feat(directory): biobank services as a separate entity

backend/molgenis-emx2-datamodels/src/test/java/org/molgenis/emx2/datamodels/TestLoaders.java

@@ -90,7 +90,7 @@ public void test08DataCatalogueNetworkStagingLoader() {
   public void test09DirectoryLoader() {
     Schema directory = database.createSchema(DIRECTORY_TEST);
     DataModels.Regular.BIOBANK_DIRECTORY.getImportTask(directory, true).run();
-    assertEquals(10, directory.getTableNames().size());
+    assertEquals(11, directory.getTableNames().size());
   }
 
   @Test

data/biobank-directory/demo/Biobanks.csv

@@ -1,3 +1,3 @@
-id,pid,name,acronym,description,url,location,country,latitude,longitude,head,contact,juridical_person,network,also_known,capabilities,collaboration_commercial,collaboration_non_for_profit,national_node,withdrawn
-bbmri-eric:ID:DE_biobank1,pid_biobank1,Biobank1,bb1,The description of biobank1,,Berlin,DE,,,bbmri-eric:contactID:DE_head_bb1,bbmri-eric:contactID:contact_bb1,A university,bbmri-eric:networkID:DE_network1,bbmri-eric:akiID:DE_00001,"covid19,nucleic-acid-extraction",true,false,DE,false
-bbmri-eric:ID:NL_biobank2,pid_biobank2,Biobank2,bb2,The description of biobank2,,Amsterdam,NL,,,bbmri-eric:contactID:NL_person1,bbmri-eric:contactID:NL_person1,An institute,bbmri-eric:networkID:EU_network,bbmri-eric:akiID:NL_00001,"cell-culture,pathology-archive-access,Testing_Facility_Animal",false,true,NL,false
+id,pid,name,acronym,description,url,location,country,latitude,longitude,head,contact,juridical_person,network,also_known,services,collaboration_commercial,collaboration_non_for_profit,national_node,withdrawn
+bbmri-eric:ID:DE_biobank1,pid_biobank1,Biobank1,bb1,The description of biobank1,,Berlin,DE,,,bbmri-eric:contactID:DE_head_bb1,bbmri-eric:contactID:contact_bb1,A university,bbmri-eric:networkID:DE_network1,bbmri-eric:akiID:DE_00001,"bbmri-eric:serviceID:DE_1234",true,false,DE,false
+bbmri-eric:ID:NL_biobank2,pid_biobank2,Biobank2,bb2,The description of biobank2,,Amsterdam,NL,,,bbmri-eric:contactID:NL_person1,bbmri-eric:contactID:NL_person1,An institute,bbmri-eric:networkID:EU_network,bbmri-eric:akiID:NL_00001,"bbmri-eric:serviceID:NL_541",false,true,NL,false

data/biobank-directory/demo/Services.csv

@@ -0,0 +1,3 @@
+id,name,acronym,description,serviceTypes,device,deviceSystem,tRL,accessDescription,unitOfAccess,unitCost,accreditation
+bbmri-eric:serviceID:DE_1234,Biobank Service,,Service provided by this biobank,dataSampleProcessing,,,4,https://myservice-access.de,,,
+bbmri-eric:serviceID:NL_541,Dutch Biobank Service,,Services provided by Biobank2,"technologiesBioanalytics, dataSampleProcessing",,,2,https://biobank2-service-access.nl,,,

data/biobank-directory/molgenis.csv

@@ -31,7 +31,7 @@ Biobanks,,juridical_person,Juridical Person,string,,false,,Juristic person of a
 Biobanks,,network,Networks,ref_array,,false,,"Reference to a biobank network ID, to which the biobank belongs; this attribute can also be used for biobank network, where it refers to the superior biobank network.",,Networks,,${name},,,,,
 Biobanks,,also_known,Also Known In,ref_array,,false,,The biobank also exists in …,,AlsoKnownIn,,${name_system},,,,,
 Biobanks,,collections,Collections,refback,,false,,Collections belonging to the biobank.,,Collections,biobank,,,,,,
-Biobanks,,capabilities,Capabilities Provided,ontology_array,,false,,Capabilities that the biobank organisation can offer to a researcher.,DirectoryOntologies,Capabilities,,${label},,,,,
+Biobanks,,services,Services,ref_array,,false,,Capabilities and services that the biobank organisation can offer to a researcher.,,Services,,${name},,,,,
 Biobanks,,quality,Quality Standards,refback,,false,true,The biobank is marked with this/these quality standard(s).,,QualityInfoBiobanks,biobank,,,,,,
 Biobanks,,collaboration_commercial,Commercial Collaboration,bool,,false,,The biobank can be used for collaboration with commercial partners.,,,,,,,,,
 Biobanks,,collaboration_non_for_profit,Non-for-profit Collaboration,bool,,false,,The biobank can be used for collaboration with non-for-profit partners.,,,,,,,,,
@@ -161,4 +161,17 @@ Persons,,role,Role of the Person,text,,false,,Official role of the person.,,,,,,
 Persons,,biobanks,Biobanks,refback,,false,true,Biobanks the person is connected to.,,Biobanks,contact,,,,,,
 Persons,,collections,Collections,refback,,false,true,Collections the person is connected to.,,Collections,contact,,,,,,
 Persons,,networks,Networks,refback,,false,true,Networks the person is connected to.,,Networks,contact,,,,,,
-Persons,,national_node,National Node,ref,,true,,The person originates from this national node.,,NationalNodes,,${description},,,,,
+Persons,,national_node,National Node,ref,,true,,The person originates from this national node.,,NationalNodes,,${description},,,,,
+Services,,,,,,,,Biobank Capabilities and Services
+Services,,id,ID,string,1,true,,"Unique ID of the service, prefixed with bbmri-eric:serviceID:"
+Services,,name,Service Name,string,2,true,,Name given to the service locally by the biobank staff.,,,,,,,,,
+Services,,acronym,Acronym,string,,false,,Short symbol simplifying communication.,,,,,,,,,
+Services,,description,Description,string,,false,,Full description of the service. If the description of this particular service exists on the internet - the URL to the relevant page is welcome.,,,,,,,,,
+Services,,serviceTypes,Service Types,ontology_array,,false,,Service Types,DirectoryOntologies,ServiceTypes,
+Services,,device,Device,string,,false,,"If the service is provided with the use of a certain device or instrument - especially when it is novel, rare or sophisticated.",,,,,,,,,
+Services,,deviceSystem,Device System,string,,false,,The system or platform describing the functioning of the used device - if needed.,,,,,,,,,
+Services,,tRL,Technology Readiness Level ,ontology,,false,,"Technology Readiness Level - concept for self-assessment of the service, used in some European projects (https://en.wikipedia.org/wiki/Technology_readiness_level). Can take values from 1 to 9.",DirectoryOntologies,TRLs,,,,,,,
+Services,,accessDescription,Access Description,string,,false,,Description of the access rules to the service. If the description is published on the internet - the URL to the relevant page is welcome.,,,,,,,,,
+Services,,unitOfAccess,Unit of Access,string,,false,,Information about a standard unit used in calculations of costs of service provision.,,,,,,,,,
+Services,,unitCost,Unit Cost,string,,false,,Actual costs of the unit.,,,,,,,,,
+Services,,accreditation,Accreditation,string,,false,,"General information, Yes or No, about accreditation referring to the provided service.",,,,,,,,,

data/biobank-directory/ontologies/ServiceTypes.csv

@@ -0,0 +1,7 @@
+order,name,label,parent,codesystem,code,ontologyTermURI,definition
+1,dataSampleProcessing,Data and Sample processing,,,,,Data and Sample processing
+2,researchDomains,Research domains,,,,,Research domains
+3,technologiesBioanalytics,"Technologies, Bioanalytics",,,,,"Technologies, Bioanalytics"
+4,expertiseOrganisation,"Expertise,
+Organisation",,,,,"Expertise,
+Organisation"

data/biobank-directory/ontologies/TRLs.csv

@@ -0,0 +1,10 @@
+order,name,label,parent,codesystem,code,ontologyTermURI,definition
+1,1,Basic principles observed,,,1,,Basic principles observed
+2,2,Technology concept formulated,,,2,,Technology concept formulated
+3,3,Experimental proof of concept,,,3,,Experimental proof of concept
+4,4,Technology validated in lab,,,4,,Technology validated in lab
+5,5,Technology validated in relevant environment (industrially relevant environment in the case of key enabling technologies),,,5,,Technology validated in relevant environment (industrially relevant environment in the case of key enabling technologies)
+6,6,Technology demonstrated in relevant environment (industrially relevant environment in the case of key enabling technologies),,,6,,Technology demonstrated in relevant environment (industrially relevant environment in the case of key enabling technologies)
+7,7,System prototype demonstration in operational environment,,,7,,System prototype demonstration in operational environment
+8,8,System complete and qualified,,,8,,System complete and qualified
+9,9,Actual system proven in operational environment (competitive manufacturing in the case of key enabling technologies; or in space),,,9,,Actual system proven in operational environment (competitive manufacturing in the case of key enabling technologies; or in space)