipe a sh:NodeShape ; +linkml_common:EnvironmentalSite a sh:NodeShape ; sh:closed true ; + sh:description "A location or site that is the subject of environmental monitoring" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path schema1:name ], - [ sh:datatype xsd:string ; sh:description "An enum with a more specific type" ; sh:maxCount 1 ; sh:order 5 ; sh:path linkml_common:subtype ], - [ sh:class linkml_common:FoodProcessing ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path linkml_common:steps ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path schema:identifier ], [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path linkml_common:type ], + [ sh:class schema:PostalAddress ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path linkml_common:address ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path schema:name ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; sh:order 7 ; - sh:path schema1:description ], - [ sh:description "A unique identifier for a thing" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path schema1:identifier ], - [ sh:class linkml_common:FoodIngredient ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path linkml_common:ingredients ], + sh:path schema:description ], [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path linkml_common:ontology_types ] ; - sh:targetClass linkml_common:FoodRecipe . + sh:path linkml_common:ontology_types ], + [ sh:class linkml_common:GeoPointLocation ; + sh:description "The geolocation of the place" ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path linkml_common:geolocation ] ; + sh:targetClass linkml_common:EnvironmentalSite . -linkml_common:FoodTypeConcept a sh:NodeShape ; +linkml_common:FinancialAccount a sh:NodeShape ; sh:closed true ; + sh:description "A bank account" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; + sh:description "The account number" ; sh:maxCount 1 ; + sh:order 0 ; + sh:path linkml_common:account_number ], + [ sh:class linkml_common:Person ; + sh:description "The person or organization that holds the account" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path linkml_common:type ], + sh:path linkml_common:account_holder ], [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path linkml_common:type ], + [ sh:class linkml_common:Organization ; + sh:description "The bank that holds the account" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path linkml_common:bank ] ; + sh:targetClass linkml_common:FinancialAccount . + +linkml_common:FinancialProduct a sh:NodeShape ; + sh:closed true ; + sh:description "A product or service offered by a bank whereby one may deposit, withdraw or transfer money and in some cases be paid interest." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path linkml_common:type ] ; + sh:targetClass linkml_common:FinancialProduct . + +linkml_common:FoodRecipe a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:description ], + sh:order 7 ; + sh:path schema:description ], [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 0 ; - sh:path schema1:identifier ], + sh:order 2 ; + sh:path schema:identifier ], + [ sh:class linkml_common:FoodProcessing ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path linkml_common:steps ], [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path linkml_common:ontology_types ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path schema:name ], + [ sh:class linkml_common:FoodIngredient ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path linkml_common:ingredients ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path linkml_common:type ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path linkml_common:subtype ] ; + sh:targetClass linkml_common:FoodRecipe . + +linkml_common:FoodTypeConcept a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path linkml_common:ontology_types ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path schema:identifier ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path linkml_common:type ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; sh:order 1 ; - sh:path schema1:name ], + sh:path schema:name ], [ sh:datatype xsd:string ; sh:description "An enum with a more specific type" ; sh:maxCount 1 ; sh:order 3 ; - sh:path linkml_common:subtype ] ; + sh:path linkml_common:subtype ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path schema:description ] ; sh:targetClass linkml_common:FoodTypeConcept . linkml_common:HealthcareConditionOccurrence a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml_common:Patient ; + sh:property [ sh:class linkml_common:TemporalInterval ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 5 ; + sh:path linkml_common:has_interval ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path linkml_common:starts_at ], + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path linkml_common:ontology_types ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path schema:identifier ], + [ sh:class linkml_common:HealthcareEncounter ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path linkml_common:observed_during ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path linkml_common:subtype ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path linkml_common:ends_at ], + [ sh:class linkml_common:Patient ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; sh:order 0 ; sh:path linkml_common:patient ], - [ sh:description "A unique identifier for a thing" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ], [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:order 6 ; + sh:order 9 ; sh:path linkml_common:type ], [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path linkml_common:starts_at ], + sh:order 4 ; + sh:path linkml_common:happens_at ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; + sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:name ], + sh:order 12 ; + sh:path schema:description ], [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path linkml_common:subtype ], - [ sh:class linkml_common:TimePoint ; + sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path linkml_common:ends_at ], - [ sh:class linkml_common:Concept ; - sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path linkml_common:ontology_types ], - [ sh:class linkml_common:HealthcareEncounter ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path linkml_common:observed_during ], - [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; + sh:path schema:name ], + [ sh:class linkml_common:Duration ; sh:maxCount 1 ; - sh:order 9 ; - sh:path schema1:description ] ; + sh:nodeKind sh:BlankNode ; + sh:order 6 ; + sh:path linkml_common:has_duration ] ; sh:targetClass linkml_common:HealthcareConditionOccurrence . linkml_common:HealthcareOrganization a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path linkml_common:type ], - [ sh:datatype xsd:string ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; sh:order 1 ; - sh:path schema1:name ], - [ sh:class linkml_common:Concept ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path linkml_common:ontology_types ], + sh:path schema:name ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path schema:identifier ], [ sh:datatype xsd:string ; sh:description "An enum with a more specific type" ; sh:maxCount 1 ; sh:order 3 ; sh:path linkml_common:subtype ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path linkml_common:type ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; sh:order 5 ; - sh:path schema1:description ], - [ sh:description "A unique identifier for a thing" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path schema1:identifier ] ; + sh:path schema:description ], + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path linkml_common:ontology_types ] ; sh:targetClass linkml_common:HealthcareOrganization . linkml_common:HealthcareRole a sh:NodeShape ; @@ -589,7 +944,12 @@ linkml_common:HealthcareRole a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path linkml_common:is_person ] ; + sh:path linkml_common:is_person ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path linkml_common:type ] ; sh:targetClass linkml_common:HealthcareRole . linkml_common:InformationEntity a sh:NodeShape ; @@ -601,674 +961,884 @@ linkml_common:InformationEntity a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; sh:order 0 ; - sh:path schema1:describes ], + sh:path schema:describes ], + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path linkml_common:ontology_types ], [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; - sh:path schema1:identifier ], + sh:path schema:identifier ], [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; sh:order 3 ; sh:path linkml_common:type ], [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; + sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path schema1:description ], + sh:order 2 ; + sh:path schema:name ], [ sh:datatype xsd:string ; sh:description "An enum with a more specific type" ; sh:maxCount 1 ; sh:order 4 ; sh:path linkml_common:subtype ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path schema:description ] ; + sh:targetClass linkml_common:InformationEntity . + +linkml_common:InvestigativeProcess a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class linkml_common:InvestigativeProtocol ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path linkml_common:follows_procedure ], + [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 5 ; + sh:path linkml_common:happens_at ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path linkml_common:starts_at ], + [ sh:class linkml_common:PhysicalDevice ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path schema1:name ], + sh:path linkml_common:uses_physical_device ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 8 ; + sh:path schema:identifier ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + sh:path linkml_common:ends_at ], + [ sh:class linkml_common:TemporalInterval ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 6 ; + sh:path linkml_common:has_interval ], + [ sh:class linkml_common:Investigation ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path linkml_common:part_of ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path schema:name ], [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path linkml_common:ontology_types ] ; - sh:targetClass linkml_common:InformationEntity . + sh:order 12 ; + sh:path linkml_common:ontology_types ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path linkml_common:type ], + [ sh:class linkml_common:Duration ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 7 ; + sh:path linkml_common:has_duration ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path linkml_common:subtype ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path schema:description ] ; + sh:targetClass linkml_common:InvestigativeProcess . -linkml_common:InvestigativeProcess a sh:NodeShape ; +linkml_common:Landform a sh:NodeShape ; sh:closed true ; + sh:description "A natural feature of the solid surface of the Earth or other planetary body" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; + sh:order 3 ; + sh:path schema:name ], + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path schema1:name ], + sh:path linkml_common:ontology_types ], + [ sh:class schema:PostalAddress ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path linkml_common:address ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path schema:description ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path linkml_common:subtype ], + [ sh:class linkml_common:GeoPointLocation ; + sh:description "The geolocation of the place" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path linkml_common:geolocation ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path schema:identifier ], [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path linkml_common:type ] ; + sh:targetClass linkml_common:Landform . + +linkml_common:LifeEvent a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; sh:order 7 ; sh:path linkml_common:type ], - [ sh:class linkml_common:Investigation ; + [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path linkml_common:starts_at ], + [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path linkml_common:ontology_types ], + [ sh:class linkml_common:Duration ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + sh:path linkml_common:has_duration ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path linkml_common:subtype ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path schema:name ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; sh:order 1 ; - sh:path linkml_common:part_of ], + sh:path linkml_common:ends_at ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path linkml_common:happens_at ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path schema:identifier ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; sh:order 10 ; - sh:path schema1:description ], - [ sh:class linkml_common:InvestigativeProtocol ; + sh:path schema:description ], + [ sh:class linkml_common:TemporalInterval ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path linkml_common:has_interval ] ; + sh:targetClass linkml_common:LifeEvent . + +linkml_common:Location a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass linkml_common:Location . + +linkml_common:MaterialCollection a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path schema:identifier ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path linkml_common:ends_at ], + [ sh:class linkml_common:Procedure ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path linkml_common:follows_procedure ], - [ sh:class linkml_common:PhysicalDevice ; + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path linkml_common:uses_physical_device ], + sh:order 10 ; + sh:path linkml_common:subtype ], [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; - sh:order 3 ; + sh:order 2 ; sh:path linkml_common:starts_at ], - [ sh:description "A unique identifier for a thing" ; + [ sh:class linkml_common:TemporalInterval ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; sh:order 5 ; - sh:path schema1:identifier ], - [ sh:class linkml_common:Concept ; - sh:nodeKind sh:IRI ; + sh:path linkml_common:has_interval ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; sh:order 9 ; - sh:path linkml_common:ontology_types ], + sh:path linkml_common:type ], [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; + sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; - sh:path linkml_common:subtype ], + sh:path schema:name ], + [ sh:class linkml_common:PhysicalDevice ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path linkml_common:uses_physical_device ], [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; sh:order 4 ; - sh:path linkml_common:ends_at ] ; - sh:targetClass linkml_common:InvestigativeProcess . + sh:path linkml_common:happens_at ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path schema:description ], + [ sh:class linkml_common:Duration ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 6 ; + sh:path linkml_common:has_duration ], + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path linkml_common:ontology_types ] ; + sh:targetClass linkml_common:MaterialCollection . -linkml_common:Landform a sh:NodeShape ; +linkml_common:MaterialProcessing a sh:NodeShape ; sh:closed true ; - sh:description "A natural feature of the solid surface of the Earth or other planetary body" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml_common:Concept ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path linkml_common:ontology_types ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path schema1:name ], + sh:order 8 ; + sh:path schema:name ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path linkml_common:starts_at ], + [ sh:class linkml_common:Procedure ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path linkml_common:follows_procedure ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path schema1:description ], - [ sh:class linkml_common:GeoPointLocation ; - sh:description "The geolocation of the place" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path linkml_common:geolocation ], + sh:order 12 ; + sh:path schema:description ], [ sh:datatype xsd:string ; sh:description "An enum with a more specific type" ; sh:maxCount 1 ; - sh:order 5 ; + sh:order 10 ; sh:path linkml_common:subtype ], + [ sh:class linkml_common:TemporalInterval ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 5 ; + sh:path linkml_common:has_interval ], [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; - sh:path schema1:identifier ], - [ sh:class schema1:PostalAddress ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path linkml_common:address ], + sh:order 7 ; + sh:path schema:identifier ], [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path linkml_common:type ] ; - sh:targetClass linkml_common:Landform . - -linkml_common:LifeEvent a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; + sh:order 9 ; + sh:path linkml_common:type ], + [ sh:class linkml_common:PhysicalDevice ; sh:maxCount 1 ; - sh:order 7 ; - sh:path schema1:description ], + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path linkml_common:uses_physical_device ], [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 11 ; sh:path linkml_common:ontology_types ], [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path linkml_common:starts_at ], - [ sh:description "A unique identifier for a thing" ; + sh:order 3 ; + sh:path linkml_common:ends_at ], + [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path schema1:identifier ], - [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + sh:path linkml_common:happens_at ], + [ sh:class linkml_common:Duration ; sh:maxCount 1 ; - sh:order 5 ; - sh:path linkml_common:subtype ], + sh:nodeKind sh:BlankNode ; + sh:order 6 ; + sh:path linkml_common:has_duration ] ; + sh:targetClass linkml_common:MaterialProcessing . + +linkml_common:Measurement a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class linkml_common:Variable ; + sh:description "The variable being measured" ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path linkml_common:variable_measured ], [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:order 4 ; + sh:order 2 ; sh:path linkml_common:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path schema1:name ], - [ sh:class linkml_common:TimePoint ; + [ sh:class ; + sh:description "The quantity being measured" ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path linkml_common:ends_at ] ; - sh:targetClass linkml_common:LifeEvent . + sh:order 0 ; + sh:path linkml_common:quantity_measured ] ; + sh:targetClass linkml_common:Measurement . -linkml_common:Location a sh:NodeShape ; - sh:closed false ; +linkml_common:Observation a sh:NodeShape ; + sh:closed true ; + sh:description "A statement about the state of something" ; sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml_common:Location . + sh:property [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path linkml_common:type ] ; + sh:targetClass linkml_common:Observation . -linkml_common:MaterialCollection a sh:NodeShape ; +linkml_common:PlannedProcess a sh:NodeShape ; sh:closed true ; + sh:description "A process that follows a defined procedure or plan" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; + sh:property [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; - sh:order 9 ; - sh:path schema1:description ], + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path linkml_common:ends_at ], [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path linkml_common:starts_at ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path linkml_common:subtype ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path schema:description ], [ sh:class linkml_common:Procedure ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path linkml_common:follows_procedure ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path schema:identifier ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + sh:path linkml_common:happens_at ], [ sh:class linkml_common:PhysicalDevice ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path linkml_common:uses_physical_device ], - [ sh:description "A unique identifier for a thing" ; + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ], + sh:order 9 ; + sh:path linkml_common:type ], [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 11 ; sh:path linkml_common:ontology_types ], - [ sh:class linkml_common:TimePoint ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path linkml_common:ends_at ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; + sh:order 8 ; + sh:path schema:name ], + [ sh:class linkml_common:TemporalInterval ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; sh:order 5 ; - sh:path schema1:name ], - [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; + sh:path linkml_common:has_interval ], + [ sh:class linkml_common:Duration ; sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; sh:order 6 ; - sh:path linkml_common:type ], - [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path linkml_common:subtype ] ; - sh:targetClass linkml_common:MaterialCollection . + sh:path linkml_common:has_duration ] ; + sh:targetClass linkml_common:PlannedProcess . -linkml_common:MaterialProcessing a sh:NodeShape ; +linkml_common:PointLocation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass linkml_common:PointLocation . + +linkml_common:Publication a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; + sh:description "The title of the item" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path linkml_common:title ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path schema:description ], + [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path schema:identifier ], + [ sh:datatype xsd:string ; + sh:description "Keywords or tags used to describe this item" ; sh:order 6 ; - sh:path linkml_common:type ], + sh:path schema:keywords ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; + sh:description "A summary of the item" ; sh:maxCount 1 ; + sh:order 1 ; + sh:path linkml_common:abstract ], + [ sh:class linkml_common:Agent ; + sh:description "A contact point for a person or organization" ; + sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path schema1:name ], - [ sh:class linkml_common:TimePoint ; + sh:path schema:contactPoint ], + [ sh:datatype xsd:string ; + sh:description "Information about rights held in and over the item" ; sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; sh:order 2 ; - sh:path linkml_common:starts_at ], - [ sh:class linkml_common:PhysicalDevice ; - sh:maxCount 1 ; + sh:path linkml_common:rights ], + [ sh:class linkml_common:Agent ; + sh:description "The person or organization who created the work" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path linkml_common:uses_physical_device ], - [ sh:class linkml_common:TimePoint ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; sh:order 3 ; - sh:path linkml_common:ends_at ], + sh:path ], [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; + sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path linkml_common:subtype ], + sh:order 9 ; + sh:path linkml_common:type ], [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 11 ; sh:path linkml_common:ontology_types ], [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path schema1:description ], - [ sh:description "A unique identifier for a thing" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ], - [ sh:class linkml_common:Procedure ; + sh:description "An enum with a more specific type" ; sh:maxCount 1 ; + sh:order 10 ; + sh:path linkml_common:subtype ], + [ sh:class linkml_common:Agent ; + sh:description "A person or organization that contributed to the creation of the work" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path linkml_common:follows_procedure ] ; - sh:targetClass linkml_common:MaterialProcessing . + sh:order 4 ; + sh:path ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path schema:name ] ; + sh:targetClass linkml_common:Publication . -linkml_common:Measurement a sh:NodeShape ; +linkml_common:RawMaterial a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml_common:Variable ; - sh:description "The variable being measured" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; sh:order 1 ; - sh:path linkml_common:variable_measured ], + sh:path schema:name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path schema:description ], [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path linkml_common:type ], - [ sh:class ; - sh:description "The quantity being measured" ; + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path linkml_common:ontology_types ], + [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; + sh:minCount 1 ; sh:order 0 ; - sh:path linkml_common:quantity_measured ] ; - sh:targetClass linkml_common:Measurement . + sh:path schema:identifier ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path linkml_common:subtype ] ; + sh:targetClass linkml_common:RawMaterial . -linkml_common:Observation a sh:NodeShape ; - sh:closed true ; - sh:description "A statement about the state of something" ; +linkml_common:Relationship a sh:NodeShape ; + sh:closed false ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; sh:order 0 ; sh:path linkml_common:type ] ; - sh:targetClass linkml_common:Observation . + sh:targetClass linkml_common:Relationship . -linkml_common:Organization a sh:NodeShape ; +linkml_common:SampleCollectionProcess a sh:NodeShape ; sh:closed true ; - sh:description "Represents an Organization" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path schema:description ], + [ sh:class linkml_common:InvestigativeProtocol ; sh:maxCount 1 ; - sh:order 2 ; - sh:path linkml_common:type ], - [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path linkml_common:ontology_types ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; + sh:order 2 ; + sh:path linkml_common:follows_procedure ], + [ sh:class linkml_common:SampleMaterial ; sh:maxCount 1 ; - sh:order 1 ; - sh:path schema1:name ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path linkml_common:material_collected ], [ sh:datatype xsd:string ; sh:description "An enum with a more specific type" ; sh:maxCount 1 ; - sh:order 3 ; + sh:order 13 ; sh:path linkml_common:subtype ], - [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:description ], [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 0 ; - sh:path schema1:identifier ] ; - sh:targetClass linkml_common:Organization . - -linkml_common:PlannedProcess a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml_common:TimePoint ; + sh:order 10 ; + sh:path schema:identifier ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path linkml_common:type ], + [ sh:class linkml_common:Duration ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path linkml_common:starts_at ], + sh:order 9 ; + sh:path linkml_common:has_duration ], + [ sh:class linkml_common:TemporalInterval ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 8 ; + sh:path linkml_common:has_interval ], + [ sh:class linkml_common:PhysicalDevice ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path linkml_common:uses_physical_device ], [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 14 ; sh:path linkml_common:ontology_types ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:name ], - [ sh:class linkml_common:Procedure ; + sh:order 11 ; + sh:path schema:name ], + [ sh:class linkml_common:Investigation ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path linkml_common:follows_procedure ], - [ sh:class linkml_common:TimePoint ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; sh:order 3 ; - sh:path linkml_common:ends_at ], - [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path linkml_common:type ], - [ sh:class linkml_common:PhysicalDevice ; + sh:path linkml_common:part_of ], + [ sh:class linkml_common:NamedThing ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path linkml_common:uses_physical_device ], - [ sh:description "A unique identifier for a thing" ; + sh:path linkml_common:collected_from ], + [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; + sh:nodeKind sh:BlankNode ; + sh:order 5 ; + sh:path linkml_common:starts_at ], + [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; - sh:order 9 ; - sh:path schema1:description ], - [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; + sh:nodeKind sh:BlankNode ; + sh:order 6 ; + sh:path linkml_common:ends_at ], + [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; sh:order 7 ; - sh:path linkml_common:subtype ] ; - sh:targetClass linkml_common:PlannedProcess . - -linkml_common:PointLocation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml_common:PointLocation . + sh:path linkml_common:happens_at ] ; + sh:targetClass linkml_common:SampleCollectionProcess . -linkml_common:Publication a sh:NodeShape ; +linkml_common:SampleProcessing a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; + sh:property [ sh:class linkml_common:PhysicalDevice ; sh:maxCount 1 ; - sh:order 2 ; - sh:path linkml_common:type ], + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path linkml_common:uses_physical_device ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path linkml_common:ends_at ], + [ sh:class linkml_common:TemporalInterval ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 5 ; + sh:path linkml_common:has_interval ], [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 7 ; + sh:path schema:identifier ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + sh:path linkml_common:happens_at ], + [ sh:class linkml_common:Procedure ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path schema1:identifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; + sh:path linkml_common:follows_procedure ], + [ sh:class linkml_common:Duration ; sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:description ], + sh:nodeKind sh:BlankNode ; + sh:order 6 ; + sh:path linkml_common:has_duration ], [ sh:datatype xsd:string ; sh:description "An enum with a more specific type" ; sh:maxCount 1 ; - sh:order 3 ; + sh:order 10 ; sh:path linkml_common:subtype ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path schema:description ], [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; - sh:order 4 ; + sh:order 11 ; sh:path linkml_common:ontology_types ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path schema1:name ] ; - sh:targetClass linkml_common:Publication . + sh:order 8 ; + sh:path schema:name ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path linkml_common:type ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path linkml_common:starts_at ] ; + sh:targetClass linkml_common:SampleProcessing . -linkml_common:RawMaterial a sh:NodeShape ; +linkml_common:Service a sh:NodeShape ; + sh:closed true ; + sh:description "A service provided by an organization" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path linkml_common:type ] ; + sh:targetClass linkml_common:Service . + +linkml_common:Specification a sh:NodeShape ; sh:closed true ; + sh:description "A specification of a thing" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path linkml_common:ontology_types ], - [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path linkml_common:subtype ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; sh:order 1 ; - sh:path schema1:name ], - [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path linkml_common:type ], + sh:path schema:name ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; sh:order 5 ; - sh:path schema1:description ], + sh:path schema:description ], [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; - sh:path schema1:identifier ] ; - sh:targetClass linkml_common:RawMaterial . - -linkml_common:Relationship a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml_common:Relationship . - -linkml_common:SampleCollectionProcess a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml_common:TimePoint ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path linkml_common:starts_at ], - [ sh:class linkml_common:TimePoint ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path linkml_common:ends_at ], + sh:path schema:identifier ], [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path linkml_common:type ], - [ sh:class linkml_common:Investigation ; + sh:description "An enum with a more specific type" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path linkml_common:part_of ], - [ sh:class linkml_common:NamedThing ; + sh:path linkml_common:subtype ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path linkml_common:collected_from ], - [ sh:class linkml_common:SampleMaterial ; + sh:order 2 ; + sh:path linkml_common:type ] ; + sh:targetClass linkml_common:Specification . + +linkml_common:StudyDesign a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:minCount 1 ; sh:order 0 ; - sh:path linkml_common:material_collected ], + sh:path schema:identifier ], [ sh:datatype xsd:string ; sh:description "An enum with a more specific type" ; sh:maxCount 1 ; - sh:order 10 ; + sh:order 3 ; sh:path linkml_common:subtype ], [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; + sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path schema1:description ], - [ sh:description "A unique identifier for a thing" ; + sh:order 1 ; + sh:path schema:name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path schema1:identifier ], + sh:order 5 ; + sh:path schema:description ], [ sh:class linkml_common:Concept ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path linkml_common:ontology_types ], - [ sh:class linkml_common:InvestigativeProtocol ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path linkml_common:follows_procedure ], - [ sh:class linkml_common:PhysicalDevice ; - sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; - sh:path linkml_common:uses_physical_device ], + sh:path linkml_common:ontology_types ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; + sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path schema1:name ] ; - sh:targetClass linkml_common:SampleCollectionProcess . + sh:order 2 ; + sh:path linkml_common:type ] ; + sh:targetClass linkml_common:StudyDesign . -linkml_common:SampleProcessing a sh:NodeShape ; +linkml_common:TemporalRelationship a sh:NodeShape ; sh:closed true ; + sh:description "A relationship to another time point" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path linkml_common:type ], - [ sh:class linkml_common:TimePoint ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; sh:order 2 ; - sh:path linkml_common:starts_at ], - [ sh:class linkml_common:Procedure ; + sh:path linkml_common:type ], + [ sh:description "The relationship between the two time points" ; + sh:in ( "BEFORE" "AFTER" "AT_SAME_TIME_AS" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path linkml_common:follows_procedure ], - [ sh:class linkml_common:TimePoint ; + sh:path linkml_common:predicate ], + [ sh:class schema:Thing ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path linkml_common:ends_at ], - [ sh:class linkml_common:Concept ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path linkml_common:ontology_types ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:name ], - [ sh:class linkml_common:PhysicalDevice ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path linkml_common:uses_physical_device ], - [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; + sh:path linkml_common:relative_to ] ; + sh:targetClass linkml_common:TemporalRelationship . + +linkml_common:TimePointOrTemporalInterval a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path linkml_common:subtype ], - [ sh:description "A unique identifier for a thing" ; + sh:order 2 ; + sh:path linkml_common:type ], + [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path linkml_common:ends_at ], + [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; - sh:order 9 ; - sh:path schema1:description ] ; - sh:targetClass linkml_common:SampleProcessing . + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path linkml_common:starts_at ] ; + sh:targetClass linkml_common:TimePointOrTemporalInterval . linkml_common:UnitConversionOperation a sh:NodeShape ; sh:closed true ; sh:description "A unit conversion operation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml_common:MathematicalOperation ; - sh:description "The steps that immediately precede this step" ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path linkml_common:immediate_preceding_steps ], - [ sh:class ; + sh:property [ sh:class ; sh:description "The output unit" ; sh:nodeKind sh:BlankNode ; sh:order 1 ; sh:path linkml_common:outputs ], + [ sh:class ; + sh:description "The input unit" ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path linkml_common:inputs ], [ sh:class linkml_common:MathematicalOperation ; sh:description "The parts of the process" ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path linkml_common:parts ], - [ sh:class ; - sh:description "The input unit" ; + [ sh:class linkml_common:MathematicalOperation ; + sh:description "The steps that immediately precede this step" ; sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path linkml_common:inputs ] ; + sh:order 3 ; + sh:path linkml_common:immediate_preceding_steps ] ; sh:targetClass linkml_common:UnitConversionOperation . -linkml_common:XProcess a sh:NodeShape ; - sh:closed true ; - sh:description "A series of actions or steps taken in order to achieve a particular end" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path linkml_common:type ] ; - sh:targetClass linkml_common:XProcess . - -schema1:Thing a sh:NodeShape ; - sh:closed false ; - sh:description "A physical, digital, conceptual, or other kind of thing with some common characteristics" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path linkml_common:type ] ; - sh:targetClass schema1:Thing . - linkml_common:ClinicalCohort a sh:NodeShape ; sh:closed true ; + sh:description "A group of patients who share a common set of characteristics" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:class linkml_common:ClinicalCohortDefinition ; sh:maxCount 1 ; @@ -1279,41 +1849,42 @@ linkml_common:ClinicalCohort a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path linkml_common:ontology_types ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path schema:identifier ], [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; sh:order 3 ; sh:path linkml_common:type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; + sh:description "An enum with a more specific type" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path schema1:name ], + sh:order 4 ; + sh:path linkml_common:subtype ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; sh:order 6 ; - sh:path schema1:description ], + sh:path schema:description ], [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path linkml_common:subtype ], - [ sh:description "A unique identifier for a thing" ; + sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path schema1:identifier ] ; + sh:order 2 ; + sh:path schema:name ] ; sh:targetClass linkml_common:ClinicalCohort . linkml_common:ClinicalCohortDefinition a sh:NodeShape ; sh:closed true ; + sh:description "A definition of a clinical cohort" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; + sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:description ], + sh:order 1 ; + sh:path schema:name ], [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; sh:order 4 ; @@ -1323,6 +1894,11 @@ linkml_common:ClinicalCohortDefinition a sh:NodeShape ; sh:maxCount 1 ; sh:order 3 ; sh:path linkml_common:subtype ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path schema:description ], [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; @@ -1332,12 +1908,7 @@ linkml_common:ClinicalCohortDefinition a sh:NodeShape ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; - sh:path schema1:identifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path schema1:name ] ; + sh:path schema:identifier ] ; sh:targetClass linkml_common:ClinicalCohortDefinition . linkml_common:CurrencyConcept a sh:NodeShape ; @@ -1350,15 +1921,10 @@ linkml_common:CurrencyConcept a sh:NodeShape ; sh:order 3 ; sh:path linkml_common:subtype ], [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:description ], - [ sh:description "A unique identifier for a thing" ; + sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path schema1:identifier ], + sh:order 1 ; + sh:path schema:name ], [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; sh:order 4 ; @@ -1369,40 +1935,30 @@ linkml_common:CurrencyConcept a sh:NodeShape ; sh:order 2 ; sh:path linkml_common:type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; + sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path schema1:name ] ; + sh:order 5 ; + sh:path schema:description ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path schema:identifier ] ; sh:targetClass linkml_common:CurrencyConcept . linkml_common:EngineeringProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path linkml_common:subtype ], - [ sh:class linkml_common:TimePoint ; + sh:property [ sh:class linkml_common:TemporalInterval ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path linkml_common:starts_at ], - [ sh:class linkml_common:EngineeringSpecification ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path linkml_common:follows_procedure ], - [ sh:description "A unique identifier for a thing" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ], + sh:order 5 ; + sh:path linkml_common:has_interval ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path schema1:description ], + sh:order 12 ; + sh:path schema:description ], [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; @@ -1411,46 +1967,62 @@ linkml_common:EngineeringProcess a sh:NodeShape ; [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:order 6 ; + sh:order 9 ; sh:path linkml_common:type ], [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 11 ; sh:path linkml_common:ontology_types ], - [ sh:class linkml_common:EngineeringProcess ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path schema:name ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path linkml_common:starts_at ], + [ sh:class linkml_common:EngineeringSpecification ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path linkml_common:part_of ], + sh:order 0 ; + sh:path linkml_common:follows_procedure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; + sh:description "An enum with a more specific type" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:name ] ; + sh:order 10 ; + sh:path linkml_common:subtype ], + [ sh:class linkml_common:Duration ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 6 ; + sh:path linkml_common:has_duration ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + sh:path linkml_common:happens_at ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path schema:identifier ], + [ sh:class linkml_common:EngineeringProcess ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path linkml_common:part_of ] ; sh:targetClass linkml_common:EngineeringProcess . linkml_common:EngineeringSpecification a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path schema1:name ], - [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path linkml_common:type ], - [ sh:class linkml_common:Concept ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path linkml_common:ontology_types ], [ sh:datatype xsd:string ; sh:description "An enum with a more specific type" ; sh:maxCount 1 ; @@ -1460,51 +2032,80 @@ linkml_common:EngineeringSpecification a sh:NodeShape ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; - sh:path schema1:identifier ] ; + sh:path schema:identifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path schema:name ], + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path linkml_common:ontology_types ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path schema:description ] ; sh:targetClass linkml_common:EngineeringSpecification . linkml_common:Event a sh:NodeShape ; sh:closed true ; sh:description "A thing that happens" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml_common:TimePoint ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path schema:description ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path linkml_common:type ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path linkml_common:happens_at ], + [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; sh:order 0 ; sh:path linkml_common:starts_at ], - [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; + [ sh:class linkml_common:TemporalInterval ; sh:maxCount 1 ; - sh:order 5 ; - sh:path linkml_common:subtype ], + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path linkml_common:has_interval ], [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path schema:name ], + [ sh:class linkml_common:Duration ; sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; sh:order 4 ; - sh:path linkml_common:type ], - [ sh:description "A unique identifier for a thing" ; + sh:path linkml_common:has_duration ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path schema1:identifier ], + sh:order 8 ; + sh:path linkml_common:subtype ], [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 9 ; sh:path linkml_common:ontology_types ], [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; sh:order 1 ; sh:path linkml_common:ends_at ], - [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path schema1:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; + [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path schema1:name ] ; + sh:order 5 ; + sh:path schema:identifier ] ; sh:targetClass linkml_common:Event . linkml_common:FoodIngredient a sh:NodeShape ; @@ -1513,122 +2114,168 @@ linkml_common:FoodIngredient a sh:NodeShape ; sh:property [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; + sh:order 1 ; + sh:path linkml_common:type ], + [ sh:class linkml_common:QuantityKind ; + sh:description "The kind of quantity" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path linkml_common:type ] ; + sh:path linkml_common:has_quantity_kind ] ; sh:targetClass linkml_common:FoodIngredient . linkml_common:FoodProcessing a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml_common:Procedure ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path schema:name ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path schema:identifier ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path linkml_common:subtype ], + [ sh:class linkml_common:TemporalInterval ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 5 ; + sh:path linkml_common:has_interval ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path schema:description ], + [ sh:class linkml_common:PhysicalDevice ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path linkml_common:uses_physical_device ], + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path linkml_common:ontology_types ], + [ sh:class linkml_common:Procedure ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path linkml_common:follows_procedure ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path linkml_common:type ], [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path linkml_common:starts_at ], - [ sh:description "A unique identifier for a thing" ; + [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; sh:order 4 ; - sh:path schema1:identifier ], - [ sh:class linkml_common:PhysicalDevice ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path linkml_common:uses_physical_device ], + sh:path linkml_common:happens_at ], [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; sh:order 3 ; sh:path linkml_common:ends_at ], - [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; + [ sh:class linkml_common:Duration ; sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; sh:order 6 ; - sh:path linkml_common:type ], - [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path linkml_common:subtype ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:name ], - [ sh:class linkml_common:Concept ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path linkml_common:ontology_types ], - [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path schema1:description ] ; + sh:path linkml_common:has_duration ] ; sh:targetClass linkml_common:FoodProcessing . linkml_common:HealthcareEncounter a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for a thing" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ], + sh:property [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path linkml_common:ontology_types ], [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:order 6 ; + sh:order 9 ; sh:path linkml_common:type ], - [ sh:class linkml_common:Concept ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path linkml_common:ontology_types ], [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path linkml_common:starts_at ], - [ sh:class linkml_common:HealthcareProvider ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path linkml_common:provider ], [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; sh:order 3 ; sh:path linkml_common:ends_at ], + [ sh:class linkml_common:TemporalInterval ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 5 ; + sh:path linkml_common:has_interval ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path schema:name ], [ sh:description "An enum with a more specific type" ; sh:in ( "Inpatient Visit" "Emergency Room Visit" "Emergency Room and Inpatient Visit" "Non-hospital institution Visit" "Outpatient Visit" "Home Visit" "Telehealth Visit" "Pharmacy Visit" "Laboratory Visit" "Ambulance Visit" "Case Management Visit" ) ; sh:maxCount 1 ; - sh:order 7 ; + sh:order 10 ; sh:path linkml_common:subtype ], - [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; + [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path schema1:description ], + sh:minCount 1 ; + sh:order 7 ; + sh:path schema:identifier ], + [ sh:class linkml_common:HealthcareProvider ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path linkml_common:provider ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + sh:path linkml_common:happens_at ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; + sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:name ], + sh:order 12 ; + sh:path schema:description ], [ sh:class linkml_common:Patient ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; sh:order 0 ; - sh:path linkml_common:patient ] ; + sh:path linkml_common:patient ], + [ sh:class linkml_common:Duration ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 6 ; + sh:path linkml_common:has_duration ] ; sh:targetClass linkml_common:HealthcareEncounter . linkml_common:HealthcareProvider a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml_common:Concept ; + sh:property [ sh:class linkml_common:Person ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path linkml_common:is_person ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path linkml_common:type ], + [ sh:class linkml_common:Concept ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; @@ -1637,67 +2284,127 @@ linkml_common:HealthcareProvider a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path linkml_common:care_site ], - [ sh:class linkml_common:Person ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path linkml_common:is_person ] ; + sh:path linkml_common:care_site ] ; sh:targetClass linkml_common:HealthcareProvider . linkml_common:HealthcareSite a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class schema1:PostalAddress ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path schema:description ], + [ sh:class linkml_common:GeoPointLocation ; + sh:description "The geolocation of the place" ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path linkml_common:geolocation ], + [ sh:class schema:PostalAddress ; sh:maxCount 1 ; sh:nodeKind sh:BlankNode ; sh:order 0 ; sh:path linkml_common:address ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path linkml_common:subtype ], + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path linkml_common:ontology_types ], [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; - sh:path schema1:identifier ], + sh:path schema:identifier ], [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; + sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path linkml_common:subtype ], + sh:order 3 ; + sh:path schema:name ], [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; sh:order 4 ; + sh:path linkml_common:type ] ; + sh:targetClass linkml_common:HealthcareSite . + +linkml_common:NamedThing a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path schema:identifier ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; sh:path linkml_common:type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path schema:description ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; sh:maxCount 1 ; sh:order 3 ; - sh:path schema1:name ], - [ sh:class linkml_common:GeoPointLocation ; - sh:description "The geolocation of the place" ; + sh:path linkml_common:subtype ], + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path linkml_common:ontology_types ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; sh:order 1 ; - sh:path linkml_common:geolocation ], + sh:path schema:name ] ; + sh:targetClass linkml_common:NamedThing . + +linkml_common:Organization a sh:NodeShape ; + sh:closed true ; + sh:description "Represents an Organization" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path schema:identifier ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path linkml_common:subtype ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path schema:description ], [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 4 ; sh:path linkml_common:ontology_types ], [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; + sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path schema1:description ] ; - sh:targetClass linkml_common:HealthcareSite . + sh:order 2 ; + sh:path linkml_common:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path schema:name ] ; + sh:targetClass linkml_common:Organization . -linkml_common:NamedThing a sh:NodeShape ; +linkml_common:SampleMaterial a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml_common:Concept ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path linkml_common:ontology_types ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "An enum with a more specific type" ; sh:maxCount 1 ; sh:order 3 ; @@ -1706,74 +2413,89 @@ linkml_common:NamedThing a sh:NodeShape ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; sh:order 1 ; - sh:path schema1:name ], - [ sh:description "A unique identifier for a thing" ; + sh:path schema:name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path schema1:identifier ], + sh:order 5 ; + sh:path schema:description ], + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path linkml_common:ontology_types ], [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path linkml_common:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; + [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:description ] ; - sh:targetClass linkml_common:NamedThing . + sh:minCount 1 ; + sh:order 0 ; + sh:path schema:identifier ] ; + sh:targetClass linkml_common:SampleMaterial . -linkml_common:SampleMaterial a sh:NodeShape ; - sh:closed true ; +schema:Thing a sh:NodeShape ; + sh:closed false ; + sh:description "A physical, digital, conceptual, or other kind of thing with some common characteristics" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:order 0 ; - sh:path schema1:identifier ], + sh:path linkml_common:type ] ; + sh:targetClass schema:Thing . + +linkml_common:UnitConcept a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path linkml_common:subtype ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path schema:description ], [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path linkml_common:type ], - [ sh:class linkml_common:Concept ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path linkml_common:ontology_types ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; sh:order 1 ; - sh:path schema1:name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:description ], - [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; + sh:path schema:name ], + [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path linkml_common:subtype ] ; - sh:targetClass linkml_common:SampleMaterial . + sh:minCount 1 ; + sh:order 0 ; + sh:path schema:identifier ], + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path linkml_common:ontology_types ] ; + sh:targetClass linkml_common:UnitConcept . linkml_common:Variable a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path linkml_common:type ], - [ sh:class linkml_common:UnitConcept ; + sh:property [ sh:class linkml_common:UnitConcept ; sh:description "The units that are allowed for this variable" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path linkml_common:allowed_units ] ; + sh:path linkml_common:allowed_units ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path linkml_common:type ] ; sh:targetClass linkml_common:Variable . -linkml_common:UnitConcept a sh:NodeShape ; +linkml_common:InvestigativeProtocol a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:class linkml_common:Concept ; @@ -1784,53 +2506,78 @@ linkml_common:UnitConcept a sh:NodeShape ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; sh:order 5 ; - sh:path schema1:description ], + sh:path schema:description ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path linkml_common:type ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path linkml_common:subtype ], [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; - sh:path schema1:identifier ], + sh:path schema:identifier ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; sh:order 1 ; - sh:path schema1:name ], - [ sh:datatype xsd:string ; + sh:path schema:name ] ; + sh:targetClass linkml_common:InvestigativeProtocol . + +linkml_common:Patient a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:order 2 ; + sh:order 1 ; sh:path linkml_common:type ], - [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; + [ sh:class linkml_common:Person ; sh:maxCount 1 ; - sh:order 3 ; - sh:path linkml_common:subtype ] ; - sh:targetClass linkml_common:UnitConcept . + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path linkml_common:is_person ] ; + sh:targetClass linkml_common:Patient . + +linkml:Any a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass linkml:Any . -schema1:PostalAddress a sh:NodeShape ; +schema:PostalAddress a sh:NodeShape ; sh:closed true ; sh:description "Represents an Address" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "The state" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path linkml_common:state ], + [ sh:datatype xsd:string ; sh:description "The postal code or zip code" ; sh:maxCount 1 ; sh:order 4 ; sh:path linkml_common:postal_code ], - [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path linkml_common:type ], [ sh:datatype xsd:string ; sh:description "The city" ; sh:maxCount 1 ; sh:order 2 ; sh:path linkml_common:city ], [ sh:datatype xsd:string ; - sh:description "The state" ; + sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path linkml_common:state ], + sh:order 6 ; + sh:path linkml_common:type ], + [ sh:datatype xsd:string ; + sh:description "The country" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path linkml_common:country ], [ sh:datatype xsd:string ; sh:description "The street address" ; sh:maxCount 1 ; @@ -1839,13 +2586,8 @@ schema1:PostalAddress a sh:NodeShape ; [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 1 ; - sh:path linkml_common:street_address_additional ], - [ sh:datatype xsd:string ; - sh:description "The country" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path linkml_common:country ] ; - sh:targetClass schema1:PostalAddress . + sh:path linkml_common:street_address_additional ] ; + sh:targetClass schema:PostalAddress . linkml_common:GeoPointLocation a sh:NodeShape ; sh:closed true ; @@ -1855,60 +2597,185 @@ linkml_common:GeoPointLocation a sh:NodeShape ; sh:maxCount 1 ; sh:order 2 ; sh:path linkml_common:altitude ], + [ sh:datatype xsd:decimal ; + sh:description "The longitude of the location" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path linkml_common:longitude ], [ sh:datatype xsd:decimal ; sh:description "The latitude of the location" ; sh:maxCount 1 ; sh:order 0 ; - sh:path linkml_common:latitude ], - [ sh:datatype xsd:decimal ; - sh:description "The longitude of the location" ; + sh:path linkml_common:latitude ] ; + sh:targetClass linkml_common:GeoPointLocation . + +linkml_common:Investigation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path schema:identifier ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path linkml_common:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; + sh:order 3 ; + sh:path schema:name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path schema:description ], + [ sh:class linkml_common:Variable ; + sh:nodeKind sh:BlankNode ; sh:order 1 ; - sh:path linkml_common:longitude ] ; - sh:targetClass linkml_common:GeoPointLocation . + sh:path linkml_common:variables ], + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path linkml_common:ontology_types ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path linkml_common:subtype ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path linkml_common:objectives ] ; + sh:targetClass linkml_common:Investigation . + +linkml_common:MathematicalOperation a sh:NodeShape ; + sh:closed true ; + sh:description "Application of a mathematical operation to one or more inputs to produce one or more outputs" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class linkml:Any ; + sh:description "The inputs to the operation" ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path linkml_common:inputs ], + [ sh:class linkml:Any ; + sh:description "The outputs of the operation" ; + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path linkml_common:outputs ], + [ sh:class linkml_common:MathematicalOperation ; + sh:description "The parts of the process" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path linkml_common:parts ], + [ sh:class linkml_common:MathematicalOperation ; + sh:description "The steps that immediately precede this step" ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path linkml_common:immediate_preceding_steps ] ; + sh:targetClass linkml_common:MathematicalOperation . + +linkml_common:Person a sh:NodeShape ; + sh:closed true ; + sh:description "Represents a Person" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path schema:identifier ], + [ sh:description "living or dead status" ; + sh:in ( PATO:0001421 PATO:0001422 "UNKNOWN" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path linkml_common:vital_status ], + [ sh:datatype xsd:string ; + sh:description "An enum with a more specific type" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path linkml_common:subtype ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path schema:name ], + [ sh:datatype xsd:string ; + sh:description "The main email address of a person" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path schema:email ; + sh:pattern "^\\S+@[\\S+\\.]+\\S+" ], + [ sh:datatype xsd:integer ; + sh:description "Number of years since birth" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path linkml_common:age_in_years ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path linkml_common:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path schema:description ], + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path linkml_common:ontology_types ], + [ sh:datatype xsd:date ; + sh:description "Date on which a person is born" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path schema:birthDate ] ; + sh:targetClass linkml_common:Person . -linkml_common:Investigation a sh:NodeShape ; +linkml_common:Procedure a sh:NodeShape ; sh:closed true ; + sh:description "A canonical series of actions conducted in a certain order or manner" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path schema1:name ], - [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; + sh:description "An enum with a more specific type" ; sh:maxCount 1 ; sh:order 3 ; - sh:path linkml_common:type ], - [ sh:class linkml_common:Concept ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path linkml_common:ontology_types ], + sh:path linkml_common:subtype ], [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path schema1:identifier ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; sh:order 0 ; - sh:path linkml_common:objectives ], + sh:path schema:identifier ], [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; + sh:description "A type for a thing" ; sh:maxCount 1 ; + sh:order 2 ; + sh:path linkml_common:type ], + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; sh:order 4 ; - sh:path linkml_common:subtype ], + sh:path linkml_common:ontology_types ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path schema1:description ] ; - sh:targetClass linkml_common:Investigation . + sh:order 5 ; + sh:path schema:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path schema:name ] ; + sh:targetClass linkml_common:Procedure . -linkml_common:InvestigativeProtocol a sh:NodeShape ; +linkml_common:QuantityKind a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path linkml_common:ontology_types ], + [ sh:datatype xsd:string ; sh:description "An enum with a more specific type" ; sh:maxCount 1 ; sh:order 3 ; @@ -1918,261 +2785,224 @@ linkml_common:InvestigativeProtocol a sh:NodeShape ; sh:maxCount 1 ; sh:order 2 ; sh:path linkml_common:type ], - [ sh:class linkml_common:Concept ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path linkml_common:ontology_types ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; sh:order 1 ; - sh:path schema1:name ], - [ sh:description "A unique identifier for a thing" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path schema1:identifier ], + sh:path schema:name ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; sh:order 5 ; - sh:path schema1:description ] ; - sh:targetClass linkml_common:InvestigativeProtocol . + sh:path schema:description ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path schema:identifier ] ; + sh:targetClass linkml_common:QuantityKind . -linkml_common:Patient a sh:NodeShape ; + a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml_common:Person ; + sh:property [ sh:class linkml_common:QuantityKind ; + sh:description "The kind of quantity" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path linkml_common:is_person ] ; - sh:targetClass linkml_common:Patient . + sh:path linkml_common:has_quantity_kind ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path linkml_common:type ] ; + sh:targetClass . -linkml_common:Person a sh:NodeShape ; +linkml_common:Agent a sh:NodeShape ; sh:closed true ; - sh:description "Represents a Person" ; + sh:description "Represents an Agent" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The main email address of a person" ; + sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path schema1:email ; - sh:pattern "^\\S+@[\\S+\\.]+\\S+" ], + sh:order 2 ; + sh:path linkml_common:type ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:name ], + sh:order 1 ; + sh:path schema:name ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path schema1:description ], - [ sh:datatype xsd:integer ; - sh:description "Number of years since birth" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path linkml_common:age_in_years ], + sh:order 5 ; + sh:path schema:description ], [ sh:datatype xsd:string ; sh:description "An enum with a more specific type" ; sh:maxCount 1 ; - sh:order 7 ; + sh:order 3 ; sh:path linkml_common:subtype ], [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ], - [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path linkml_common:type ], - [ sh:datatype xsd:date ; - sh:description "Date on which a person is born" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path schema1:birthDate ], + sh:order 0 ; + sh:path schema:identifier ], [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path linkml_common:ontology_types ], - [ sh:description "living or dead status" ; - sh:in ( PATO:0001421 PATO:0001422 "UNKNOWN" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path linkml_common:vital_status ] ; - sh:targetClass linkml_common:Person . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . + sh:order 4 ; + sh:path linkml_common:ontology_types ] ; + sh:targetClass linkml_common:Agent . -linkml_common:MathematicalOperation a sh:NodeShape ; +linkml_common:PhysicalDevice a sh:NodeShape ; sh:closed true ; - sh:description "Application of a mathematical operation to one or more inputs to produce one or more outputs" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml_common:MathematicalOperation ; - sh:description "The parts of the process" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path linkml_common:parts ], - [ sh:class linkml:Any ; - sh:description "The inputs to the operation" ; - sh:nodeKind sh:BlankNode ; + sh:property [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:order 0 ; - sh:path linkml_common:inputs ], - [ sh:class linkml:Any ; - sh:description "The outputs of the operation" ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path linkml_common:outputs ], - [ sh:class linkml_common:MathematicalOperation ; - sh:description "The steps that immediately precede this step" ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path linkml_common:immediate_preceding_steps ] ; - sh:targetClass linkml_common:MathematicalOperation . - -linkml_common:Procedure a sh:NodeShape ; - sh:closed true ; - sh:description "A canonical series of actions conducted in a certain order or manner" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:path schema:identifier ], + [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; sh:order 5 ; - sh:path schema1:description ], + sh:path schema:description ], [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path linkml_common:type ], - [ sh:class linkml_common:Concept ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path linkml_common:ontology_types ], [ sh:datatype xsd:string ; sh:description "An enum with a more specific type" ; sh:maxCount 1 ; sh:order 3 ; sh:path linkml_common:subtype ], + [ sh:class linkml_common:Concept ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path linkml_common:ontology_types ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; sh:order 1 ; - sh:path schema1:name ], - [ sh:description "A unique identifier for a thing" ; + sh:path schema:name ] ; + sh:targetClass linkml_common:PhysicalDevice . + +linkml_common:Duration a sh:NodeShape ; + sh:closed true ; + sh:description "A length of time" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class linkml_common:QuantityKind ; + sh:description "The kind of quantity" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path schema1:identifier ] ; - sh:targetClass linkml_common:Procedure . + sh:path linkml_common:has_quantity_kind ], + [ sh:datatype xsd:string ; + sh:description "A type for a thing" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path linkml_common:type ] ; + sh:targetClass linkml_common:Duration . - a sh:NodeShape ; +linkml_common:TemporalInterval a sh:NodeShape ; sh:closed true ; + sh:description "A period of time" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; + sh:order 2 ; + sh:path linkml_common:type ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path linkml_common:ends_at ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; sh:order 0 ; - sh:path linkml_common:type ] ; - sh:targetClass . + sh:path linkml_common:starts_at ] ; + sh:targetClass linkml_common:TemporalInterval . -linkml_common:PhysicalDevice a sh:NodeShape ; +linkml_common:Concept a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml_common:Concept ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path schema:name ], + [ sh:class linkml_common:Concept ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path linkml_common:ontology_types ], - [ sh:description "A unique identifier for a thing" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path schema1:identifier ], + sh:order 5 ; + sh:path schema:description ], [ sh:datatype xsd:string ; sh:description "A type for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path linkml_common:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path schema1:name ], [ sh:datatype xsd:string ; sh:description "An enum with a more specific type" ; sh:maxCount 1 ; sh:order 3 ; sh:path linkml_common:subtype ], - [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; + [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:description ] ; - sh:targetClass linkml_common:PhysicalDevice . + sh:minCount 1 ; + sh:order 0 ; + sh:path schema:identifier ] ; + sh:targetClass linkml_common:Concept . linkml_common:TimePoint a sh:NodeShape ; sh:closed true ; + sh:description "A point in time. Can be fully specified, or specified in relative terms." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:dateTime ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path linkml_common:datetime_value ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path schema1:description ], - [ sh:datatype xsd:time ; + sh:order 5 ; + sh:path schema:description ], + [ sh:datatype xsd:date ; sh:maxCount 1 ; sh:order 1 ; - sh:path linkml_common:time_value ], + sh:path linkml_common:date_value ], [ sh:class linkml_common:Event ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; + sh:order 4 ; sh:path linkml_common:marker_event ], - [ sh:datatype xsd:date ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path linkml_common:date_value ] ; - sh:targetClass linkml_common:TimePoint . - -linkml_common:Concept a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A type for a thing" ; + [ sh:datatype xsd:time ; sh:maxCount 1 ; sh:order 2 ; - sh:path linkml_common:type ], - [ sh:datatype xsd:string ; - sh:description "An enum with a more specific type" ; + sh:path linkml_common:time_value ], + [ sh:datatype xsd:dateTime ; sh:maxCount 1 ; sh:order 3 ; - sh:path linkml_common:subtype ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; + sh:path linkml_common:datetime_value ], + [ sh:class linkml_common:TimePoint ; sh:maxCount 1 ; - sh:order 1 ; - sh:path schema1:name ], - [ sh:class linkml_common:Concept ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path linkml_common:ontology_types ], - [ sh:description "A unique identifier for a thing" ; + sh:nodeKind sh:BlankNode ; + sh:order 7 ; + sh:path linkml_common:ends_at ], + [ sh:datatype xsd:integer ; sh:maxCount 1 ; - sh:minCount 1 ; sh:order 0 ; - sh:path schema1:identifier ], + sh:path linkml_common:year_value ], + [ sh:class linkml_common:TimePoint ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 6 ; + sh:path linkml_common:starts_at ], [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; + sh:description "A type for a thing" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:description ] ; - sh:targetClass linkml_common:Concept . + sh:order 8 ; + sh:path linkml_common:type ] ; + sh:targetClass linkml_common:TimePoint . diff --git a/project/shex/linkml_common.shex b/project/shex/linkml_common.shex index e54872b..c204475 100644 --- a/project/shex/linkml_common.shex +++ b/project/shex/linkml_common.shex @@ -2,8 +2,9 @@ BASE PREFIX rdf: PREFIX xsd: PREFIX linkml: -PREFIX schema1: +PREFIX schema: PREFIX fhir: +PREFIX dcterms: linkml:String xsd:string @@ -44,12 +45,30 @@ linkml:Jsonpath xsd:string linkml:Sparqlpath xsd:string + ( + CLOSED { + ( $ ( & ; + rdf:type [ ] ? + ) ; + rdf:type [ ] + ) + } OR @ OR @ OR @ +) + CLOSED { ( $ rdf:type . * ; rdf:type [ linkml:Any ] ? ) } + CLOSED { + ( $ ( & ; + rdf:type [ ] ? + ) ; + rdf:type [ ] + ) +} + CLOSED { ( $ ( & ; rdf:type [ ] ? @@ -87,7 +106,7 @@ linkml:Sparqlpath xsd:string CLOSED { ( $ ( & ; - rdf:type [ schema1:Intangible ] ? ; + rdf:type [ schema:Intangible ] ? ; @ * ) ; rdf:type [ ] ? @@ -109,7 +128,24 @@ linkml:Sparqlpath xsd:string ) ; rdf:type [ ] ) - } OR @ OR @ + } OR @ OR @ OR @ +) + + ( + CLOSED { + ( $ ( & ; + rdf:type [ ] ? ; + @linkml:String ? ; + <abstract> @linkml:String ? ; + <rights> @linkml:String ? ; + dcterms:creator @<Agent> * ; + dcterms:contributor @<Agent> * ; + schema:contactPoint @<Agent> * ; + schema:keywords @linkml:String * + ) ; + rdf:type [ <CreativeWork> ] + ) + } OR @<Dataset> OR @<Publication> ) <DataGenerationFromSample> CLOSED { @@ -120,14 +156,31 @@ linkml:Sparqlpath xsd:string ) } +<Dataset> CLOSED { + ( $<Dataset_tes> ( &<CreativeWork_tes> ; + rdf:type [ <CreativeWork> ] ? ; + <collected_as_part_of> @<Investigation> * + ) ; + rdf:type [ <Dataset> ] + ) +} + <DataStructure> CLOSED { ( $<DataStructure_tes> ( &<Intangible_tes> ; - rdf:type [ schema1:Intangible ] ? + rdf:type [ schema:Intangible ] ? ) ; rdf:type [ <DataStructure> ] ? ) } +<Duration> CLOSED { + ( $<Duration_tes> ( &<Quantity_tes> ; + rdf:type [ fhir:Quantity ] ? + ) ; + rdf:type [ <Duration> ] ? + ) +} + <EngineeringMaterialProcessing> CLOSED { ( $<EngineeringMaterialProcessing_tes> ( &<MaterialProcessing_tes> ; rdf:type [ <MaterialProcessing> ] ? @@ -155,18 +208,36 @@ linkml:Sparqlpath xsd:string } <Entity> ( - @<Intangible> OR @<NamedThing> OR @<Observation> OR @<PostalAddress> OR @<Variable> OR @<XProcess> + @<Intangible> OR @<NamedThing> OR @<Observation> OR @<PostalAddress> OR @<Variable> ) <Entity_struct> { ( $<Entity_tes> <type> @linkml:String ? ; - rdf:type [ schema1:Thing ] ? + rdf:type [ schema:Thing ] ? + ) +} + +<EnvironmentalMonitoring> CLOSED { + ( $<EnvironmentalMonitoring_tes> ( &<EnvironmentalProcess_tes> ; + rdf:type [ <EnvironmentalProcess> ] ? + ) ; + rdf:type [ <EnvironmentalMonitoring> ] ? ) } -<EnvironmentalProcess> CLOSED { - ( $<EnvironmentalProcess_tes> rdf:type . * ; - rdf:type [ <EnvironmentalProcess> ] ? +<EnvironmentalProcess> ( + CLOSED { + ( $<EnvironmentalProcess_tes> rdf:type . * ; + rdf:type [ <EnvironmentalProcess> ] ? + ) + } OR @<EnvironmentalMonitoring> +) + +<EnvironmentalSite> CLOSED { + ( $<EnvironmentalSite_tes> ( &<Place_tes> ; + rdf:type [ schema:Place ] ? + ) ; + rdf:type [ <EnvironmentalSite> ] ) } @@ -175,7 +246,10 @@ linkml:Sparqlpath xsd:string ( $<Event_tes> ( &<NamedThing_tes> ; rdf:type [ <NamedThing> ] ? ; <starts_at> @<TimePoint> ? ; - <ends_at> @<TimePoint> ? + <ends_at> @<TimePoint> ? ; + <happens_at> @<TimePoint> ? ; + <has_interval> @<TemporalInterval> ? ; + <has_duration> @<Duration> ? ) ; rdf:type [ <Event> ] ) @@ -245,7 +319,17 @@ linkml:Sparqlpath xsd:string rdf:type [ <Event> ] ? ; <patient> @<Patient> ? ; <provider> @<HealthcareProvider> ? ; - <subtype> @<HealthcareEncounterClassification> ? + <subtype> [ <https://w3id.org/linkml-common/HealthcareEncounterClassification#Inpatient%20Visit> + <https://w3id.org/linkml-common/HealthcareEncounterClassification#Emergency%20Room%20Visit> + <https://w3id.org/linkml-common/HealthcareEncounterClassification#Emergency%20Room%20and%20Inpatient%20Visit> + <https://w3id.org/linkml-common/HealthcareEncounterClassification#Non-hospital%20institution%20Visit> + <https://w3id.org/linkml-common/HealthcareEncounterClassification#Outpatient%20Visit> + <https://w3id.org/linkml-common/HealthcareEncounterClassification#Home%20Visit> + <https://w3id.org/linkml-common/HealthcareEncounterClassification#Telehealth%20Visit> + <https://w3id.org/linkml-common/HealthcareEncounterClassification#Pharmacy%20Visit> + <https://w3id.org/linkml-common/HealthcareEncounterClassification#Laboratory%20Visit> + <https://w3id.org/linkml-common/HealthcareEncounterClassification#Ambulance%20Visit> + <https://w3id.org/linkml-common/HealthcareEncounterClassification#Case%20Management%20Visit> ] ? ) ; rdf:type [ <HealthcareEncounter> ] ) @@ -271,7 +355,10 @@ linkml:Sparqlpath xsd:string <HealthcareRole> ( CLOSED { - ( $<HealthcareRole_tes> <is_person> @<Person> ? ; + ( $<HealthcareRole_tes> ( &<Role_tes> ; + rdf:type [ schema:Role ] ? ; + <is_person> @<Person> ? + ) ; rdf:type [ <HealthcareRole> ] ? ) } OR @<HealthcareProvider> OR @<Patient> @@ -279,7 +366,7 @@ linkml:Sparqlpath xsd:string <HealthcareSite> CLOSED { ( $<HealthcareSite_tes> ( &<Place_tes> ; - rdf:type [ schema1:Place ] ? + rdf:type [ schema:Place ] ? ) ; rdf:type [ <HealthcareSite> ] ) @@ -288,7 +375,7 @@ linkml:Sparqlpath xsd:string <InformationEntity> CLOSED { ( $<InformationEntity_tes> ( &<NamedThing_tes> ; rdf:type [ <NamedThing> ] ? ; - schema1:describes @<Any> ? + schema:describes @<Any> ? ) ; rdf:type [ <InformationEntity> ] ) @@ -297,17 +384,19 @@ linkml:Sparqlpath xsd:string <Intangible> ( CLOSED { ( $<Intangible_tes> ( &<Entity_tes> ; - rdf:type [ schema1:Thing ] ? + rdf:type [ schema:Thing ] ? ) ; - rdf:type [ schema1:Intangible ] ? + rdf:type [ schema:Intangible ] ? ) - } OR @<Collection> OR @<DataStructure> OR @<Quantity> OR @<QuantityRange> + } OR @<Collection> OR @<DataStructure> OR @<Quantity> OR @<QuantityRange> OR @<Relationship> OR @<Role> OR @<Service> OR + @<TimePointOrTemporalInterval> ) <Investigation> CLOSED { ( $<Investigation_tes> ( &<NamedThing_tes> ; rdf:type [ <NamedThing> ] ? ; - <objectives> @linkml:String ? + <objectives> @linkml:String ? ; + <variables> @<Variable> * ) ; rdf:type [ <Investigation> ] ) @@ -335,7 +424,7 @@ linkml:Sparqlpath xsd:string <Landform> CLOSED { ( $<Landform_tes> ( &<Place_tes> ; - rdf:type [ schema1:Place ] ? ; + rdf:type [ schema:Place ] ? ; <geolocation> @<GeoPointLocation> ) ; rdf:type [ <Landform> ] @@ -401,23 +490,23 @@ linkml:Sparqlpath xsd:string <NamedThing> ( CLOSED { ( $<NamedThing_tes> ( &<Entity_tes> ; - rdf:type [ schema1:Thing ] ? ; - schema1:name @linkml:String ? ; + rdf:type [ schema:Thing ] ? ; + schema:name @linkml:String ? ; <subtype> @linkml:String ? ; <ontology_types> @<Concept> * ; - schema1:description @linkml:String ? + schema:description @linkml:String ? ) ; rdf:type [ <NamedThing> ] ) - } OR @<ClinicalCohort> OR @<ClinicalCohortDefinition> OR @<Concept> OR @<Event> OR @<InformationEntity> OR @<Investigation> OR - @<Organization> OR @<Person> OR @<PhysicalDevice> OR @<Place> OR @<Procedure> OR @<Publication> OR @<RawMaterial> OR - @<SampleMaterial> + } OR @<Agent> OR @<ClinicalCohort> OR @<ClinicalCohortDefinition> OR @<Concept> OR @<CreativeWork> OR @<Event> OR + @<InformationEntity> OR @<Investigation> OR @<PhysicalDevice> OR @<Place> OR @<RawMaterial> OR @<SampleMaterial> OR + @<Specification> ) <Observation> ( CLOSED { ( $<Observation_tes> ( &<Entity_tes> ; - rdf:type [ schema1:Thing ] ? + rdf:type [ schema:Thing ] ? ) ; rdf:type [ <Observation> ] ? ) @@ -426,8 +515,8 @@ linkml:Sparqlpath xsd:string <Organization> ( CLOSED { - ( $<Organization_tes> ( &<NamedThing_tes> ; - rdf:type [ <NamedThing> ] ? + ( $<Organization_tes> ( &<Agent_tes> ; + rdf:type [ <Agent> ] ? ) ; rdf:type [ <Organization> ] ) @@ -443,12 +532,13 @@ linkml:Sparqlpath xsd:string } <Person> CLOSED { - ( $<Person_tes> ( &<NamedThing_tes> ; - rdf:type [ <NamedThing> ] ? ; - schema1:email @linkml:String ? ; - schema1:birthDate @linkml:Date ? ; + ( $<Person_tes> ( &<Agent_tes> ; + rdf:type [ <Agent> ] ? ; + schema:email @linkml:String ? ; + schema:birthDate @linkml:Date ? ; <age_in_years> @linkml:Integer ? ; - <vital_status> @<PersonStatus> ? + <vital_status> [ <http://purl.obolibrary.org/obo/PATO_0001421> <http://purl.obolibrary.org/obo/PATO_0001422> + <https://w3id.org/linkml-common/PersonStatus#UNKNOWN> ] ? ) ; rdf:type [ <Person> ] ) @@ -469,9 +559,9 @@ linkml:Sparqlpath xsd:string <address> @<PostalAddress> ? ; <geolocation> @<GeoPointLocation> ? ) ; - rdf:type [ schema1:Place ] + rdf:type [ schema:Place ] ) - } OR @<HealthcareSite> OR @<Landform> + } OR @<EnvironmentalSite> OR @<HealthcareSite> OR @<Landform> ) <PlannedProcess> ( @@ -498,7 +588,7 @@ linkml:Sparqlpath xsd:string <PostalAddress> CLOSED { ( $<PostalAddress_tes> ( &<Entity_tes> ; - rdf:type [ schema1:Thing ] ? ; + rdf:type [ schema:Thing ] ? ; <street_address> @linkml:String ? ; <street_address_additional> @linkml:String ? ; <city> @linkml:String ? ; @@ -506,23 +596,23 @@ linkml:Sparqlpath xsd:string <postal_code> @linkml:String ? ; <country> @linkml:String ? ) ; - rdf:type [ schema1:PostalAddress ] ? + rdf:type [ schema:PostalAddress ] ? ) } <Procedure> ( CLOSED { - ( $<Procedure_tes> ( &<NamedThing_tes> ; - rdf:type [ <NamedThing> ] ? + ( $<Procedure_tes> ( &<Specification_tes> ; + rdf:type [ <Specification> ] ? ) ; rdf:type [ <Procedure> ] ) - } OR @<EngineeringSpecification> OR @<FoodRecipe> OR @<InvestigativeProtocol> + } OR @<EngineeringSpecification> OR @<FoodRecipe> OR @<InvestigativeProtocol> OR @<StudyDesign> ) <Publication> CLOSED { - ( $<Publication_tes> ( &<NamedThing_tes> ; - rdf:type [ <NamedThing> ] ? + ( $<Publication_tes> ( &<CreativeWork_tes> ; + rdf:type [ <CreativeWork> ] ? ) ; rdf:type [ <Publication> ] ) @@ -531,16 +621,25 @@ linkml:Sparqlpath xsd:string <Quantity> ( CLOSED { ( $<Quantity_tes> ( &<Intangible_tes> ; - rdf:type [ schema1:Intangible ] ? + rdf:type [ schema:Intangible ] ? ; + <has_quantity_kind> @<QuantityKind> ? ) ; rdf:type [ fhir:Quantity ] ? ) - } OR @<FoodIngredient> OR @<Ratio> OR @<SimpleQuantity> + } OR @<Duration> OR @<FoodIngredient> OR @<Ratio> OR @<SimpleQuantity> ) +<QuantityKind> CLOSED { + ( $<QuantityKind_tes> ( &<Concept_tes> ; + rdf:type [ <Concept> ] ? + ) ; + rdf:type [ <QuantityKind> ] + ) +} + <QuantityRange> CLOSED { ( $<QuantityRange_tes> ( &<Intangible_tes> ; - rdf:type [ schema1:Intangible ] ? ; + rdf:type [ schema:Intangible ] ? ; <lower_bound> @<Quantity> ? ; <upper_bound> @<Quantity> ? ) ; @@ -566,11 +665,25 @@ linkml:Sparqlpath xsd:string ) } -<Relationship> { - ( $<Relationship_tes> rdf:type . * ; - rdf:type [ <Relationship> ] ? - ) -} +<Relationship> ( + { + ( $<Relationship_tes> ( &<Intangible_tes> ; + rdf:type [ schema:Intangible ] ? + ) ; + rdf:type [ <Relationship> ] ? + ) + } OR @<TemporalRelationship> +) + +<Role> ( + { + ( $<Role_tes> ( &<Intangible_tes> ; + rdf:type [ schema:Intangible ] ? + ) ; + rdf:type [ schema:Role ] ? + ) + } OR @<HealthcareRole> +) <SampleCollectionProcess> CLOSED { ( $<SampleCollectionProcess_tes> ( &<InvestigativeProcess_tes> ; @@ -598,6 +711,14 @@ linkml:Sparqlpath xsd:string ) } +<Service> CLOSED { + ( $<Service_tes> ( &<Intangible_tes> ; + rdf:type [ schema:Intangible ] ? + ) ; + rdf:type [ <Service> ] ? + ) +} + <SimpleQuantity> CLOSED { ( $<SimpleQuantity_tes> ( &<Quantity_tes> ; rdf:type [ fhir:Quantity ] ? ; @@ -608,17 +729,70 @@ linkml:Sparqlpath xsd:string ) } +<Specification> ( + CLOSED { + ( $<Specification_tes> ( &<NamedThing_tes> ; + rdf:type [ <NamedThing> ] ? + ) ; + rdf:type [ <Specification> ] + ) + } OR @<Procedure> +) + +<StudyDesign> CLOSED { + ( $<StudyDesign_tes> ( &<Procedure_tes> ; + rdf:type [ <Procedure> ] ? + ) ; + rdf:type [ <StudyDesign> ] + ) +} + +<TemporalInterval> CLOSED { + ( $<TemporalInterval_tes> ( &<TimePointOrTemporalInterval_tes> ; + rdf:type [ <TimePointOrTemporalInterval> ] ? + ) ; + rdf:type [ <TemporalInterval> ] ? + ) +} + +<TemporalRelationship> CLOSED { + ( $<TemporalRelationship_tes> ( &<Relationship_tes> ; + rdf:type [ <Relationship> ] ? ; + <predicate> [ <https://w3id.org/linkml-common/RelativeTimeEnum#BEFORE> + <https://w3id.org/linkml-common/RelativeTimeEnum#AFTER> + <https://w3id.org/linkml-common/RelativeTimeEnum#AT_SAME_TIME_AS> ] ? ; + <relative_to> @<Entity> ? + ) ; + rdf:type [ <TemporalRelationship> ] ? + ) +} + <TimePoint> CLOSED { - ( $<TimePoint_tes> ( <date_value> @linkml:Date ? ; + ( $<TimePoint_tes> ( &<TimePointOrTemporalInterval_tes> ; + rdf:type [ <TimePointOrTemporalInterval> ] ? ; + <year_value> @linkml:Integer ? ; + <date_value> @linkml:Date ? ; <time_value> @linkml:Time ? ; <datetime_value> @linkml:Datetime ? ; <marker_event> @<Event> ? ; - schema1:description @linkml:String ? + schema:description @linkml:String ? ) ; rdf:type [ <TimePoint> ] ? ) } +<TimePointOrTemporalInterval> ( + CLOSED { + ( $<TimePointOrTemporalInterval_tes> ( &<Intangible_tes> ; + rdf:type [ schema:Intangible ] ? ; + <starts_at> @<TimePoint> ? ; + <ends_at> @<TimePoint> ? + ) ; + rdf:type [ <TimePointOrTemporalInterval> ] ? + ) + } OR @<TemporalInterval> OR @<TimePoint> +) + <UnitConcept> CLOSED { ( $<UnitConcept_tes> ( &<Concept_tes> ; rdf:type [ <Concept> ] ? @@ -639,19 +813,11 @@ linkml:Sparqlpath xsd:string <Variable> CLOSED { ( $<Variable_tes> ( &<Entity_tes> ; - rdf:type [ schema1:Thing ] ? ; + rdf:type [ schema:Thing ] ? ; <allowed_units> @<UnitConcept> * ) ; rdf:type [ <Variable> ] ? ) } -<XProcess> CLOSED { - ( $<XProcess_tes> ( &<Entity_tes> ; - rdf:type [ schema1:Thing ] ? - ) ; - rdf:type [ <XProcess> ] ? - ) -} - diff --git a/project/sqlschema/linkml_common.sql b/project/sqlschema/linkml_common.sql index 79a5266..0d8cc97 100644 --- a/project/sqlschema/linkml_common.sql +++ b/project/sqlschema/linkml_common.sql @@ -1,5 +1,25 @@ +CREATE TABLE "Agent" ( + id TEXT NOT NULL, + name TEXT, + type TEXT, + subtype TEXT, + ontology_types TEXT, + description TEXT, + PRIMARY KEY (id) +); + +CREATE TABLE "AutomatedAgent" ( + id TEXT NOT NULL, + name TEXT, + type TEXT, + subtype TEXT, + ontology_types TEXT, + description TEXT, + PRIMARY KEY (id) +); + CREATE TABLE "BasicFoodType" ( id TEXT NOT NULL, name TEXT, @@ -46,6 +66,39 @@ CREATE TABLE "Concept" ( PRIMARY KEY (id) ); +CREATE TABLE "CreativeWork" ( + id TEXT NOT NULL, + name TEXT, + type TEXT, + subtype TEXT, + ontology_types TEXT, + description TEXT, + title TEXT, + abstract TEXT, + rights TEXT, + creators TEXT, + contributors TEXT, + contacts TEXT, + PRIMARY KEY (id) +); + +CREATE TABLE "Dataset" ( + id TEXT NOT NULL, + name TEXT, + type TEXT, + subtype TEXT, + ontology_types TEXT, + description TEXT, + title TEXT, + abstract TEXT, + rights TEXT, + creators TEXT, + contributors TEXT, + contacts TEXT, + collected_as_part_of TEXT, + PRIMARY KEY (id) +); + CREATE TABLE "DataStructure" ( type TEXT, PRIMARY KEY (type) @@ -61,6 +114,18 @@ CREATE TABLE "EngineeringSpecification" ( PRIMARY KEY (id) ); +CREATE TABLE "EnvironmentalSite" ( + id TEXT NOT NULL, + name TEXT, + type TEXT, + subtype TEXT, + ontology_types TEXT, + description TEXT, + address TEXT, + geolocation TEXT, + PRIMARY KEY (id) +); + CREATE TABLE "Event" ( id TEXT NOT NULL, name TEXT, @@ -70,6 +135,9 @@ CREATE TABLE "Event" ( description TEXT, starts_at TEXT, ends_at TEXT, + happens_at TEXT, + has_interval TEXT, + has_duration TEXT, PRIMARY KEY (id) ); @@ -108,6 +176,9 @@ CREATE TABLE "HealthcareEncounter" ( description TEXT, starts_at TEXT, ends_at TEXT, + happens_at TEXT, + has_interval TEXT, + has_duration TEXT, patient TEXT, provider TEXT, subtype VARCHAR(34), @@ -160,6 +231,7 @@ CREATE TABLE "Investigation" ( ontology_types TEXT, description TEXT, objectives TEXT, + variables TEXT, PRIMARY KEY (id) ); @@ -194,6 +266,9 @@ CREATE TABLE "LifeEvent" ( description TEXT, starts_at TEXT, ends_at TEXT, + happens_at TEXT, + has_interval TEXT, + has_duration TEXT, PRIMARY KEY (id) ); @@ -301,12 +376,23 @@ CREATE TABLE "Publication" ( subtype TEXT, ontology_types TEXT, description TEXT, + title TEXT, + abstract TEXT, + rights TEXT, + creators TEXT, + contributors TEXT, + contacts TEXT, PRIMARY KEY (id) ); -CREATE TABLE "Quantity" ( +CREATE TABLE "QuantityKind" ( + id TEXT NOT NULL, + name TEXT, type TEXT, - PRIMARY KEY (type) + subtype TEXT, + ontology_types TEXT, + description TEXT, + PRIMARY KEY (id) ); CREATE TABLE "QuantityRange" ( @@ -316,14 +402,17 @@ CREATE TABLE "QuantityRange" ( PRIMARY KEY (type, lower_bound, upper_bound) ); -CREATE TABLE "Ratio" ( +CREATE TABLE "RawMaterial" ( + id TEXT NOT NULL, + name TEXT, type TEXT, - numerator TEXT, - denominator TEXT, - PRIMARY KEY (type, numerator, denominator) + subtype TEXT, + ontology_types TEXT, + description TEXT, + PRIMARY KEY (id) ); -CREATE TABLE "RawMaterial" ( +CREATE TABLE "SampleMaterial" ( id TEXT NOT NULL, name TEXT, type TEXT, @@ -333,7 +422,12 @@ CREATE TABLE "RawMaterial" ( PRIMARY KEY (id) ); -CREATE TABLE "SampleMaterial" ( +CREATE TABLE "Service" ( + type TEXT, + PRIMARY KEY (type) +); + +CREATE TABLE "Specification" ( id TEXT NOT NULL, name TEXT, type TEXT, @@ -343,6 +437,37 @@ CREATE TABLE "SampleMaterial" ( PRIMARY KEY (id) ); +CREATE TABLE "StudyDesign" ( + id TEXT NOT NULL, + name TEXT, + type TEXT, + subtype TEXT, + ontology_types TEXT, + description TEXT, + PRIMARY KEY (id) +); + +CREATE TABLE "TemporalInterval" ( + type TEXT, + starts_at TEXT, + ends_at TEXT, + PRIMARY KEY (type, starts_at, ends_at) +); + +CREATE TABLE "TemporalRelationship" ( + type TEXT, + predicate VARCHAR(15), + relative_to TEXT, + PRIMARY KEY (type, predicate, relative_to) +); + +CREATE TABLE "TimePointOrTemporalInterval" ( + type TEXT, + starts_at TEXT, + ends_at TEXT, + PRIMARY KEY (type, starts_at, ends_at) +); + CREATE TABLE "UnitConcept" ( id TEXT NOT NULL, name TEXT, @@ -367,11 +492,6 @@ CREATE TABLE "Variable" ( PRIMARY KEY (type, allowed_units) ); -CREATE TABLE "XProcess" ( - type TEXT, - PRIMARY KEY (type) -); - CREATE TABLE "ClinicalCohort" ( id TEXT NOT NULL, name TEXT, @@ -393,6 +513,9 @@ CREATE TABLE "DataGenerationFromSample" ( description TEXT, starts_at TEXT, ends_at TEXT, + happens_at TEXT, + has_interval TEXT, + has_duration TEXT, uses_physical_device TEXT, follows_procedure TEXT, part_of TEXT, @@ -402,6 +525,13 @@ CREATE TABLE "DataGenerationFromSample" ( FOREIGN KEY(part_of) REFERENCES "Investigation" (id) ); +CREATE TABLE "Duration" ( + type TEXT, + has_quantity_kind TEXT, + PRIMARY KEY (type, has_quantity_kind), + FOREIGN KEY(has_quantity_kind) REFERENCES "QuantityKind" (id) +); + CREATE TABLE "EngineeringMaterialProcessing" ( id TEXT NOT NULL, name TEXT, @@ -411,6 +541,9 @@ CREATE TABLE "EngineeringMaterialProcessing" ( description TEXT, starts_at TEXT, ends_at TEXT, + happens_at TEXT, + has_interval TEXT, + has_duration TEXT, follows_procedure TEXT, uses_physical_device TEXT, PRIMARY KEY (id), @@ -427,6 +560,9 @@ CREATE TABLE "EngineeringProcess" ( description TEXT, starts_at TEXT, ends_at TEXT, + happens_at TEXT, + has_interval TEXT, + has_duration TEXT, follows_procedure TEXT, part_of TEXT, PRIMARY KEY (id), @@ -436,8 +572,10 @@ CREATE TABLE "EngineeringProcess" ( CREATE TABLE "FoodIngredient" ( type TEXT, + has_quantity_kind TEXT, "FoodRecipe_id" TEXT, - PRIMARY KEY (type, "FoodRecipe_id"), + PRIMARY KEY (type, has_quantity_kind, "FoodRecipe_id"), + FOREIGN KEY(has_quantity_kind) REFERENCES "QuantityKind" (id), FOREIGN KEY("FoodRecipe_id") REFERENCES "FoodRecipe" (id) ); @@ -450,6 +588,9 @@ CREATE TABLE "FoodProcessing" ( description TEXT, starts_at TEXT, ends_at TEXT, + happens_at TEXT, + has_interval TEXT, + has_duration TEXT, follows_procedure TEXT, uses_physical_device TEXT, "FoodRecipe_id" TEXT, @@ -468,6 +609,9 @@ CREATE TABLE "HealthcareConditionOccurrence" ( description TEXT, starts_at TEXT, ends_at TEXT, + happens_at TEXT, + has_interval TEXT, + has_duration TEXT, patient TEXT, observed_during TEXT, PRIMARY KEY (id), @@ -475,18 +619,20 @@ CREATE TABLE "HealthcareConditionOccurrence" ( ); CREATE TABLE "HealthcareProvider" ( + type TEXT, is_person TEXT, speciality TEXT, care_site TEXT, - PRIMARY KEY (is_person, speciality, care_site), + PRIMARY KEY (type, is_person, speciality, care_site), FOREIGN KEY(is_person) REFERENCES "Person" (id), FOREIGN KEY(speciality) REFERENCES "Concept" (id), FOREIGN KEY(care_site) REFERENCES "HealthcareSite" (id) ); CREATE TABLE "HealthcareRole" ( + type TEXT, is_person TEXT, - PRIMARY KEY (is_person), + PRIMARY KEY (type, is_person), FOREIGN KEY(is_person) REFERENCES "Person" (id) ); @@ -499,6 +645,9 @@ CREATE TABLE "InvestigativeProcess" ( description TEXT, starts_at TEXT, ends_at TEXT, + happens_at TEXT, + has_interval TEXT, + has_duration TEXT, uses_physical_device TEXT, follows_procedure TEXT, part_of TEXT, @@ -517,6 +666,9 @@ CREATE TABLE "MaterialCollection" ( description TEXT, starts_at TEXT, ends_at TEXT, + happens_at TEXT, + has_interval TEXT, + has_duration TEXT, follows_procedure TEXT, uses_physical_device TEXT, PRIMARY KEY (id), @@ -533,6 +685,9 @@ CREATE TABLE "MaterialProcessing" ( description TEXT, starts_at TEXT, ends_at TEXT, + happens_at TEXT, + has_interval TEXT, + has_duration TEXT, follows_procedure TEXT, uses_physical_device TEXT, PRIMARY KEY (id), @@ -541,8 +696,9 @@ CREATE TABLE "MaterialProcessing" ( ); CREATE TABLE "Patient" ( + type TEXT, is_person TEXT, - PRIMARY KEY (is_person), + PRIMARY KEY (type, is_person), FOREIGN KEY(is_person) REFERENCES "Person" (id) ); @@ -555,6 +711,9 @@ CREATE TABLE "PlannedProcess" ( description TEXT, starts_at TEXT, ends_at TEXT, + happens_at TEXT, + has_interval TEXT, + has_duration TEXT, follows_procedure TEXT, uses_physical_device TEXT, PRIMARY KEY (id), @@ -562,6 +721,22 @@ CREATE TABLE "PlannedProcess" ( FOREIGN KEY(uses_physical_device) REFERENCES "PhysicalDevice" (id) ); +CREATE TABLE "Quantity" ( + type TEXT, + has_quantity_kind TEXT, + PRIMARY KEY (type, has_quantity_kind), + FOREIGN KEY(has_quantity_kind) REFERENCES "QuantityKind" (id) +); + +CREATE TABLE "Ratio" ( + type TEXT, + has_quantity_kind TEXT, + numerator TEXT, + denominator TEXT, + PRIMARY KEY (type, has_quantity_kind, numerator, denominator), + FOREIGN KEY(has_quantity_kind) REFERENCES "QuantityKind" (id) +); + CREATE TABLE "SampleCollectionProcess" ( id TEXT NOT NULL, name TEXT, @@ -571,6 +746,9 @@ CREATE TABLE "SampleCollectionProcess" ( description TEXT, starts_at TEXT, ends_at TEXT, + happens_at TEXT, + has_interval TEXT, + has_duration TEXT, uses_physical_device TEXT, follows_procedure TEXT, part_of TEXT, @@ -593,6 +771,9 @@ CREATE TABLE "SampleProcessing" ( description TEXT, starts_at TEXT, ends_at TEXT, + happens_at TEXT, + has_interval TEXT, + has_duration TEXT, follows_procedure TEXT, uses_physical_device TEXT, PRIMARY KEY (id), @@ -602,22 +783,49 @@ CREATE TABLE "SampleProcessing" ( CREATE TABLE "SimpleQuantity" ( type TEXT, + has_quantity_kind TEXT, value FLOAT, unit TEXT, - PRIMARY KEY (type, value, unit), + PRIMARY KEY (type, has_quantity_kind, value, unit), + FOREIGN KEY(has_quantity_kind) REFERENCES "QuantityKind" (id), FOREIGN KEY(unit) REFERENCES "UnitConcept" (id) ); CREATE TABLE "TimePoint" ( + type TEXT, + starts_at TEXT, + ends_at TEXT, + year_value INTEGER, date_value DATE, time_value TIME, datetime_value DATETIME, marker_event TEXT, description TEXT, - PRIMARY KEY (date_value, time_value, datetime_value, marker_event, description), + PRIMARY KEY (type, starts_at, ends_at, year_value, date_value, time_value, datetime_value, marker_event, description), FOREIGN KEY(marker_event) REFERENCES "Event" (id) ); +CREATE TABLE "CreativeWork_keywords" ( + backref_id TEXT, + keywords TEXT, + PRIMARY KEY (backref_id, keywords), + FOREIGN KEY(backref_id) REFERENCES "CreativeWork" (id) +); + +CREATE TABLE "Dataset_keywords" ( + backref_id TEXT, + keywords TEXT, + PRIMARY KEY (backref_id, keywords), + FOREIGN KEY(backref_id) REFERENCES "Dataset" (id) +); + +CREATE TABLE "Publication_keywords" ( + backref_id TEXT, + keywords TEXT, + PRIMARY KEY (backref_id, keywords), + FOREIGN KEY(backref_id) REFERENCES "Publication" (id) +); + CREATE TABLE "ClinicalCohortEnrollment" ( id TEXT NOT NULL, name TEXT, @@ -627,6 +835,9 @@ CREATE TABLE "ClinicalCohortEnrollment" ( description TEXT, starts_at TEXT, ends_at TEXT, + happens_at TEXT, + has_interval TEXT, + has_duration TEXT, patient TEXT, cohort TEXT, PRIMARY KEY (id), diff --git a/pyproject.toml b/pyproject.toml index 904e4b0..c1d485e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,7 +14,8 @@ neo4j = "^5.14.1" linkml-transformer = "^0.2.2" [tool.poetry.group.dev.dependencies] -linkml = "^1.6.8" +linkml = "^1.6.10" +schema-automator = "^0.4.0" [tool.poetry-dynamic-versioning] enable = true diff --git a/src/data/examples/valid/Dataset-001.yaml b/src/data/examples/valid/Dataset-001.yaml new file mode 100644 index 0000000..2460753 --- /dev/null +++ b/src/data/examples/valid/Dataset-001.yaml @@ -0,0 +1,11 @@ +# Example data object +id: example:Dataset001 +name: my dataset +collected_as_part_of: + - example:Investigation001 +creators: + - example:Person001 +keywords: + - sample data + - testing + diff --git a/src/data/examples/valid/Event-001.yaml b/src/data/examples/valid/Event-001.yaml new file mode 100644 index 0000000..95f341a --- /dev/null +++ b/src/data/examples/valid/Event-001.yaml @@ -0,0 +1,6 @@ +# Example data object +id: example:Event001 +name: Battle of Hastings +happens_at: + year_value: 1066 + diff --git a/src/linkml_common/datamodel/linkml_common.py b/src/linkml_common/datamodel/linkml_common.py index 517473c..be78339 100644 --- a/src/linkml_common/datamodel/linkml_common.py +++ b/src/linkml_common/datamodel/linkml_common.py @@ -1,5 +1,5 @@ # Auto generated from linkml_common.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-01-13T18:02:58 +# Generation date: 2024-02-02T17:33:04 # Schema: linkml-common # # id: https://w3id.org/linkml/linkml-common @@ -31,19 +31,29 @@ dataclasses._init_fn = dataclasses_init_fn_with_kwargs # Namespaces +BFO = CurieNamespace('BFO', 'http://purl.obolibrary.org/obo/BFO_') ENVO = CurieNamespace('ENVO', 'http://purl.obolibrary.org/obo/ENVO_') +IAO = CurieNamespace('IAO', 'http://purl.obolibrary.org/obo/IAO_') +OBI = CurieNamespace('OBI', 'http://purl.obolibrary.org/obo/OBI_') PATO = CurieNamespace('PATO', 'http://purl.obolibrary.org/obo/PATO_') UCUM = CurieNamespace('UCUM', 'http://example.org/UNKNOWN/UCUM/') UO = CurieNamespace('UO', 'http://example.org/UNKNOWN/UO/') BIOLINK = CurieNamespace('biolink', 'https://w3id.org/biolink/') +DCTERMS = CurieNamespace('dcterms', 'http://purl.org/dc/terms/') EXAMPLE = CurieNamespace('example', 'https://example.org/') FHIR = CurieNamespace('fhir', 'http://hl7.org/fhir/') +FIBO = CurieNamespace('fibo', 'http://example.org/UNKNOWN/fibo/') +FIBO_DATESANDTIMES = CurieNamespace('fibo_DatesAndTimes', 'https://www.omg.org/spec/Commons/DatesAndTimes/') +FIBO_QUANTITIESANDUNITS = CurieNamespace('fibo_QuantitiesAndUnits', 'https://www.omg.org/spec/Commons/QuantitiesAndUnits/') +FIBO_COMMONS_PARTIESANDSITUATIONS = CurieNamespace('fibo_commons_PartiesAndSituations', 'https://spec.edmcouncil.org/fibo/ontology/FBC/ommons/PartiesAndSituations/') LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') LINKML_COMMON = CurieNamespace('linkml_common', 'https://w3id.org/linkml-common/') NMDCSCHEMA = CurieNamespace('nmdcschema', 'http://example.org/UNKNOWN/nmdcschema/') OMOPSCHEMA = CurieNamespace('omopschema', 'http://example.org/omop/') -QUDT = CurieNamespace('qudt', 'http://example.org/UNKNOWN/qudt/') -RDF = CurieNamespace('rdf', 'http://example.org/UNKNOWN/rdf/') +PROV = CurieNamespace('prov', 'http://www.w3.org/ns/prov#') +QUDT = CurieNamespace('qudt', 'http://qudt.org/vocab/unit/') +RDF = CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#') +RDFS = CurieNamespace('rdfs', 'http://www.w3.org/2000/01/rdf-schema#') SCHEMA = CurieNamespace('schema', 'http://schema.org/') DEFAULT_ = LINKML_COMMON @@ -67,11 +77,11 @@ class PhysicalDeviceId(NamedThingId): pass -class ProcedureId(NamedThingId): +class SpecificationId(NamedThingId): pass -class PublicationId(NamedThingId): +class ProcedureId(SpecificationId): pass @@ -111,6 +121,10 @@ class PlaceId(NamedThingId): pass +class EnvironmentalSiteId(PlaceId): + pass + + class LandformId(PlaceId): pass @@ -127,19 +141,31 @@ class InvestigativeProtocolId(ProcedureId): pass +class StudyDesignId(ProcedureId): + pass + + class SampleMaterialId(NamedThingId): pass +class QuantityKindId(ConceptId): + pass + + class UnitConceptId(ConceptId): pass -class PersonId(NamedThingId): +class AgentId(NamedThingId): + pass + + +class PersonId(AgentId): pass -class OrganizationId(NamedThingId): +class OrganizationId(AgentId): pass @@ -147,6 +173,22 @@ class HealthcareOrganizationId(OrganizationId): pass +class AutomatedAgentId(AgentId): + pass + + +class CreativeWorkId(NamedThingId): + pass + + +class PublicationId(CreativeWorkId): + pass + + +class DatasetId(CreativeWorkId): + pass + + class EventId(NamedThingId): pass @@ -386,7 +428,22 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.type = str(self.class_name) -class Relationship(YAMLRoot): +class Role(Intangible): + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = SCHEMA["Role"] + class_class_curie: ClassVar[str] = "schema:Role" + class_name: ClassVar[str] = "Role" + class_model_uri: ClassVar[URIRef] = LINKML_COMMON.Role + + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + + super().__post_init__(**kwargs) + self.type = str(self.class_name) + + +class Relationship(Intangible): _inherited_slots: ClassVar[List[str]] = [] class_class_uri: ClassVar[URIRef] = LINKML_COMMON["Relationship"] @@ -395,6 +452,12 @@ class Relationship(YAMLRoot): class_model_uri: ClassVar[URIRef] = LINKML_COMMON.Relationship + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + + super().__post_init__(**kwargs) + self.type = str(self.class_name) + + class Location(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -432,42 +495,48 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @dataclass -class Procedure(NamedThing): +class Specification(NamedThing): """ - A canonical series of actions conducted in a certain order or manner + A specification of a thing """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = LINKML_COMMON["Procedure"] - class_class_curie: ClassVar[str] = "linkml_common:Procedure" - class_name: ClassVar[str] = "Procedure" - class_model_uri: ClassVar[URIRef] = LINKML_COMMON.Procedure + class_class_uri: ClassVar[URIRef] = LINKML_COMMON["Specification"] + class_class_curie: ClassVar[str] = "linkml_common:Specification" + class_name: ClassVar[str] = "Specification" + class_model_uri: ClassVar[URIRef] = LINKML_COMMON.Specification - id: Union[str, ProcedureId] = None + id: Union[str, SpecificationId] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): self.MissingRequiredField("id") - if not isinstance(self.id, ProcedureId): - self.id = ProcedureId(self.id) + if not isinstance(self.id, SpecificationId): + self.id = SpecificationId(self.id) super().__post_init__(**kwargs) self.type = str(self.class_name) -class XProcess(Entity): +@dataclass +class Procedure(Specification): """ - A series of actions or steps taken in order to achieve a particular end + A canonical series of actions conducted in a certain order or manner """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = LINKML_COMMON["XProcess"] - class_class_curie: ClassVar[str] = "linkml_common:XProcess" - class_name: ClassVar[str] = "XProcess" - class_model_uri: ClassVar[URIRef] = LINKML_COMMON.XProcess + class_class_uri: ClassVar[URIRef] = LINKML_COMMON["Procedure"] + class_class_curie: ClassVar[str] = "linkml_common:Procedure" + class_name: ClassVar[str] = "Procedure" + class_model_uri: ClassVar[URIRef] = LINKML_COMMON.Procedure + id: Union[str, ProcedureId] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, ProcedureId): + self.id = ProcedureId(self.id) super().__post_init__(**kwargs) self.type = str(self.class_name) @@ -527,29 +596,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): Any = Any -@dataclass -class Publication(NamedThing): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = LINKML_COMMON["Publication"] - class_class_curie: ClassVar[str] = "linkml_common:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = LINKML_COMMON.Publication - - id: Union[str, PublicationId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PublicationId): - self.id = PublicationId(self.id) - - super().__post_init__(**kwargs) - self.type = str(self.class_name) - - @dataclass class ClinicalCohort(NamedThing): + """ + A group of patients who share a common set of characteristics + """ _inherited_slots: ClassVar[List[str]] = [] class_class_uri: ClassVar[URIRef] = LINKML_COMMON["ClinicalCohort"] @@ -575,6 +626,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @dataclass class ClinicalCohortDefinition(NamedThing): + """ + A definition of a clinical cohort + """ _inherited_slots: ClassVar[List[str]] = [] class_class_uri: ClassVar[URIRef] = LINKML_COMMON["ClinicalCohortDefinition"] @@ -660,6 +714,15 @@ class EnvironmentalProcess(YAMLRoot): class_model_uri: ClassVar[URIRef] = LINKML_COMMON.EnvironmentalProcess +class EnvironmentalMonitoring(EnvironmentalProcess): + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = LINKML_COMMON["EnvironmentalMonitoring"] + class_class_curie: ClassVar[str] = "linkml_common:EnvironmentalMonitoring" + class_name: ClassVar[str] = "EnvironmentalMonitoring" + class_model_uri: ClassVar[URIRef] = LINKML_COMMON.EnvironmentalMonitoring + + @dataclass class FoodRecipe(Procedure): _inherited_slots: ClassVar[List[str]] = [] @@ -786,6 +849,30 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.type = str(self.class_name) +@dataclass +class EnvironmentalSite(Place): + """ + A location or site that is the subject of environmental monitoring + """ + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = LINKML_COMMON["EnvironmentalSite"] + class_class_curie: ClassVar[str] = "linkml_common:EnvironmentalSite" + class_name: ClassVar[str] = "EnvironmentalSite" + class_model_uri: ClassVar[URIRef] = LINKML_COMMON.EnvironmentalSite + + id: Union[str, EnvironmentalSiteId] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, EnvironmentalSiteId): + self.id = EnvironmentalSiteId(self.id) + + super().__post_init__(**kwargs) + self.type = str(self.class_name) + + @dataclass class Landform(Place): """ @@ -906,7 +993,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @dataclass -class HealthcareRole(YAMLRoot): +class HealthcareRole(Role): _inherited_slots: ClassVar[List[str]] = [] class_class_uri: ClassVar[URIRef] = LINKML_COMMON["HealthcareRole"] @@ -921,6 +1008,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.is_person = PersonId(self.is_person) super().__post_init__(**kwargs) + self.type = str(self.class_name) @dataclass @@ -943,6 +1031,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.care_site = HealthcareSiteId(self.care_site) super().__post_init__(**kwargs) + self.type = str(self.class_name) class Patient(HealthcareRole): @@ -954,6 +1043,12 @@ class Patient(HealthcareRole): class_model_uri: ClassVar[URIRef] = LINKML_COMMON.Patient + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + + super().__post_init__(**kwargs) + self.type = str(self.class_name) + + @dataclass class Investigation(NamedThing): _inherited_slots: ClassVar[List[str]] = [] @@ -965,6 +1060,7 @@ class Investigation(NamedThing): id: Union[str, InvestigationId] = None objectives: Optional[str] = None + variables: Optional[Union[Union[dict, "Variable"], List[Union[dict, "Variable"]]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -975,6 +1071,10 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.objectives is not None and not isinstance(self.objectives, str): self.objectives = str(self.objectives) + if not isinstance(self.variables, list): + self.variables = [self.variables] if self.variables is not None else [] + self.variables = [v if isinstance(v, Variable) else Variable(**as_dict(v)) for v in self.variables] + super().__post_init__(**kwargs) self.type = str(self.class_name) @@ -1000,6 +1100,27 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.type = str(self.class_name) +@dataclass +class StudyDesign(Procedure): + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = LINKML_COMMON["StudyDesign"] + class_class_curie: ClassVar[str] = "linkml_common:StudyDesign" + class_name: ClassVar[str] = "StudyDesign" + class_model_uri: ClassVar[URIRef] = LINKML_COMMON.StudyDesign + + id: Union[str, StudyDesignId] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, StudyDesignId): + self.id = StudyDesignId(self.id) + + super().__post_init__(**kwargs) + self.type = str(self.class_name) + + @dataclass class SampleMaterial(NamedThing): _inherited_slots: ClassVar[List[str]] = [] @@ -1064,6 +1185,28 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.type = str(self.class_name) +@dataclass +class QuantityKind(Concept): + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = LINKML_COMMON["QuantityKind"] + class_class_curie: ClassVar[str] = "linkml_common:QuantityKind" + class_name: ClassVar[str] = "QuantityKind" + class_model_uri: ClassVar[URIRef] = LINKML_COMMON.QuantityKind + + id: Union[str, QuantityKindId] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, QuantityKindId): + self.id = QuantityKindId(self.id) + + super().__post_init__(**kwargs) + self.type = str(self.class_name) + + +@dataclass class Quantity(Intangible): _inherited_slots: ClassVar[List[str]] = [] @@ -1072,8 +1215,11 @@ class Quantity(Intangible): class_name: ClassVar[str] = "Quantity" class_model_uri: ClassVar[URIRef] = LINKML_COMMON.Quantity + has_quantity_kind: Optional[Union[str, QuantityKindId]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self.has_quantity_kind is not None and not isinstance(self.has_quantity_kind, QuantityKindId): + self.has_quantity_kind = QuantityKindId(self.has_quantity_kind) super().__post_init__(**kwargs) self.type = str(self.class_name) @@ -1221,7 +1367,31 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @dataclass -class Person(NamedThing): +class Agent(NamedThing): + """ + Represents an Agent + """ + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = LINKML_COMMON["Agent"] + class_class_curie: ClassVar[str] = "linkml_common:Agent" + class_name: ClassVar[str] = "Agent" + class_model_uri: ClassVar[URIRef] = LINKML_COMMON.Agent + + id: Union[str, AgentId] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, AgentId): + self.id = AgentId(self.id) + + super().__post_init__(**kwargs) + self.type = str(self.class_name) + + +@dataclass +class Person(Agent): """ Represents a Person """ @@ -1261,7 +1431,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @dataclass -class Organization(NamedThing): +class Organization(Agent): """ Represents an Organization """ @@ -1305,6 +1475,151 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.type = str(self.class_name) +@dataclass +class AutomatedAgent(Agent): + """ + Represents an Automated Agent + """ + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = LINKML_COMMON["AutomatedAgent"] + class_class_curie: ClassVar[str] = "linkml_common:AutomatedAgent" + class_name: ClassVar[str] = "AutomatedAgent" + class_model_uri: ClassVar[URIRef] = LINKML_COMMON.AutomatedAgent + + id: Union[str, AutomatedAgentId] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, AutomatedAgentId): + self.id = AutomatedAgentId(self.id) + + super().__post_init__(**kwargs) + self.type = str(self.class_name) + + +@dataclass +class CreativeWork(NamedThing): + """ + The most generic kind of creative work, including books, movies, photographs, software programs, etc. + """ + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = LINKML_COMMON["CreativeWork"] + class_class_curie: ClassVar[str] = "linkml_common:CreativeWork" + class_name: ClassVar[str] = "CreativeWork" + class_model_uri: ClassVar[URIRef] = LINKML_COMMON.CreativeWork + + id: Union[str, CreativeWorkId] = None + title: Optional[str] = None + abstract: Optional[str] = None + rights: Optional[str] = None + creators: Optional[Union[Union[str, AgentId], List[Union[str, AgentId]]]] = empty_list() + contributors: Optional[Union[Union[str, AgentId], List[Union[str, AgentId]]]] = empty_list() + contacts: Optional[Union[Union[str, AgentId], List[Union[str, AgentId]]]] = empty_list() + keywords: Optional[Union[str, List[str]]] = empty_list() + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, CreativeWorkId): + self.id = CreativeWorkId(self.id) + + if self.title is not None and not isinstance(self.title, str): + self.title = str(self.title) + + if self.abstract is not None and not isinstance(self.abstract, str): + self.abstract = str(self.abstract) + + if self.rights is not None and not isinstance(self.rights, str): + self.rights = str(self.rights) + + if not isinstance(self.creators, list): + self.creators = [self.creators] if self.creators is not None else [] + self.creators = [v if isinstance(v, AgentId) else AgentId(v) for v in self.creators] + + if not isinstance(self.contributors, list): + self.contributors = [self.contributors] if self.contributors is not None else [] + self.contributors = [v if isinstance(v, AgentId) else AgentId(v) for v in self.contributors] + + if not isinstance(self.contacts, list): + self.contacts = [self.contacts] if self.contacts is not None else [] + self.contacts = [v if isinstance(v, AgentId) else AgentId(v) for v in self.contacts] + + if not isinstance(self.keywords, list): + self.keywords = [self.keywords] if self.keywords is not None else [] + self.keywords = [v if isinstance(v, str) else str(v) for v in self.keywords] + + super().__post_init__(**kwargs) + self.type = str(self.class_name) + + +@dataclass +class Publication(CreativeWork): + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = LINKML_COMMON["Publication"] + class_class_curie: ClassVar[str] = "linkml_common:Publication" + class_name: ClassVar[str] = "Publication" + class_model_uri: ClassVar[URIRef] = LINKML_COMMON.Publication + + id: Union[str, PublicationId] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, PublicationId): + self.id = PublicationId(self.id) + + super().__post_init__(**kwargs) + self.type = str(self.class_name) + + +@dataclass +class Dataset(CreativeWork): + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = LINKML_COMMON["Dataset"] + class_class_curie: ClassVar[str] = "linkml_common:Dataset" + class_name: ClassVar[str] = "Dataset" + class_model_uri: ClassVar[URIRef] = LINKML_COMMON.Dataset + + id: Union[str, DatasetId] = None + collected_as_part_of: Optional[Union[Union[str, InvestigationId], List[Union[str, InvestigationId]]]] = empty_list() + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, DatasetId): + self.id = DatasetId(self.id) + + if not isinstance(self.collected_as_part_of, list): + self.collected_as_part_of = [self.collected_as_part_of] if self.collected_as_part_of is not None else [] + self.collected_as_part_of = [v if isinstance(v, InvestigationId) else InvestigationId(v) for v in self.collected_as_part_of] + + super().__post_init__(**kwargs) + self.type = str(self.class_name) + + +class Service(Intangible): + """ + A service provided by an organization + """ + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = LINKML_COMMON["Service"] + class_class_curie: ClassVar[str] = "linkml_common:Service" + class_name: ClassVar[str] = "Service" + class_model_uri: ClassVar[URIRef] = LINKML_COMMON.Service + + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + + super().__post_init__(**kwargs) + self.type = str(self.class_name) + + @dataclass class Event(NamedThing): """ @@ -1320,6 +1635,9 @@ class Event(NamedThing): id: Union[str, EventId] = None starts_at: Optional[Union[dict, "TimePoint"]] = None ends_at: Optional[Union[dict, "TimePoint"]] = None + happens_at: Optional[Union[dict, "TimePoint"]] = None + has_interval: Optional[Union[dict, "TemporalInterval"]] = None + has_duration: Optional[Union[dict, "Duration"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -1333,12 +1651,24 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.ends_at is not None and not isinstance(self.ends_at, TimePoint): self.ends_at = TimePoint(**as_dict(self.ends_at)) + if self.happens_at is not None and not isinstance(self.happens_at, TimePoint): + self.happens_at = TimePoint(**as_dict(self.happens_at)) + + if self.has_interval is not None and not isinstance(self.has_interval, TemporalInterval): + self.has_interval = TemporalInterval(**as_dict(self.has_interval)) + + if self.has_duration is not None and not isinstance(self.has_duration, Duration): + self.has_duration = Duration(**as_dict(self.has_duration)) + super().__post_init__(**kwargs) self.type = str(self.class_name) @dataclass class ClinicalCohortEnrollment(Event): + """ + An event relating a patient to a clinical cohort + """ _inherited_slots: ClassVar[List[str]] = [] class_class_uri: ClassVar[URIRef] = LINKML_COMMON["ClinicalCohortEnrollment"] @@ -1479,7 +1809,59 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @dataclass -class TimePoint(YAMLRoot): +class TimePointOrTemporalInterval(Intangible): + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = LINKML_COMMON["TimePointOrTemporalInterval"] + class_class_curie: ClassVar[str] = "linkml_common:TimePointOrTemporalInterval" + class_name: ClassVar[str] = "TimePointOrTemporalInterval" + class_model_uri: ClassVar[URIRef] = LINKML_COMMON.TimePointOrTemporalInterval + + starts_at: Optional[Union[dict, "TimePoint"]] = None + ends_at: Optional[Union[dict, "TimePoint"]] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self.starts_at is not None and not isinstance(self.starts_at, TimePoint): + self.starts_at = TimePoint(**as_dict(self.starts_at)) + + if self.ends_at is not None and not isinstance(self.ends_at, TimePoint): + self.ends_at = TimePoint(**as_dict(self.ends_at)) + + super().__post_init__(**kwargs) + self.type = str(self.class_name) + + +@dataclass +class TemporalInterval(TimePointOrTemporalInterval): + """ + A period of time + """ + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = LINKML_COMMON["TemporalInterval"] + class_class_curie: ClassVar[str] = "linkml_common:TemporalInterval" + class_name: ClassVar[str] = "TemporalInterval" + class_model_uri: ClassVar[URIRef] = LINKML_COMMON.TemporalInterval + + starts_at: Optional[Union[dict, "TimePoint"]] = None + ends_at: Optional[Union[dict, "TimePoint"]] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self.starts_at is not None and not isinstance(self.starts_at, TimePoint): + self.starts_at = TimePoint(**as_dict(self.starts_at)) + + if self.ends_at is not None and not isinstance(self.ends_at, TimePoint): + self.ends_at = TimePoint(**as_dict(self.ends_at)) + + super().__post_init__(**kwargs) + self.type = str(self.class_name) + + +@dataclass +class TimePoint(TimePointOrTemporalInterval): + """ + A point in time. Can be fully specified, or specified in relative terms. + """ _inherited_slots: ClassVar[List[str]] = [] class_class_uri: ClassVar[URIRef] = LINKML_COMMON["TimePoint"] @@ -1487,6 +1869,7 @@ class TimePoint(YAMLRoot): class_name: ClassVar[str] = "TimePoint" class_model_uri: ClassVar[URIRef] = LINKML_COMMON.TimePoint + year_value: Optional[int] = None date_value: Optional[Union[str, XSDDate]] = None time_value: Optional[Union[str, XSDTime]] = None datetime_value: Optional[Union[str, XSDDateTime]] = None @@ -1494,6 +1877,9 @@ class TimePoint(YAMLRoot): description: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self.year_value is not None and not isinstance(self.year_value, int): + self.year_value = int(self.year_value) + if self.date_value is not None and not isinstance(self.date_value, XSDDate): self.date_value = XSDDate(self.date_value) @@ -1510,10 +1896,58 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.description = str(self.description) super().__post_init__(**kwargs) + self.type = str(self.class_name) + + +class Duration(Quantity): + """ + A length of time + """ + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = LINKML_COMMON["Duration"] + class_class_curie: ClassVar[str] = "linkml_common:Duration" + class_name: ClassVar[str] = "Duration" + class_model_uri: ClassVar[URIRef] = LINKML_COMMON.Duration + + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + + super().__post_init__(**kwargs) + self.type = str(self.class_name) + + +@dataclass +class TemporalRelationship(Relationship): + """ + A relationship to another time point + """ + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = LINKML_COMMON["TemporalRelationship"] + class_class_curie: ClassVar[str] = "linkml_common:TemporalRelationship" + class_name: ClassVar[str] = "TemporalRelationship" + class_model_uri: ClassVar[URIRef] = LINKML_COMMON.TemporalRelationship + + predicate: Optional[Union[str, "RelativeTimeEnum"]] = None + relative_to: Optional[Union[dict, Entity]] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self.predicate is not None and not isinstance(self.predicate, RelativeTimeEnum): + self.predicate = RelativeTimeEnum(self.predicate) + + if self.relative_to is not None and not isinstance(self.relative_to, Entity): + self.relative_to = Entity(**as_dict(self.relative_to)) + + super().__post_init__(**kwargs) + self.type = str(self.class_name) @dataclass class PlannedProcess(Event): + """ + A process that follows a defined procedure or plan + """ _inherited_slots: ClassVar[List[str]] = [] class_class_uri: ClassVar[URIRef] = LINKML_COMMON["PlannedProcess"] @@ -1779,6 +2213,34 @@ def _addvals(cls): text="Case Management Visit", description="""Person interacting with healthcare system, without a Care Site, within a day, with no Providers involved, for administrative purposes""")) +class CaseOrControlEnum(EnumDefinitionImpl): + + CASE = PermissibleValue( + text="CASE", + meaning=OBI["0002492"]) + CONTROL = PermissibleValue( + text="CONTROL", + meaning=OBI["0002493"]) + + _defn = EnumDefinition( + name="CaseOrControlEnum", + ) + +class StudyDesignEnum(EnumDefinitionImpl): + + _defn = EnumDefinition( + name="StudyDesignEnum", + ) + +class HumanLanguageCodeEnum(EnumDefinitionImpl): + """ + An enumeration of languages + """ + _defn = EnumDefinition( + name="HumanLanguageCodeEnum", + description="An enumeration of languages", + ) + class PersonStatus(EnumDefinitionImpl): ALIVE = PermissibleValue( @@ -1797,6 +2259,16 @@ class PersonStatus(EnumDefinitionImpl): name="PersonStatus", ) +class RelativeTimeEnum(EnumDefinitionImpl): + + BEFORE = PermissibleValue(text="BEFORE") + AFTER = PermissibleValue(text="AFTER") + AT_SAME_TIME_AS = PermissibleValue(text="AT_SAME_TIME_AS") + + _defn = EnumDefinition( + name="RelativeTimeEnum", + ) + # Slots class slots: pass @@ -1852,6 +2324,12 @@ class slots: slots.ends_at = Slot(uri=LINKML_COMMON.ends_at, name="ends_at", curie=LINKML_COMMON.curie('ends_at'), model_uri=LINKML_COMMON.ends_at, domain=None, range=Optional[Union[dict, TimePoint]]) +slots.happens_at = Slot(uri=LINKML_COMMON.happens_at, name="happens_at", curie=LINKML_COMMON.curie('happens_at'), + model_uri=LINKML_COMMON.happens_at, domain=None, range=Optional[Union[dict, TimePoint]]) + +slots.year_value = Slot(uri=LINKML_COMMON.year_value, name="year_value", curie=LINKML_COMMON.curie('year_value'), + model_uri=LINKML_COMMON.year_value, domain=None, range=Optional[int]) + slots.date_value = Slot(uri=LINKML_COMMON.date_value, name="date_value", curie=LINKML_COMMON.curie('date_value'), model_uri=LINKML_COMMON.date_value, domain=None, range=Optional[Union[str, XSDDate]]) @@ -1864,6 +2342,12 @@ class slots: slots.marker_event = Slot(uri=LINKML_COMMON.marker_event, name="marker_event", curie=LINKML_COMMON.curie('marker_event'), model_uri=LINKML_COMMON.marker_event, domain=None, range=Optional[Union[str, EventId]]) +slots.has_interval = Slot(uri=LINKML_COMMON.has_interval, name="has_interval", curie=LINKML_COMMON.curie('has_interval'), + model_uri=LINKML_COMMON.has_interval, domain=None, range=Optional[Union[dict, TemporalInterval]]) + +slots.has_duration = Slot(uri=LINKML_COMMON.has_duration, name="has_duration", curie=LINKML_COMMON.curie('has_duration'), + model_uri=LINKML_COMMON.has_duration, domain=None, range=Optional[Union[dict, Duration]]) + slots.mathematicalOperation__inputs = Slot(uri=LINKML_COMMON.inputs, name="mathematicalOperation__inputs", curie=LINKML_COMMON.curie('inputs'), model_uri=LINKML_COMMON.mathematicalOperation__inputs, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) @@ -1879,6 +2363,9 @@ class slots: slots.collection__members = Slot(uri=LINKML_COMMON.members, name="collection__members", curie=LINKML_COMMON.curie('members'), model_uri=LINKML_COMMON.collection__members, domain=None, range=Optional[Union[Union[dict, Entity], List[Union[dict, Entity]]]]) +slots.dataset__collected_as_part_of = Slot(uri=LINKML_COMMON.collected_as_part_of, name="dataset__collected_as_part_of", curie=LINKML_COMMON.curie('collected_as_part_of'), + model_uri=LINKML_COMMON.dataset__collected_as_part_of, domain=None, range=Optional[Union[Union[str, InvestigationId], List[Union[str, InvestigationId]]]]) + slots.clinicalCohort__definition = Slot(uri=LINKML_COMMON.definition, name="clinicalCohort__definition", curie=LINKML_COMMON.curie('definition'), model_uri=LINKML_COMMON.clinicalCohort__definition, domain=None, range=Optional[Union[str, ClinicalCohortDefinitionId]]) @@ -1951,6 +2438,9 @@ class slots: slots.investigation__objectives = Slot(uri=LINKML_COMMON.objectives, name="investigation__objectives", curie=LINKML_COMMON.curie('objectives'), model_uri=LINKML_COMMON.investigation__objectives, domain=None, range=Optional[str]) +slots.investigation__variables = Slot(uri=LINKML_COMMON.variables, name="investigation__variables", curie=LINKML_COMMON.curie('variables'), + model_uri=LINKML_COMMON.investigation__variables, domain=None, range=Optional[Union[Union[dict, Variable], List[Union[dict, Variable]]]]) + slots.investigativeProcess__follows_procedure = Slot(uri=LINKML_COMMON.follows_procedure, name="investigativeProcess__follows_procedure", curie=LINKML_COMMON.curie('follows_procedure'), model_uri=LINKML_COMMON.investigativeProcess__follows_procedure, domain=None, range=Optional[Union[str, InvestigativeProtocolId]]) @@ -1972,6 +2462,9 @@ class slots: slots.variable__allowed_units = Slot(uri=LINKML_COMMON.allowed_units, name="variable__allowed_units", curie=LINKML_COMMON.curie('allowed_units'), model_uri=LINKML_COMMON.variable__allowed_units, domain=None, range=Optional[Union[Union[str, UnitConceptId], List[Union[str, UnitConceptId]]]]) +slots.quantity__has_quantity_kind = Slot(uri=LINKML_COMMON.has_quantity_kind, name="quantity__has_quantity_kind", curie=LINKML_COMMON.curie('has_quantity_kind'), + model_uri=LINKML_COMMON.quantity__has_quantity_kind, domain=None, range=Optional[Union[str, QuantityKindId]]) + slots.simpleQuantity__value = Slot(uri=LINKML_COMMON.value, name="simpleQuantity__value", curie=LINKML_COMMON.curie('value'), model_uri=LINKML_COMMON.simpleQuantity__value, domain=None, range=Optional[float]) @@ -1990,6 +2483,33 @@ class slots: slots.quantityRange__upper_bound = Slot(uri=LINKML_COMMON.upper_bound, name="quantityRange__upper_bound", curie=LINKML_COMMON.curie('upper_bound'), model_uri=LINKML_COMMON.quantityRange__upper_bound, domain=None, range=Optional[Union[dict, Quantity]]) +slots.creativeWork__title = Slot(uri=LINKML_COMMON.title, name="creativeWork__title", curie=LINKML_COMMON.curie('title'), + model_uri=LINKML_COMMON.creativeWork__title, domain=None, range=Optional[str]) + +slots.creativeWork__abstract = Slot(uri=LINKML_COMMON.abstract, name="creativeWork__abstract", curie=LINKML_COMMON.curie('abstract'), + model_uri=LINKML_COMMON.creativeWork__abstract, domain=None, range=Optional[str]) + +slots.creativeWork__rights = Slot(uri=LINKML_COMMON.rights, name="creativeWork__rights", curie=LINKML_COMMON.curie('rights'), + model_uri=LINKML_COMMON.creativeWork__rights, domain=None, range=Optional[str]) + +slots.creativeWork__creators = Slot(uri=DCTERMS.creator, name="creativeWork__creators", curie=DCTERMS.curie('creator'), + model_uri=LINKML_COMMON.creativeWork__creators, domain=None, range=Optional[Union[Union[str, AgentId], List[Union[str, AgentId]]]]) + +slots.creativeWork__contributors = Slot(uri=DCTERMS.contributor, name="creativeWork__contributors", curie=DCTERMS.curie('contributor'), + model_uri=LINKML_COMMON.creativeWork__contributors, domain=None, range=Optional[Union[Union[str, AgentId], List[Union[str, AgentId]]]]) + +slots.creativeWork__contacts = Slot(uri=SCHEMA.contactPoint, name="creativeWork__contacts", curie=SCHEMA.curie('contactPoint'), + model_uri=LINKML_COMMON.creativeWork__contacts, domain=None, range=Optional[Union[Union[str, AgentId], List[Union[str, AgentId]]]]) + +slots.creativeWork__keywords = Slot(uri=SCHEMA.keywords, name="creativeWork__keywords", curie=SCHEMA.curie('keywords'), + model_uri=LINKML_COMMON.creativeWork__keywords, domain=None, range=Optional[Union[str, List[str]]]) + +slots.temporalRelationship__predicate = Slot(uri=LINKML_COMMON.predicate, name="temporalRelationship__predicate", curie=LINKML_COMMON.curie('predicate'), + model_uri=LINKML_COMMON.temporalRelationship__predicate, domain=None, range=Optional[Union[str, "RelativeTimeEnum"]]) + +slots.temporalRelationship__relative_to = Slot(uri=LINKML_COMMON.relative_to, name="temporalRelationship__relative_to", curie=LINKML_COMMON.curie('relative_to'), + model_uri=LINKML_COMMON.temporalRelationship__relative_to, domain=None, range=Optional[Union[dict, Entity]]) + slots.plannedProcess__follows_procedure = Slot(uri=LINKML_COMMON.follows_procedure, name="plannedProcess__follows_procedure", curie=LINKML_COMMON.curie('follows_procedure'), model_uri=LINKML_COMMON.plannedProcess__follows_procedure, domain=None, range=Optional[Union[str, ProcedureId]]) diff --git a/src/linkml_common/schema/bibliographic.yaml b/src/linkml_common/schema/bibliographic.yaml index 0d506e0..e98060d 100644 --- a/src/linkml_common/schema/bibliographic.yaml +++ b/src/linkml_common/schema/bibliographic.yaml @@ -2,7 +2,7 @@ id: https://w3id.org/linkml-common/financial name: linkml-common-financial title: linkml-common-financial description: |- - Common Data Model Elements + Common Data Model Elements: Bibliographic and Publishing Data license: MIT see_also: - https://linkml.github.io/linkml-common @@ -24,5 +24,5 @@ imports: classes: Publication: - is_a: NamedThing + is_a: CreativeWork diff --git a/src/linkml_common/schema/clinicalresearch.yaml b/src/linkml_common/schema/clinicalresearch.yaml index ec08343..d916c7c 100644 --- a/src/linkml_common/schema/clinicalresearch.yaml +++ b/src/linkml_common/schema/clinicalresearch.yaml @@ -1,8 +1,8 @@ id: https://w3id.org/linkml-common/clinicalresearch name: linkml-common-clinicalresearch -title: linkml-common-clinicalresearch +title: "LinkML Common Schema Components: Clinical Research" description: |- - Common Data Model Elements + Common Schema Components: Clinical Research license: MIT see_also: - https://linkml.github.io/linkml-common @@ -26,17 +26,20 @@ imports: classes: ClinicalCohort: + description: A group of patients who share a common set of characteristics is_a: NamedThing attributes: definition: range: ClinicalCohortDefinition ClinicalCohortDefinition: + description: A definition of a clinical cohort is_a: NamedThing exact_mappings: - omopschema:COHORT_DEFINITION ClinicalCohortEnrollment: + description: An event relating a patient to a clinical cohort is_a: Event exact_mappings: - omopschema:COHORT diff --git a/src/linkml_common/schema/computational.yaml b/src/linkml_common/schema/computational.yaml index 2da151b..f7e383a 100644 --- a/src/linkml_common/schema/computational.yaml +++ b/src/linkml_common/schema/computational.yaml @@ -19,7 +19,6 @@ default_range: string imports: - linkml:types - - quantities classes: diff --git a/src/linkml_common/schema/core.yaml b/src/linkml_common/schema/core.yaml index c6d3451..1b79158 100644 --- a/src/linkml_common/schema/core.yaml +++ b/src/linkml_common/schema/core.yaml @@ -13,7 +13,10 @@ prefixes: biolink: https://w3id.org/biolink/ schema: http://schema.org/ BFO: http://purl.obolibrary.org/obo/BFO_ + IAO: http://purl.obolibrary.org/obo/IAO_ fhir: http://hl7.org/fhir/ + rdfs: http://www.w3.org/2000/01/rdf-schema# + rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# default_prefix: linkml_common default_range: string @@ -63,8 +66,18 @@ classes: class_uri: schema:Intangible is_a: Entity + Role: + is_a: Intangible + abstract: true + class_uri: schema:Role + close_mappings: + - BFO:0000023 + Relationship: + is_a: Intangible abstract: true + close_mappings: + - rdfs:Statement Location: @@ -74,14 +87,19 @@ classes: is_a: Location Observation: - description: >- - A statement about the state of something + description: A statement about the state of something is_a: Entity - Procedure: - description: >- - A canonical series of actions conducted in a certain order or manner + + Specification: + description: A specification of a thing is_a: NamedThing + exact_mappings: + - IAO:0000104 + + Procedure: + description: A canonical series of actions conducted in a certain order or manner + is_a: Specification MathematicalOperation: description: >- diff --git a/src/linkml_common/schema/datasets.yaml b/src/linkml_common/schema/datasets.yaml new file mode 100644 index 0000000..6c7b187 --- /dev/null +++ b/src/linkml_common/schema/datasets.yaml @@ -0,0 +1,33 @@ +id: https://w3id.org/linkml-common/datasets +name: linkml-common-datasets +title: linkml-common-datasets +description: |- + Common Data Model Elements +license: MIT +see_also: + - https://linkml.github.io/linkml-common + +prefixes: + linkml_common: https://w3id.org/linkml-common/ + linkml: https://w3id.org/linkml/ + biolink: https://w3id.org/biolink/ + schema: http://schema.org/ + PATO: http://purl.obolibrary.org/obo/PATO_ + fhir: http://hl7.org/fhir/ +default_prefix: linkml_common +default_range: string + +imports: + - linkml:types + - bibliographic + - investigations + +classes: + + Dataset: + is_a: CreativeWork + attributes: + collected_as_part_of: + range: Investigation + multivalued: true + diff --git a/src/linkml_common/schema/environmental.yaml b/src/linkml_common/schema/environmental.yaml index 1cb3141..0ca172d 100644 --- a/src/linkml_common/schema/environmental.yaml +++ b/src/linkml_common/schema/environmental.yaml @@ -24,7 +24,14 @@ imports: classes: + EnvironmentalSite: + description: A location or site that is the subject of environmental monitoring + is_a: Place + EnvironmentalProcess: comments: - TODO #is_a: Process + + EnvironmentalMonitoring: + is_a: EnvironmentalProcess diff --git a/src/linkml_common/schema/financial.yaml b/src/linkml_common/schema/financial.yaml index 29019d6..8f31816 100644 --- a/src/linkml_common/schema/financial.yaml +++ b/src/linkml_common/schema/financial.yaml @@ -14,7 +14,7 @@ prefixes: schema: http://schema.org/ PATO: http://purl.obolibrary.org/obo/PATO_ fhir: http://hl7.org/fhir/ - fibo: https://spec.edmcouncil.org/fibo/ontology/ + fibo: https://spec.edmcouncil.org/fibo/ontology/FBC default_prefix: linkml_common default_range: string @@ -43,3 +43,25 @@ classes: A currency is_a: Concept + FinancialProduct: + description: A product or service offered by a bank whereby one may deposit, + withdraw or transfer money and in some cases be paid interest. + is_a: Service + + FinancialAccount: + description: A bank account + is_a: FinancialProduct + attributes: + account_number: + range: string + description: The account number + bank: + range: Organization + description: The bank that holds the account + account_holder: + range: Person + description: The person or organization that holds the account + exact_mappings: + - fibo:ProductsAndServices/ClientsAndAccounts/Account + - schema:BankAccount + diff --git a/src/linkml_common/schema/foods.yaml b/src/linkml_common/schema/foods.yaml index 9aa61d1..1ee0f07 100644 --- a/src/linkml_common/schema/foods.yaml +++ b/src/linkml_common/schema/foods.yaml @@ -47,4 +47,6 @@ classes: CompositeFoodType: is_a: FoodTypeConcept + implements: + - linkml_common:Composable diff --git a/src/linkml_common/schema/healthcare.yaml b/src/linkml_common/schema/healthcare.yaml index d325c77..0dd5222 100644 --- a/src/linkml_common/schema/healthcare.yaml +++ b/src/linkml_common/schema/healthcare.yaml @@ -47,6 +47,7 @@ classes: is_a: Organization HealthcareRole: + is_a: Role attributes: is_person: range: Person diff --git a/src/linkml_common/schema/investigations.yaml b/src/linkml_common/schema/investigations.yaml index 539f5ae..a3e3ea0 100644 --- a/src/linkml_common/schema/investigations.yaml +++ b/src/linkml_common/schema/investigations.yaml @@ -6,6 +6,7 @@ description: |- license: MIT see_also: - https://linkml.github.io/linkml-common + - https://obi-ontology.org/ prefixes: linkml_common: https://w3id.org/linkml-common/ @@ -32,10 +33,16 @@ classes: attributes: objectives: range: string + variables: + range: Variable + multivalued: true InvestigativeProtocol: is_a: Procedure + StudyDesign: + is_a: Procedure + SampleMaterial: is_a: NamedThing @@ -63,3 +70,21 @@ classes: DataGenerationFromSample: is_a: InvestigativeProcess +enums: + + CaseOrControlEnum: + permissible_values: + CASE: + title: case role in case-control study + meaning: OBI:0002492 + CONTROL: + title: control role in case-control study + meaning: OBI:0002493 + + StudyDesignEnum: + reachable_from: + source_nodes: + - OBI:0500000 + is_direct: false + relationship_types: + - rdfs:subClassOf \ No newline at end of file diff --git a/src/linkml_common/schema/linkml_common.yaml b/src/linkml_common/schema/linkml_common.yaml index e952d70..0ed535a 100644 --- a/src/linkml_common/schema/linkml_common.yaml +++ b/src/linkml_common/schema/linkml_common.yaml @@ -21,6 +21,7 @@ imports: - linkml:types - core - bibliographic + - datasets - clinicalresearch - computational - engineering diff --git a/src/linkml_common/schema/plannedprocess.yaml b/src/linkml_common/schema/plannedprocess.yaml index 17249ef..7c353fa 100644 --- a/src/linkml_common/schema/plannedprocess.yaml +++ b/src/linkml_common/schema/plannedprocess.yaml @@ -25,12 +25,15 @@ imports: classes: PlannedProcess: + description: A process that follows a defined procedure or plan is_a: Event attributes: follows_procedure: range: Procedure uses_physical_device: range: PhysicalDevice + exact_mappings: + - OBI:0000011 MaterialCollection: is_a: PlannedProcess diff --git a/src/linkml_common/schema/quantities.yaml b/src/linkml_common/schema/quantities.yaml index d17aa55..a469cfe 100644 --- a/src/linkml_common/schema/quantities.yaml +++ b/src/linkml_common/schema/quantities.yaml @@ -14,6 +14,8 @@ prefixes: schema: http://schema.org/ PATO: http://purl.obolibrary.org/obo/PATO_ fhir: http://hl7.org/fhir/ + qudt: http://qudt.org/vocab/unit/ + fibo.QuantitiesAndUnits: https://www.omg.org/spec/Commons/QuantitiesAndUnits/ default_prefix: linkml_common default_range: string @@ -23,6 +25,12 @@ imports: classes: + QuantityKind: + is_a: Concept + exact_mappings: + - qudt:QuantityKind + - fibo.QuantitiesAndUnits:ScalarQuantity + Quantity: is_a: Intangible class_uri: fhir:Quantity @@ -30,6 +38,12 @@ classes: - Quantity - QuantityRange - Ratio + attributes: + has_quantity_kind: + range: QuantityKind + description: The kind of quantity + exact_mappings: + - schema:Quantity SimpleQuantity: description: >- @@ -42,6 +56,12 @@ classes: description: The value of the quantity unit: range: UnitConcept + exact_mappings: + - schema:unitCode + - qudt:unit + exact_mappings: + - fibo:ScalarQuantityValue + Ratio: description: >- diff --git a/src/linkml_common/schema/social.yaml b/src/linkml_common/schema/social.yaml index 86bb511..a2cca18 100644 --- a/src/linkml_common/schema/social.yaml +++ b/src/linkml_common/schema/social.yaml @@ -2,7 +2,7 @@ id: https://w3id.org/linkml-common/social name: linkml-common-social title: linkml-common-social description: |- - Common Data Model Elements + Common Data Model Elements: Human and social activities license: MIT see_also: - https://linkml.github.io/linkml-common @@ -14,6 +14,9 @@ prefixes: schema: http://schema.org/ PATO: http://purl.obolibrary.org/obo/PATO_ fhir: http://hl7.org/fhir/ + prov: http://www.w3.org/ns/prov# + dcterms: http://purl.org/dc/terms/ + fibo.commons.PartiesAndSituations: https://spec.edmcouncil.org/fibo/ontology/FBC/ommons/PartiesAndSituations/ default_prefix: linkml_common default_range: string @@ -23,10 +26,16 @@ imports: classes: - Person: + Agent: is_a: NamedThing - description: >- - Represents a Person + description: Represents an Agent + exact_mappings: + - prov:Agent + - fibo.commons.PartiesAndSituations:Agent + + Person: + is_a: Agent + description: Represents a Person slots: - primary_email - birth_date @@ -35,15 +44,66 @@ classes: slot_usage: primary_email: pattern: "^\\S+@[\\S+\\.]+\\S+" + exact_mappings: + - schema:Person Organization: - is_a: NamedThing - description: >- - Represents an Organization + is_a: Agent + description: Represents an Organization + exact_mappings: + - schema:Organization + + AutomatedAgent: + is_a: Agent + description: Represents an Automated Agent LifeEvent: is_a: Event + CreativeWork: + description: The most generic kind of creative work, including books, movies, photographs, software programs, etc. + is_a: NamedThing + exact_mappings: + - schema:CreativeWork + attributes: + title: + range: string + description: The title of the item + exact_mappings: + - dcterms:title + abstract: + range: string + description: A summary of the item + rights: + range: string + description: Information about rights held in and over the item + creators: + range: Agent + slot_uri: dcterms:creator + description: The person or organization who created the work + multivalued: true + contributors: + range: Agent + slot_uri: dcterms:contributor + description: A person or organization that contributed to the creation of the work + multivalued: true + contacts: + range: Agent + slot_uri: schema:contactPoint + description: A contact point for a person or organization + multivalued: true + keywords: + range: string + slot_uri: schema:keywords + description: Keywords or tags used to describe this item + multivalued: true + + Service: + description: A service provided by an organization + is_a: Intangible + exact_mappings: + - schema:Service + slots: primary_email: @@ -61,6 +121,8 @@ slots: description: living or dead status enums: + HumanLanguageCodeEnum: + description: An enumeration of languages PersonStatus: permissible_values: ALIVE: diff --git a/src/linkml_common/schema/time.yaml b/src/linkml_common/schema/time.yaml index 8422613..ea358c4 100644 --- a/src/linkml_common/schema/time.yaml +++ b/src/linkml_common/schema/time.yaml @@ -14,6 +14,7 @@ prefixes: schema: http://schema.org/ PATO: http://purl.obolibrary.org/obo/PATO_ fhir: http://hl7.org/fhir/ + fibo.DatesAndTimes: https://www.omg.org/spec/Commons/DatesAndTimes/ default_prefix: linkml_common default_range: string @@ -25,20 +26,60 @@ imports: classes: Event: - description: >- - A thing that happens + description: A thing that happens is_a: NamedThing slots: - starts_at - ends_at + - happens_at + - has_interval + - has_duration + + + TimePointOrTemporalInterval: + is_a: Intangible + slots: + - starts_at + - ends_at + + TemporalInterval: + description: A period of time + is_a: TimePointOrTemporalInterval + slots: + - starts_at + - ends_at TimePoint: + description: A point in time. Can be fully specified, or specified in relative terms. + is_a: TimePointOrTemporalInterval slots: + - year_value - date_value - time_value - datetime_value - marker_event - description + exact_mappings: + - fibo.DatesAndTimes:TimeInstant + + Duration: + description: A length of time + is_a: Quantity + + + TemporalRelationship: + description: A relationship to another time point + is_a: Relationship + attributes: + predicate: + range: RelativeTimeEnum + description: The relationship between the two time points + relative_to: + range: Entity + any_of: + - range: TimePoint + - range: TemporalInterval + - range: Event slots: @@ -49,6 +90,15 @@ slots: ends_at: range: TimePoint + happens_at: + range: TimePoint + + year_value: + range: integer + unit: + symbol: year + ucum_code: a + date_value: range: date @@ -60,3 +110,17 @@ slots: marker_event: range: Event + + has_interval: + range: TemporalInterval + + has_duration: + range: Duration + +enums: + + RelativeTimeEnum: + permissible_values: + BEFORE: + AFTER: + AT_SAME_TIME_AS: \ No newline at end of file