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simleosimleo
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Merge pull request crs4#149 from nfdi4plants/isa-profile-setup
ISA Profile Setup
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‎CITATION.cff‎

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- family-names: Bauer
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given-names: Daniel
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orcid: https://orcid.org/0000-0001-9447-460X
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- family-names: "Wetzels"
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given-names: "Florian"
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orcid: https://orcid.org/0000-0002-5526-7138
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- family-names: "Weil"
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given-names: "Heinrich Lukas"
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orcid: https://orcid.org/0000-0003-1945-6342
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repository-code: "https://github.com/crs4/rocrate-validator"
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url: "https://github.com/crs4/rocrate-validator"
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keywords:

‎rocrate_validator/profiles/isa-ro-crate/0_investigation.ttl‎

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# Copyright (c) 2026 DataPLANT
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# Copyright (c) 2026 The University of Manchester
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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@prefix ro: <./> .
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@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
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@prefix isa-ro-crate: <https://github.com/crs4/rocrate-validator/profiles/isa-ro-crate/> .
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@prefix bioschemas: <https://bioschemas.org/> .
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@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
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@prefix schema: <http://schema.org/> .
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@prefix sh: <http://www.w3.org/ns/shacl#> .
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@prefix validator: <https://github.com/crs4/rocrate-validator/> .
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@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
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isa-ro-crate:RootDataEntityMustBeInvestigation a sh:NodeShape ;
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sh:name "Root Data Entity must be Investigation" ;
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sh:description "The root data entity must follow the investigation profile" ;
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sh:targetClass ro-crate:RootDataEntity ;
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sh:property [
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a sh:PropertyShape ;
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sh:path schema:additionalType ;
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sh:minCount 1 ;
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sh:hasValue "Investigation";
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sh:description "Check if the root data entity is specified as an investigation through additionalType" ;
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sh:message "The root data entity must have additionalType of `Investigation`" ;
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sh:severity sh:Violation ;
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:path schema:identifier ;
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sh:minCount 1 ;
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sh:datatype xsd:string ;
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sh:not [
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sh:hasValue ""
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] ;
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sh:description "Check if the root data entity (investigation) has an identifier" ;
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sh:message "The root data entity must have a non-empty identifier" ;
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sh:severity sh:Violation ;
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] ;
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# sh:property [
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# a sh:PropertyShape ;
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# sh:path schema:name ;
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# sh:minCount 1 ;
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# sh:not [
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# sh:hasValue ""
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# ] ;
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# sh:description "Check if the root data entity (investigation) has a name" ;
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# sh:message "The root data entity must have a non-empty name" ;
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# sh:severity sh:Violation ;
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# ] ;
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# sh:property [
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# a sh:PropertyShape ;
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# sh:path schema:description ;
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# sh:minCount 1 ;
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# sh:not [
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# sh:hasValue ""
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# ] ;
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# sh:description "Check if the root data entity (investigation) has a description" ;
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# sh:message "The root data entity must have a non-empty description" ;
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# sh:severity sh:Violation ;
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# ] ;
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# sh:property [
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# a sh:PropertyShape ;
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# sh:path schema:license ;
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# sh:minCount 1 ;
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# sh:description "Check if the root data entity (investigation) specifies a license" ;
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# sh:message "The root data entity must specify a license" ;
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# sh:severity sh:Violation ;
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# ] ;
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# sh:property [
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# a sh:PropertyShape ;
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# sh:path schema:datePublished ;
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# sh:minCount 1 ;
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# sh:nodeKind sh:Literal ;
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# sh:pattern "^([\\+-]?\\d{4})((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))|W([0-4]\\d|5[0-2])(-?[1-7])|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)?[0-5]\\d)?|24:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)$" ;
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# sh:description "Check if the root data entity (investigation) has a datePublished" ;
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# sh:message "The root data entity must have a datePublished" ;
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# sh:severity sh:Violation ;
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# ] ;
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.
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isa-ro-crate:InvestigationShouldHaveCreator a sh:NodeShape ;
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sh:name "Investigation SHOULD have creator" ;
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sh:description "An Investigation SHOULD have a creator" ;
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sh:targetClass ro-crate:RootDataEntity ;
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sh:property [
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a sh:PropertyShape ;
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sh:path schema:creator ;
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sh:minCount 1 ;
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sh:description "Check that investigation does have at least one creator" ;
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sh:message "Investigation entity SHOULD have a creator" ;
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sh:severity sh:Warning ;
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:path schema:creator ;
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sh:class schema:Person ;
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sh:description "Check that if investigation does have at least one creator, it MUST be of type Person" ;
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sh:message "Investigation creator MUST be of type Person" ;
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sh:severity sh:Violation ;
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]
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.
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isa-ro-crate:InvestigationShouldHaveDateCreated a sh:NodeShape ;
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sh:name "Investigation SHOULD have dateCreated" ;
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sh:description "An Investigation SHOULD have a dateCreated" ;
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sh:targetClass ro-crate:RootDataEntity ;
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sh:property [
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a sh:PropertyShape ;
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sh:path schema:dateCreated ;
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sh:minCount 1 ;
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sh:description "Check that investigation does have at least one dateCreated" ;
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sh:message "Investigation entity SHOULD have a dateCreated" ;
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sh:severity sh:Warning ;
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:path schema:dateCreated ;
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sh:nodeKind sh:Literal ;
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sh:pattern "^([\\+-]?\\d{4})((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))|W([0-4]\\d|5[0-2])(-?[1-7])|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)?[0-5]\\d)?|24:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)$" ;
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sh:description "Check that if investigation does have at least one dateCreated, it MUST be a valid ISO 8601 date." ;
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sh:message "Investigation dateCreated MUST be a valid ISO 8601 date" ;
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sh:severity sh:Violation ;
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]
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.

‎rocrate_validator/profiles/isa-ro-crate/10_definedterm.ttl‎

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# Copyright (c) 2026 DataPLANT
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# Copyright (c) 2026 The University of Manchester
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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@prefix ro: <./> .
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@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
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@prefix isa-ro-crate: <https://github.com/crs4/rocrate-validator/profiles/isa-ro-crate/> .
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@prefix bioschemas: <https://bioschemas.org/> .
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@prefix bioschemas-prop: <https://bioschemas.org/properties/> .
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@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
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@prefix schema: <http://schema.org/> .
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@prefix sh: <http://www.w3.org/ns/shacl#> .
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@prefix validator: <https://github.com/crs4/rocrate-validator/> .
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@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
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isa-ro-crate:DefinedTermMustHaveName a sh:NodeShape ;
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sh:name "DefinedTerm MUST have a name" ;
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sh:description "A DefinedTerm MUST have a name" ;
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sh:targetClass schema:DefinedTerm ;
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sh:property [
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a sh:PropertyShape ;
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sh:path schema:name ;
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sh:datatype xsd:string ;
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sh:minCount 1 ;
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sh:maxCount 1 ;
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sh:not [
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sh:hasValue ""
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] ;
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sh:description "Check that DefinedTerm does have non-empty name and it's a string" ;
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sh:message "DefinedTerm entity MUST have a non-empty name of type string" ;
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sh:severity sh:Violation ;
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]
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.
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isa-ro-crate:DefinedTermShouldHaveTermCodeOfCorrectType a sh:NodeShape ;
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sh:name "DefinedTerm SHOULD have termCode of correct type" ;
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sh:description "A DefinedTerm SHOULD have at least one termCode of correct type" ;
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sh:targetClass schema:DefinedTerm ;
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sh:property [
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a sh:PropertyShape ;
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sh:path schema:termCode ;
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sh:minCount 1 ;
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sh:not [
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sh:hasValue ""
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] ;
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sh:description "Check that DefinedTerm does have at least one termCode" ;
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sh:message "DefinedTerm entity SHOULD have at least one termCode" ;
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sh:severity sh:Warning ;
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:path schema:termCode ;
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sh:datatype xsd:string ;
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sh:description "The termCode of a DefinedTerm MUST be of type string" ;
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sh:message "DefinedTerm termCode MUST be of type string" ;
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sh:severity sh:Violation ;
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]
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.

‎rocrate_validator/profiles/isa-ro-crate/11_propertyvalue.ttl‎

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# Copyright (c) 2026 DataPLANT
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# Copyright (c) 2026 The University of Manchester
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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@prefix ro: <./> .
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@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
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@prefix isa-ro-crate: <https://github.com/crs4/rocrate-validator/profiles/isa-ro-crate/> .
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@prefix bioschemas: <https://bioschemas.org/> .
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@prefix bioschemas-prop: <https://bioschemas.org/properties/> .
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@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
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@prefix schema: <http://schema.org/> .
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@prefix sh: <http://www.w3.org/ns/shacl#> .
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@prefix validator: <https://github.com/crs4/rocrate-validator/> .
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@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
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ro-crate:FindPropertyValueSubtypes a sh:NodeShape, validator:HiddenShape;
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sh:name "Identify PropertyValue subtypes within the RO-Crate" ;
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sh:description "A PropertyValue has type Parameter, Characteristic, Factor or Component if additionalType is set accordingly." ;
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sh:targetClass schema:PropertyValue ;
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# Expand data graph with triples from the file data entity
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sh:rule [
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a sh:TripleRule ;
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sh:subject sh:this ;
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sh:predicate rdf:type ;
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sh:object isa-ro-crate:Parameter ;
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# The condition: additionalType == "Parameter"
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sh:condition [
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sh:property [
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sh:path schema:additionalType ;
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sh:hasValue "Parameter" ;
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] ;
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] ;
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] ;
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sh:rule [
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a sh:TripleRule ;
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sh:subject sh:this ;
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sh:predicate rdf:type ;
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sh:object isa-ro-crate:Characteristic ;
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# The condition: additionalType == "Characteristic"
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sh:condition [
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sh:property [
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sh:path schema:additionalType ;
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sh:hasValue "Characteristic" ;
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] ;
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] ;
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] ;
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sh:rule [
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a sh:TripleRule ;
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sh:subject sh:this ;
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sh:predicate rdf:type ;
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sh:object isa-ro-crate:Factor ;
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# The condition: additionalType == "Factor"
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sh:condition [
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sh:property [
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sh:path schema:additionalType ;
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sh:hasValue "Factor" ;
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] ;
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] ;
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] ;
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sh:rule [
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a sh:TripleRule ;
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sh:subject sh:this ;
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sh:predicate rdf:type ;
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sh:object isa-ro-crate:Component ;
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# The condition: additionalType == "Component"
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sh:condition [
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sh:property [
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sh:path schema:additionalType ;
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sh:hasValue "Component" ;
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] ;
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] ;
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]
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.
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isa-ro-crate:PropertyValueMustHaveName a sh:NodeShape ;
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sh:name "PropertyValue MUST have a name" ;
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sh:description "A PropertyValue MUST have a name" ;
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sh:targetClass schema:PropertyValue ;
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sh:property [
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a sh:PropertyShape ;
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sh:path schema:name ;
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sh:datatype xsd:string ;
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sh:minCount 1 ;
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sh:maxCount 1 ;
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sh:not [
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sh:hasValue ""
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] ;
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sh:description "Check that PropertyValue does have non-empty name and it's a string" ;
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sh:message "PropertyValue entity MUST have a non-empty name of type string" ;
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sh:severity sh:Violation ;
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]
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.
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isa-ro-crate:PropertyValueShouldHaveValueOfCorrectType a sh:NodeShape ;
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sh:name "PropertyValue SHOULD have value of correct type" ;
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sh:description "A PropertyValue SHOULD have at least one value of correct type" ;
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sh:targetClass schema:PropertyValue ;
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sh:property [
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a sh:PropertyShape ;
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sh:path schema:value ;
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sh:minCount 1 ;
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sh:not [
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sh:hasValue ""
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] ;
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sh:description "Check that PropertyValue does have at least one value" ;
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sh:message "PropertyValue entity SHOULD have at least one value" ;
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sh:severity sh:Warning ;
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] ;
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sh:property [
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a sh:PropertyShape ;
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sh:path schema:value ;
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sh:or(
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[ sh:datatype xsd:string ]
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[ sh:datatype xsd:float ]
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[ sh:datatype xsd:integer ]
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) ;
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sh:description "The value of a PropertyValue MUST be of type string or a number" ;
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sh:message "PropertyValue value MUST be of type string, float, or integer" ;
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sh:severity sh:Violation ;
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]
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.

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