feat: updated models to use prefixed name instead of IRIs (#4818)

* updated models to use prefixed name instead of IRIs

* fixed some pre-existing invalid prefixed names

* replaced HTTPS IRIs with prefixed names

* fixed incorrect healthDCAT-AP prefixed names

* removed semantics from datasets/samplesets

* Fixed failing SHACL

backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/DefaultNamespace.java

@@ -15,7 +15,7 @@ public enum DefaultNamespace {
   EFO("efo", "http://www.ebi.ac.uk/efo/"),
   EJP("ejp", "https://w3id.org/ejp-rd/vocabulary#"),
   ENSEMBL("ensembl", "http://ensembl.org/glossary/"),
-  FDP("fdp-o", "http://w3id.org/fdp/fdp-o#"),
+  FDP("fdp-o", "https://w3id.org/fdp/fdp-o#"),
   FG("fg", "https://w3id.org/fair-genomes/resource/"),
   FOAF("foaf", "http://xmlns.com/foaf/0.1/"),
   HEALTHDCAT_AP("healthDCAT-AP", "urn:uuid:a7ef52b2-bd43-4294-a80f-3e7299af35e4#"),

data/_models/shared/Agent.csv

@@ -1,6 +1,6 @@
 tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles
-Agent,,,,,,,,,,,"http://xmlns.com/foaf/0.1/Agent,http://www.w3.org/2006/vcard/ns#Agent","An agent (eg. person, group, software or physical artifact).","DCAT,Beacon v2,DataCatalogueFlat"
-Agent,,name,string,1,TRUE,,,,,,"http://xmlns.com/foaf/0.1/name,http://purl.org/dc/terms/identifier",A name and identifier for this agent.,"DCAT,Beacon v2,DataCatalogueFlat"
-Agent,,logo,hyperlink,,,,,,,,"http://xmlns.com/foaf/0.1/logo",A logo representing some thing.,"DCAT,Beacon v2,DataCatalogueFlat"
-Agent,,url,hyperlink,,,,,,,,"http://www.w3.org/2006/vcard/ns#url",An URL representing some thing.,"Beacon v2,DataCatalogueFlat"
-Agent,,mbox,email,,,,,,,,"http://www.w3.org/2006/vcard/ns#hasEmail,http://xmlns.com/foaf/0.1/mbox","An email address is an identifier to send mail to particular electronic mailbox of a contact person or organization.","Beacon v2,DataCatalogueFlat"
+Agent,,,,,,,,,,,"foaf:Agent,vcard:Agent","An agent (eg. person, group, software or physical artifact).","DCAT,Beacon v2,DataCatalogueFlat"
+Agent,,name,string,1,TRUE,,,,,,"foaf:name,dcterms:identifier",A name and identifier for this agent.,"DCAT,Beacon v2,DataCatalogueFlat"
+Agent,,logo,hyperlink,,,,,,,,"foaf:logo",A logo representing some thing.,"DCAT,Beacon v2,DataCatalogueFlat"
+Agent,,url,hyperlink,,,,,,,,"vcard:url",An URL representing some thing.,"Beacon v2,DataCatalogueFlat"
+Agent,,mbox,email,,,,,,,,"vcard:hasEmail,foaf:mbox","An email address is an identifier to send mail to particular electronic mailbox of a contact person or organization.","Beacon v2,DataCatalogueFlat"

data/_models/shared/Analyses.csv

@@ -1,21 +1,21 @@
 tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles
-Analyses,,,,,,,,,,,http://edamontology.org/operation_2945,An analysis applies analytical (often computational) methods to existing data of a specific type to produce some desired output. In FAIR Genomes: Analysis.,"Beacon v2, FAIR Genomes, DCAT examples"
-Analyses,,id,string,1,TRUE,,,,,,http://purl.allotrope.org/ontologies/result#AFR_0001979,A unique proper name or character sequence that identifies this particular analysis. In FAIR Genomes: AnalysisIdentifier.,"Beacon v2, FAIR Genomes, DCAT examples"
-Analyses,,aligner,string,,,,,,,,http://edamontology.org/operation_0292,E.g. bwa-0.7.8,"Beacon v2, DCAT examples"
-Analyses,,analysisDate,date,,TRUE,,,,,,http://purl.obolibrary.org/obo/date,E.g. 2021-10-17,"Beacon v2, DCAT examples"
-Analyses,,biosampleId,ref,,,,Biosamples,,,,http://purl.obolibrary.org/obo/NCIT_C93400,E.g. S0001,"Beacon v2, DCAT examples"
-Analyses,,individualId,ref,,,,Individuals,,,,http://purl.obolibrary.org/obo/NCIT_C164337,E.g. P0001,"Beacon v2, DCAT examples"
-Analyses,,pipelineName,string,,TRUE,,,,,,http://edamontology.org/data_2531,E.g. Pipeline-panel-0001-v1,"Beacon v2, DCAT examples"
-Analyses,,pipelineRef,hyperlink,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C17564,E.g. https://doi.org/10.48511/workflowhub.workflow.111.1,"Beacon v2, DCAT examples"
-Analyses,,runId,ref,,,,Runs,,,,http://purl.obolibrary.org/obo/NCIT_C171337,E.g. SRR10903401,"Beacon v2, DCAT examples"
-Analyses,,variantCaller,string,,,,,,,,http://edamontology.org/operation_3227,E.g. GATK4.0,"Beacon v2, DCAT examples"
-"Analyses","","BelongsToSequencing","ref","","","","Runs","","","","http://purl.obolibrary.org/obo/NCIT_C25683","Reference to the sequencing that was performed, i.e. the source on which this analysis was based.","FAIR Genomes"
-"Analyses","","PhysicalDataLocation","string","","","","","","","","http://purl.obolibrary.org/obo/GAZ_00000448","A place on the Earth where the data is located, by its name or by its geographical location. This definition is intentionally vague to allow reuse locally (e.g. which computer), for contacting (e.g. which institute), broadly for logistical or legal reasons (e.g. city, country or continent).","FAIR Genomes"
-"Analyses","","AbstractDataLocation","string","","","","","","","","http://purl.obolibrary.org/obo/NCIT_C142494","The file location of the data, or a copy of the data, on an electronically accessible device for preservation (either in plain-text or encrypted format).","FAIR Genomes"
-"Analyses","","DataFormatsStored","ontology_array","","","","FileFormats","","","","http://purl.obolibrary.org/obo/NCIT_C142494","Which data file formats (i.e. defined ways or layouts of representing and structuring data in a computer file, blob, string, message, or elsewhere) are stored and potentially available.","FAIR Genomes"
-"Analyses","","AlgorithmsUsed","text","","","","","","","","http://purl.obolibrary.org/obo/NCIT_C16275","Any used problem-solving procedures implemented in software to be executed by a computer.","FAIR Genomes"
-"Analyses","","ReferenceGenomeUsed","ontology","","","","ReferenceGenomeAssemblies","","","","http://edamontology.org/data_2340","The specific build of the human genome used as reference for sequence alignment and variant calling.","FAIR Genomes"
-"Analyses","","BioinformaticProtocolUsed","text","","","","","","","","http://edamontology.org/data_2531","A human-readable collection of information about about how a scientific experiment or analysis was carried out that results in a specific set of data or results used for further analysis or to test a specific hypothesis.","FAIR Genomes"
-"Analyses","","BioinformaticProtocolDeviation","string","","","","","","","","http://purl.obolibrary.org/obo/NCIT_C50996","A variation from processes or procedures defined in the bioinformatic protocol. Deviations usually do not preclude the overall evaluability of subject data for either efficacy or safety, and are often acknowledged and accepted in advance by the sponsor.","FAIR Genomes"
-"Analyses","","ReasonForBioinformaticProtocolDeviation","string","","","","","","","","http://purl.obolibrary.org/obo/NCIT_C93529","The rationale for why a deviation from the bioinformatic protocol has occurred.","FAIR Genomes"
-"Analyses","","WgsGuidelineFollowed","string","","","","","","","","http://purl.obolibrary.org/obo/NCIT_C17564","Any followed systematic statement of policy rules or principles. Guidelines may be developed by government agencies at any level, institutions, professional societies, governing boards, or by convening expert panels.","FAIR Genomes"
+Analyses,,,,,,,,,,,edam:operation_2945,An analysis applies analytical (often computational) methods to existing data of a specific type to produce some desired output. In FAIR Genomes: Analysis.,"Beacon v2, FAIR Genomes, DCAT examples"
+Analyses,,id,string,1,TRUE,,,,,,afr:AFR_0001979,A unique proper name or character sequence that identifies this particular analysis. In FAIR Genomes: AnalysisIdentifier.,"Beacon v2, FAIR Genomes, DCAT examples"
+Analyses,,aligner,string,,,,,,,,edam:operation_0292,E.g. bwa-0.7.8,"Beacon v2, DCAT examples"
+Analyses,,analysisDate,date,,TRUE,,,,,,obo:date,E.g. 2021-10-17,"Beacon v2, DCAT examples"
+Analyses,,biosampleId,ref,,,,Biosamples,,,,obo:NCIT_C93400,E.g. S0001,"Beacon v2, DCAT examples"
+Analyses,,individualId,ref,,,,Individuals,,,,obo:NCIT_C164337,E.g. P0001,"Beacon v2, DCAT examples"
+Analyses,,pipelineName,string,,TRUE,,,,,,edam:data_2531,E.g. Pipeline-panel-0001-v1,"Beacon v2, DCAT examples"
+Analyses,,pipelineRef,hyperlink,,,,,,,,obo:NCIT_C17564,E.g. https://doi.org/10.48511/workflowhub.workflow.111.1,"Beacon v2, DCAT examples"
+Analyses,,runId,ref,,,,Runs,,,,obo:NCIT_C171337,E.g. SRR10903401,"Beacon v2, DCAT examples"
+Analyses,,variantCaller,string,,,,,,,,edam:operation_3227,E.g. GATK4.0,"Beacon v2, DCAT examples"
+"Analyses","","BelongsToSequencing","ref","","","","Runs","","","","obo:NCIT_C25683","Reference to the sequencing that was performed, i.e. the source on which this analysis was based.","FAIR Genomes"
+"Analyses","","PhysicalDataLocation","string","","","","","","","","obo:GAZ_00000448","A place on the Earth where the data is located, by its name or by its geographical location. This definition is intentionally vague to allow reuse locally (e.g. which computer), for contacting (e.g. which institute), broadly for logistical or legal reasons (e.g. city, country or continent).","FAIR Genomes"
+"Analyses","","AbstractDataLocation","string","","","","","","","","obo:NCIT_C142494","The file location of the data, or a copy of the data, on an electronically accessible device for preservation (either in plain-text or encrypted format).","FAIR Genomes"
+"Analyses","","DataFormatsStored","ontology_array","","","","FileFormats","","","","obo:NCIT_C142494","Which data file formats (i.e. defined ways or layouts of representing and structuring data in a computer file, blob, string, message, or elsewhere) are stored and potentially available.","FAIR Genomes"
+"Analyses","","AlgorithmsUsed","text","","","","","","","","obo:NCIT_C16275","Any used problem-solving procedures implemented in software to be executed by a computer.","FAIR Genomes"
+"Analyses","","ReferenceGenomeUsed","ontology","","","","ReferenceGenomeAssemblies","","","","edam:data_2340","The specific build of the human genome used as reference for sequence alignment and variant calling.","FAIR Genomes"
+"Analyses","","BioinformaticProtocolUsed","text","","","","","","","","edam:data_2531","A human-readable collection of information about about how a scientific experiment or analysis was carried out that results in a specific set of data or results used for further analysis or to test a specific hypothesis.","FAIR Genomes"
+"Analyses","","BioinformaticProtocolDeviation","string","","","","","","","","obo:NCIT_C50996","A variation from processes or procedures defined in the bioinformatic protocol. Deviations usually do not preclude the overall evaluability of subject data for either efficacy or safety, and are often acknowledged and accepted in advance by the sponsor.","FAIR Genomes"
+"Analyses","","ReasonForBioinformaticProtocolDeviation","string","","","","","","","","obo:NCIT_C93529","The rationale for why a deviation from the bioinformatic protocol has occurred.","FAIR Genomes"
+"Analyses","","WgsGuidelineFollowed","string","","","","","","","","obo:NCIT_C17564","Any followed systematic statement of policy rules or principles. Guidelines may be developed by government agencies at any level, institutions, professional societies, governing boards, or by convening expert panels.","FAIR Genomes"