feat(directory): biobank services as a separate entity (#4155)

* feat(directory): separate biobank services

* feat(directory): biobank services as a separate entity

* chore: rename FALSE to false

* chore: add NL dummy service

* chore: TRL as ontology and service types added

* chore: change service types logic

* feat(directory): update Biobank services model

* feat(directory): update Biobank services model

* feat(directory): fix typo's and add serviceCategory column

* feat(directory): add QualityInformationServices

* chore: separate ServiceCategories table

* chore: fix missing and invalid refLabels

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

@@ -93,7 +93,7 @@ public void test08DataCatalogueNetworkStagingLoader() {
   public void test09DirectoryLoader() {
     Schema directory = database.createSchema(DIRECTORY_TEST);
     DataModels.Regular.BIOBANK_DIRECTORY.getImportTask(directory, true).run();
-    assertEquals(11, directory.getTableNames().size());
+    assertEquals(13, 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withdrawn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withdrawn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/QualityInfoServices.csv

@@ -0,0 +1,4 @@
+service,qualityStandard,assessmentLevel,certificationNumber,certificationReport,certificationImageLink
+bbmri-eric:serviceID:DE_1234,iso-20184-3,accredited,,,
+bbmri-eric:serviceID:NL_541,ISO-20387-2018,accredited,,,
+bbmri-eric:serviceID:NL_541,iso-20166-1,accredited,,,

data/biobank-directory/demo/Services.csv

@@ -0,0 +1,3 @@
+id,name,serviceTypes,acronym,description,descriptionUrl,device,deviceSystem,tRL,accessDescriptionUrl,unitOfAccess,accessDescription,unitCost,contactInformation,national_node
+bbmri-eric:serviceID:DE_1234,Biobank Service,"microbiome-analysis, sample-storage",,Service provided by this biobank,,,,TRL-4,,,https://myservice-access.de,,bbmri-eric:contactID:contact_bb1,DE
+bbmri-eric:serviceID:NL_541,Dutch Biobank Service,"PET-Scans, TrainingResourceLabProtocols",,Services provided by Biobank2,,,,TRL-2,,,https://biobank2-service-access.nl,,,NL

data/biobank-directory/molgenis.csv

@@ -25,14 +25,14 @@ Biobanks,,location,Location,string,,false,,The city where the biobank is located
 Biobanks,,country,Country,ontology,,true,,Country hosting the biobank according to MIABIS 2.0 - MIABIS-2.0-06.,DirectoryOntologies,Countries,,${label},,,,,
 Biobanks,,latitude,Latitude,string,,false,,"Latitude of the biobank in the WGS84 system (the one used by GPS), positive is northern hemisphere.",,,,,,,,,
 Biobanks,,longitude,Longitude,string,,false,,"Longitude of the biobank in the WGS84 system (the one used by GPS), positive is to the East of Greenwich.",,,,,,,,,
-Biobanks,,head,Head of the Biobank,ref,,false,,Person in charge of the biobank.,,Persons,,${first_name} ${last_name},,,,,
-Biobanks,,contact,Contact Person,ref,,true,,Contact person of the biobank.,,Persons,,${first_name} ${last_name},,,,,
+Biobanks,,head,Head of the Biobank,ref,,false,,Person in charge of the biobank.,,Persons,,${email},,,,,
+Biobanks,,contact,Contact Person,ref,,true,,Contact person of the biobank.,,Persons,,${email},,,,,
 Biobanks,,juridical_person,Juridical Person,string,,true,,Juristic person of a biobank according to MIABIS 2.0 - MIABIS-2.0-05.,,,,,,,,,
 Biobanks,,network,Networks,ref_array,,false,,"Reference to a biobank network ID, to which the biobank belongs; this attribute can also be used for biobank network, where it refers to the superior biobank network.",,Networks,,${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,,quality,Quality Standards,refback,,false,true,The biobank is marked with this/these quality standard(s).,,QualityInfoBiobanks,biobank,,,,,,
+Biobanks,,collections,Collections,refback,,false,,Collections belonging to the biobank.,,Collections,biobank,${name},,,,,
+Biobanks,,services,Services,ref_array,,false,,Capabilities and services that the biobank organisation can offer to a researcher.,,Services,,${name},,,,,
+Biobanks,,quality,Quality Standards,refback,,false,true,The biobank is marked with this/these quality standard(s).,,QualityInfoBiobanks,biobank,${quality_standard.label},,,,,
 Biobanks,,collaboration_commercial,Commercial Collaboration,bool,,false,,The biobank can be used for collaboration with commercial partners.,,,,,,,,,
 Biobanks,,collaboration_non_for_profit,Non-for-profit Collaboration,bool,,false,,The biobank can be used for collaboration with non-for-profit partners.,,,,,,,,,
 Biobanks,,national_node,National Node,ref,,true,,The biobank originates from this national node.,,NationalNodes,,${description},,,,,
@@ -67,8 +67,8 @@ Collections,,location,Location,string,,false,,The city where the collection is l
 Collections,,country,Country,ontology,,true,,Country according to MIABIS 2.0 - MIABIS-2.0-07-H.,DirectoryOntologies,Countries,,${label},,,,,
 Collections,,latitude,Latitude,string,,false,,"Latitude of the collection in the WGS84 system (the one used by GPS), positive is northern hemisphere.",,,,,,,,,
 Collections,,longitude,Longitude,string,,false,,"Longitude of the collection in the WGS84 system (the one used by GPS), positive is to the East of Greenwich.",,,,,,,,,
-Collections,,head,Head of the Collection,ref,,false,,Person in charge of the collection.,,Persons,,${first_name} ${last_name},,,,,
-Collections,,contact,Contact Person,ref,,true,,Contact person of the collection.,,Persons,,${first_name} ${last_name},,,,,
+Collections,,head,Head of the Collection,ref,,false,,Person in charge of the collection.,,Persons,,${email},,,,,
+Collections,,contact,Contact Person,ref,,true,,Contact person of the collection.,,Persons,,${email},,,,,
 Collections,,national_node,National Node,ref,,true,,The collection originates from this national node.,,NationalNodes,,${description},,,,,
 Collections,,withdrawn,Withdrawn,bool,,true,,This collection is withdrawn from the Directory.,,,,,false,,,,
 Collections,,belongs_to,Belongs to,heading,,false,,The collection belongs to ...,,,,,,,,,
@@ -87,7 +87,7 @@ Collections,,order_of_magnitude,Order of Magnitude,ontology,,true,,Size of the c
 Collections,,size,Size,int,,false,,Exact size of the collection at the given date.,,,,,,,,,
 Collections,,categories,Collection Categories,ontology_array,,false,,Collection categories.,DirectoryOntologies,Categories,,${label},,,,,
 Collections,,timestamp,Timestamp,datetime,,false,,"Date to which the size of the collection was valid, format: yyyy-mm-ddThh:mm:ss+nnnn, e.g. 2016-11-15T09:53:13+0100.",,,,,,,,,
-Collections,,quality,Quality Standards,refback,,false,true,The collection is marked with this/these quality standard(s).,,QualityInfoCollections,collection,${quality_standard},,,,,
+Collections,,quality,Quality Standards,refback,,false,true,The collection is marked with this/these quality standard(s).,,QualityInfoCollections,collection,${quality_standard.label},,,,,
 Collections,,combined_quality,Combined Qualities,ontology_array,,false,,"The direct or indirect collection’s assessment level(s) (i.e., either the collection is explicitly marked with this assessment level or its biobank is).",DirectoryOntologies,AssessmentLevels,,${label},,,,,
 Collections,,donor_data,Donor Data,heading,,false,,Donor Data Characteristics,,,,,,,,,
 Collections,,number_of_donors,Number of Donors,int,,false,,Number of donors from who sample(s) were taken.,,,,,,,,,
@@ -141,7 +141,7 @@ Networks,,longitude,Longitude,string,,false,,"Longitude of the network in the WG
 Networks,,also_known,Also Known In,ref_array,,false,,The network is also known in …,,AlsoKnownIn,,${name_system},,,,,
 Networks,,url,URL,hyperlink,,false,,Network URL,,,,,,,,,
 Networks,,juridical_person,Juridical Person,string,,false,,Juristic person of the network to MIABIS 2.0 - MIABIS-2.0-05.,,,,,,,,,
-Networks,,contact,Contact Person,ref,,true,,Contact person of the network.,,Persons,,${first_name} ${last_name},,,,,
+Networks,,contact,Contact Person,ref,,true,,Contact person of the network.,,Persons,,${email},,,,,
 Networks,,parent_network,Parent Network,ref_array,,false,,"Reference to a network ID, refers to the superior network.",,Networks,,${name},,,,,
 Networks,,common_network_elements,Common Network Elements,ontology_array,,false,,Selection of elements that are the same for all biobanks/collections within the network.,DirectoryOntologies,CommonNetworkElements,,${label},,,,,
 Networks,,national_node,National Node,ref,,true,,The network originates from this national node.,,NationalNodes,,${description},,,,,
@@ -159,20 +159,46 @@ Persons,,zip,Zip code,string,,false,,ZIP or postal code according to MIABIS 2.0
 Persons,,city,City,string,,false,,City according to MIABIS 2.0 - MIABIS-2.0-07-G.,,,,,,,,,
 Persons,,country,Country,ontology,,true,,Country according to MIABIS 2.0 - MIABIS-2.0-07-H.,DirectoryOntologies,Countries,,${label},,,,,
 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,,biobanks,Biobanks,refback,,false,true,Biobanks the person is connected to.,,Biobanks,contact,${name},,,,,
+Persons,,collections,Collections,refback,,false,true,Collections the person is connected to.,,Collections,contact,${name},,,,,
+Persons,,networks,Networks,refback,,false,true,Networks the person is connected to.,,Networks,contact,${name},,,,,
 Persons,,national_node,National Node,ref,,true,,The person originates from this national node.,,NationalNodes,,${description},,,,,
+QualityInfoServices,,,,,,,,Collection Quality Information,,,,,,,,,
+QualityInfoServices,,id,ID,auto_id,1,true,true,,,,,,,,,QIS-${mg_autoid},
+QualityInfoServices,,service,Collection,ref,,true,,,,Services,,${name},,,,,
+QualityInfoServices,,qualityStandard,Quality Standard,ontology,,true,,,DirectoryOntologies,QualityStandards,,${label},,,,,
+QualityInfoServices,,assessmentLevel,Assessment Level,ontology,,true,,,DirectoryOntologies,AssessmentLevels,,${label},,,,,
+QualityInfoServices,,certificationNumber,Certification Number,string,,false,,,,,,,,,,,
+QualityInfoServices,,certificationReport,Certification Report,hyperlink,,false,,,,,,,,,,,
+QualityInfoServices,,certificationImageLink,Certification Image,hyperlink,,false,,,,,,,,,,,
+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 of the service (preferably in English).,,,,,,,,,
+Services,,serviceTypes,Service Types,ref_array,,true,,Related service types,DirectoryOntologies,ServiceTypes,,${label}
+Services,,acronym,Acronym,string,,false,,Short name in use for the service. If applicable.,,,,,,,,,
+Services,,description,Description,string,,true,,Full description of the service (in English),,,,,,,,,
+Services,,descriptionUrl,Description URL,hyperlink,,false,,URL address of the service description if available.,,,,,,,,,
+Services,,device,Device,string,,false,,Name of the device(s) if the service is provided with the use of them.,,,,,,,,,
+Services,,deviceSystem,Device System,string,,false,,Name of a software system or platform if important for the device characteristics.,,,,,,,,,
+Services,,tRL,Technology Readiness Level ,ontology,,false,,Technology Readiness Level - a concept for self-assessment of the service maturity,DirectoryOntologies,TRLs,,${label},,,,,
+Services,,accessDescription,Access Description,string,,true,,Description of the access policy of the service.,,,,,,,,,
+Services,,accessDescriptionUrl,Access Description URL,hyperlink,,false,,URL of the service access policy if available..,,,,,,,,,
+Services,,unitOfAccess,Unit of Access,string,,false,,Information about a standard unit used in calculations of costs of service provision.,,,,,,,,,
+Services,,accessDescription,Access Description,string,,true,,Description of the access policy of the service,,,,,,,,,
+Services,,unitCost,Unit Cost,string,,false,,Cost per unit.,,,,,,,,,
+Services,,qualityStandards,Quality Standards,refback,,false,true,The standards and/or technical specifications that the service is certified or accredited for.,,QualityInfoServices,service,${qualityStandard.label},,,,,
+Services,,contactInformation,Contact Information,ref,,false,,Contact information for the contact person or responsible person of the service ,,Persons,
+Services,,national_node,National Node,ref,,true,,The study originates from this national node.,,NationalNodes,,${description},,,,,
 Studies,,,,,,,,Table with information about the studies in which context the collection was generated,,,,,,,,,
 Studies,,id,ID,string,1,true,,"Unique ID of the study, prefixed with bbmri-eric:studyID:<id_of_the_study>",,,,,,,,,
 Studies,,title,Title,text,,true,,The title of the study,,,,,,,,,
 Studies,,description,Description,text,,false,,A text describing the study,,,,,,,,,
 Studies,,type,Type,string,,false,,"The type of study (Observational, Interventional).",,,,,,,,,
-Studies,,sex,Sex,ontology_array,,false,,"The sex of the individuals that participated to the study",DirectoryOntologies,SexTypes,,,,,,,
+Studies,,sex,Sex,ontology_array,,false,,"The sex of the individuals that participated to the study",DirectoryOntologies,SexTypes,,${label},,,,,
 Studies,,age_low,Age Low,int,,false,,Age of youngest sample donor at time of sample donation - MIABIS-2.0-10.,,,,,,,,,
 Studies,,age_high,Age High,int,,false,,Age of oldest sample donor at time of sample donation - MIABIS-2.0-11.,,,,,,,,,
 Studies,,age_unit,Age Unit,ontology,,false,,"Unit defining Age Low and Age High. Can be one of the following values: YEAR, MONTH, WEEK, DAY - MIABIS-2.0-08.",DirectoryOntologies,AgeUnits,,${label},,,,,
 Studies,,number_of_subjects,Number of subjects,int,,false,,"The number of subjects that participated to the study",,,,,,,,,
 Studies,,also_known,Also Known In,ref_array,,false,,The study also exists in …,,AlsoKnownIn,,${name_system},,,,,
-Studies,,collections,Collections,refback,,false,true,,,Collections,studies,,,,,,
+Studies,,collections,Collections,refback,,false,true,,,Collections,studies,${name},,,,,
 Studies,,national_node,National Node,ref,,true,,The study originates from this national node.,,NationalNodes,,${description},,,,,

data/biobank-directory/ontologies/ServiceCategories.csv

@@ -0,0 +1,7 @@
+order,name,label,parent,codesystem,code,ontologyTermURI,definition
+1,biobankingElsiServices,Biobanking & ELSI Services,,,,,,
+2,sampleBioanalyticServices,Sample & Bioanalytical Services,,,,,,
+3,imagingServices,Imaging Services,,,,,,
+4,bioinformaticsDataScienceServices,Bioinformatics & Data Science Services,,,,,,
+5,consultingTrainingEducationServices,Consulting & Training & Education Services,,,,,,
+6,specializationsInResearchAreas,Specializations in Areas of Research,,,,,,