fix: minor revisions to ontologies to fix import errors

backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/RD3v2Loader.java

@@ -5,6 +5,7 @@
 import java.util.List;
 import org.molgenis.emx2.*;
 import org.molgenis.emx2.io.ImportDataModelTask;
+import org.molgenis.emx2.io.MolgenisIO;
 import org.molgenis.emx2.io.emx2.Emx2;
 import org.molgenis.emx2.tasks.Task;
 
@@ -32,6 +33,7 @@ public void run() {
       }
       List<Row> rows = getProfilesFromAllModels("/portal", List.of());
       getSchema().migrate(Emx2.fromRowList(rows));
+      MolgenisIO.fromClasspathDirectory("/_ontologies", getSchema(), false);
       this.complete();
     } catch (Exception e) {
       this.completeWithError(e.getMessage());

data/_ontologies/Consent document types.csv

@@ -1,5 +1,5 @@
-name,definition,codesystem,code,ontologyTermURI
-informed consent form,"A document that explains all relevant information to assist a human being in understanding the expectations and requirements of participation in a process, and is an instrument in obtaining consent and, after having obtained consent, is a record that such a consent has occurred.",ICO,ICO:0000001,http://purl.obolibrary.org/obo/ICO_0000001
+name,definition,codesystem,code,ontologyTermURI
+informed consent form,A document that explains all relevant information to assist a human being in understanding the expectations and requirements of participation in a process and is an instrument in obtaining consent and after having obtained consent is a record that such a consent has occurred.,ICO,ICO:0000001,http://purl.obolibrary.org/obo/ICO_0000001
 informed consent form containing questionnaire,An informed consent form that contains a questionnaire section.,ICO,ICO:0000104,http://purl.obolibrary.org/obo/ICO_0000104
 informed consent form for clinical research involving children,An informed consent form for clinical study that involves children.,ICO,ICO:0000034,http://purl.obolibrary.org/obo/ICO_0000034
 informed consent form for clinical study,An informed consent form that is used for a clinical study.,ICO,ICO:0000029,http://purl.obolibrary.org/obo/ICO_0000029

data/_ontologies/Organisations.csv

@@ -1,27 +1,27 @@
-name,definition,codesystem,code,ontologyTermURI,type,parent
-ERN Board of Member States,ERN Board of Member States,ROR,00r7apq26,https://ror.org/00r7apq26,index,European Commission
-European Commission,European Commission,ROR,00k4n6c32,https://ror.org/00k4n6c32,Parent,
-ERN BOND,European Reference Network on rare bone diseases,ROR,04crk2m06,https://ror.org/04crk2m06,Child,ERN Board of Member States
-ERN CRANIO,"European Reference Network for rare and/or complex craniofacial anomalies and ear, nose and throat disorders",ROR,032gggv33,https://ror.org/032gggv33,Child,ERN Board of Member States
-Endo-ERN,European Reference Network on Rare Endocrine Conditions,ROR,05s4nk876,https://ror.org/05s4nk876,Child,ERN Board of Member States
-ERN EpiCARE,European Reference Network for rare and complex epilepsies,ROR,0214h3370,https://ror.org/0214h3370,Child,ERN Board of Member States
-ERKNet,"European Reference Network for Rare Kidney Diseases,European Rare Kidney Disease Reference Network",ROR,04x2ddb07,https://ror.org/04x2ddb07,Child,ERN Board of Member States
-ERN-RND,European Reference Network for Rare Neurological Diseases,ROR,05a27za87,https://ror.org/05a27za87,Child,ERN Board of Member States
-ERNICA,European Reference Network for Rare Inherited and Congenital Anomalies,ROR,02h9n4675,https://ror.org/02h9n4675,Child,ERN Board of Member States
-ERN LUNG,European Reference Network on respiratory diseases,ROR,0279ntc65,https://ror.org/0279ntc65,Child,ERN Board of Member States
-ERN Skin,European Reference Network on skin disorders,ROR,0446wcg70,https://ror.org/0446wcg70,Child,ERN Board of Member States
-ERN EURACAN,European Reference Network on rare adult solid cancers,ROR,01rq5e797,https://ror.org/01rq5e797,Child,ERN Board of Member States
-ERN EuroBloodNet,European Reference Network on rare haematological diseases,ROR,04dng8q18,https://ror.org/04dng8q18,Child,ERN Board of Member States
-ERN eUROGEN,European Reference Network on urogenital diseases and conditions,ROR,00y7tet25,https://ror.org/00y7tet25,Child,ERN Board of Member States
-ERN EURO-NMD,European Reference Network on rare neuromuscular diseases,ROR,04x3ta798,https://ror.org/04x3ta798,Child,ERN Board of Member States
-ERN EYE,European Reference Network on rare eye diseases,ROR,029nm1m14,https://ror.org/029nm1m14,Child,ERN Board of Member States
-ERN GENTURIS,European Reference Network on rare genetic tumour risk syndromes,ROR,03pbpa834,https://ror.org/03pbpa834,Child,ERN Board of Member States
-ERN ITHACA,"European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies",ROR,03va0yq34,https://ror.org/03va0yq34,Child,ERN Board of Member States
-MetabERN,European Reference Network on hereditary metabolic disorders,ROR,00xdsr520,https://ror.org/00xdsr520,Child,ERN Board of Member States
-ERN PaedCan,European Reference Network on paediatric cancer,ROR,02dk8t214,https://ror.org/02dk8t214,Child,ERN Board of Member States
-ERN RARE-LIVER,European Reference Network on rare liver diseases,ROR,036e61f39,https://ror.org/036e61f39,Child,ERN Board of Member States
-ERN ReCONNET,European Reference Network on Rare and Complex Connective Tissue and Musculoskeletal Diseases,ROR,04069k268,https://ror.org/04069k268,Child,ERN Board of Member States
-ERN RITA,"European Reference Network on immunodeficiency, autoinflammatory and autoimmune diseases",ROR,0208ges23,https://ror.org/0208ges23,Child,ERN Board of Member States
-ERN TRANSPLANT-CHILD,European Reference Network on Transplantation in Children,ROR,04rr75245,https://ror.org/04rr75245,Child,ERN Board of Member States
-VASCERN,European Reference Network on Rare Multisystemic Vascular Diseases,ROR,005pygq66,https://ror.org/005pygq66,Child,ERN Board of Member States
-UMCG,University Medical Center Groningen,ROR,03cv38k47,https://ror.org/03cv38k47,,
+resource,id,name,pid
+RD3,ERN Board of Member States,ERN Board of Member States,https://ror.org/00r7apq26
+RD3,European Commission,European Commission,https://ror.org/00k4n6c32
+RD3,ERN BOND,ERN BOND,https://ror.org/04crk2m06
+RD3,ERN CRANIO,ERN CRANIO,https://ror.org/032gggv33
+RD3,Endo-ERN,Endo-ERN,https://ror.org/05s4nk876
+RD3,ERN EpiCARE,ERN EpiCARE,https://ror.org/0214h3370
+RD3,ERKNet,ERKNet,https://ror.org/04x2ddb07
+RD3,ERN-RND,ERN-RND,https://ror.org/05a27za87
+RD3,ERNICA,ERNICA,https://ror.org/02h9n4675
+RD3,ERN LUNG,ERN LUNG,https://ror.org/0279ntc65
+RD3,ERN Skin,ERN Skin,https://ror.org/0446wcg70
+RD3,ERN EURACAN,ERN EURACAN,https://ror.org/01rq5e797
+RD3,ERN EuroBloodNet,ERN EuroBloodNet,https://ror.org/04dng8q18
+RD3,ERN eUROGEN,ERN eUROGEN,https://ror.org/00y7tet25
+RD3,ERN EURO-NMD,ERN EURO-NMD,https://ror.org/04x3ta798
+RD3,ERN EYE,ERN EYE,https://ror.org/029nm1m14
+RD3,ERN GENTURIS,ERN GENTURIS,https://ror.org/03pbpa834
+RD3,ERN ITHACA,ERN ITHACA,https://ror.org/03va0yq34
+RD3,MetabERN,MetabERN,https://ror.org/00xdsr520
+RD3,ERN PaedCan,ERN PaedCan,https://ror.org/02dk8t214
+RD3,ERN RARE-LIVER,ERN RARE-LIVER,https://ror.org/036e61f39
+RD3,ERN ReCONNET,ERN ReCONNET,https://ror.org/04069k268
+RD3,ERN RITA,ERN RITA,https://ror.org/0208ges23
+RD3,ERN TRANSPLANT-CHILD,ERN TRANSPLANT-CHILD,https://ror.org/04rr75245
+RD3,VASCERN,VASCERN,https://ror.org/005pygq66
+RD3,UMCG,UMCG,https://ror.org/03cv38k47

data/_ontologies/Resources.csv

@@ -0,0 +1,2 @@
+id,name,type
+RD3,Solve-RD RD3,Other type

data/portal/Biosamples.csv

@@ -6,12 +6,12 @@ Biosamples,,material type,ontology,,,,BiospecimenType,,,,http://purl.obolibrary.
 Biosamples,,pathological state,ontology,,TRUE,,PathologicalState,,,,http://purl.obolibrary.org/obo/NCIT_C28257,"An examination that is performed to determine the extent of the spread of cancer based on histopathologic examination of one or more pathology specimens. Pathologic staging uses evidence acquired during the process of clinical staging, supplemented by histopathologic examination of surgical specimens.","Beacon v2, FAIR Genomes, DCAT examples, RD3"
 Biosamples,,anatomical location,ontology,,TRUE,,AnatomicalLocation,,,,http://purl.obolibrary.org/obo/NCIT_C170983,The specific anatomical or biological region associated with a tissue or organ specimen.,"Beacon v2, FAIR Genomes, DCAT examples, RD3"
 Biosamples,,anatomical location other,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C170983,Additional description on the anatomical or biological region associated with a tissue or organ specimen,"Beacon v2, FAIR Genomes, DCAT examples, RD3"
-Biosamples,,collected at organisation,ontology,,,,Organisations,,,,http://purl.obolibrary.org/obo/OBIB_0000085,The geographic location where biosample collection took place,RD3
+Biosamples,,collected at organisation,ref,,,,Organisations,,,,http://purl.obolibrary.org/obo/OBIB_0000085,The geographic location where biosample collection took place,RD3
 Biosamples,,collected by,ontology_array,,,,Contacts,,,,http://purl.obolibrary.org/obo/OBI_0001769,The person or persons responsible for biosample collection,RD3
 Biosamples,,date of collection,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C82515,Date on which the material was collected,"Beacon v2, FAIR Genomes, DCAT examples"
 Biosamples,,age group of individual at collection,ontology,,,,Age groups,,,,http://purl.obolibrary.org/obo/NCIT_C20587,"A categorical value that groups this individual by age at the time of sample collection (e.g., ""Adult"", ""18-24 years"", etc.)",
 Biosamples,,age of individual at collection,period,,,,,,,,http://purl.obolibrary.org/obo/GENEPIO_0001775,The age of the individual at the time of sample collection,"Beacon v2, DCAT examples"
-Biosamples,,affiliated organisations,ontology_array,,,,Organisations,,,,http://purl.obolibrary.org/obo/NCIT_C25412,One or more associations between the record and an organisation or institution.,RD3
+Biosamples,,affiliated organisations,ref_array,,,,Organisations,,,,http://purl.obolibrary.org/obo/NCIT_C25412,One or more associations between the record and an organisation or institution.,RD3
 Biosamples,,collected from individual,ref,,,,Individuals,,,,http://semanticscience.org/resource/SIO_000244,Reference to the person from whom this material was collected.,"FAIR Genomes, RD3"
 Biosamples,,protocol used,refback,,,,Protocol parameters,,identifier,,http://www.ebi.ac.uk/efo/EFO_0005518,A description of the procedures whereby biological samples for an experiment are sourced.,"Beacon v2, FAIR Genomes, DCAT examples, RD3"
 Biosamples,,registration timestamp,datetime,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25646,"Date and time at which this material was listed or recorded officially, i.e. officially qualified or enrolled.",FAIR Genomes

data/portal/Files.csv

@@ -6,7 +6,7 @@ Files,,path,hyperlink_array,,TRUE,,,,,,http://purl.allotrope.org/ontologies/resu
 Files,,md5 checksum,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C171276,A 32-character hexadecimal number that is computed on a file.,"RD3, DCAT files add-on"
 Files,,format,ontology,,TRUE,,FileFormats,,,,"http://purl.org/dc/terms/FileFormat,http://purl.obolibrary.org/obo/NCIT_C171252","A digital resource format (e.g. BAM, FastQ, gVCF, phenopacket, BED)","Beacon v2 EMX2 add-on, RD3, DCAT files add-on"
 Files,,individuals,ref_array,,,,Individuals,,,,http://purl.obolibrary.org/obo/IAO_0000136,A reference to the individual whom this file is about,"Beacon v2 EMX2 add-on, RD3"
-Files,,biosamples,ref_array,,,,Biosamples,,output samples,,http://purl.obolibrary.org/obo/NCIT_C43376,A reference to one or more samples that are associated with this file,"Beacon v2 EMX2 add-on, RD3"
+Files,,biosamples,ref_array,,,,Biosamples,,,,http://purl.obolibrary.org/obo/NCIT_C43376,A reference to one or more samples that are associated with this file,"Beacon v2 EMX2 add-on, RD3"
 Files,,generated by protocol,ref,,,,Protocol parameters,,,,http://purl.obolibrary.org/obo/OBI_0000272,A reference to the protocol and parameters used to produce this file,RD3
 Files,,included of datasets,ref_array,,,,Datasets,,,,http://purl.obolibrary.org/obo/HSO_0000370,"A reference to one or more datasets that organises records for in a meaningful way (e.g., data releases, subpopulations, cohorts, etc.)",RD3
 Files,,comments,text,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25393,"A written explanation, observation or criticism added to textual material.",RD3

data/portal/Protocol parameters.csv

@@ -4,7 +4,7 @@ Protocol parameters,,identifier,auto_id,1,,,,,,,http://purl.obolibrary.org/obo/N
 Protocol parameters,,protocol,ontology,,,,Protocols,,,,,Link to the protocol that was used,RD3
 Protocol parameters,,date,datetime,,,,,,,,,"When the processing happened","RD3"
 Protocol parameters,,persons involved,ref_array,,,,Contacts,,,,,"Who was involved in the processing","RD3"
-Protocol parameters,,institutions involved,ontology_array,,,,Organisations,,,,http://purl.obolibrary.org/obo/NCIT_C25412,One or more associations between the individual and a organisation or institution.,Delete?
+Protocol parameters,,institutions involved,ref_array,,,,Organisations,,,,http://purl.obolibrary.org/obo/NCIT_C25412,One or more associations between the individual and a organisation or institution.,Delete?
 Protocol parameters,,description,text,,,,,,,,,"Human readible description of the protocol used. In case of standard protocol describe deviations. Could also be a log","RD3"
 Protocol parameters,,input files,ref_array,,,,Files,,,,,"links to files used as input","RD3"
 Protocol parameters,,input samples,ref_array,,,,Biosamples,,,,,"links to samples used as input","RD3"
@@ -20,7 +20,7 @@ Sample preparations,,intended read length,int,,,,,,,,http://purl.obolibrary.org/
 Sample preparations,,barcode,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C43361,A machine-readable representation of information in a visual format on a surface.,RD3
 Sequencing runs,Protocol parameters,,,,,,,,,,http://edamontology.org/topic_3168,"The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes. In FAIR Genomes: Sequencing. Ideally: SequencingRuns.","Beacon v2, FAIR Genomes, DCAT examples,RD3"
 Sequencing runs,,individualId,ref,,,,Individuals,,,,http://purl.obolibrary.org/obo/NCIT_C164337,E.g. Ind001,"Beacon v2,RD3"
-Sequencing runs,,Sequencing centre,ontology,,,,Organisations,,,,http://purl.obolibrary.org/obo/GENEPIO_0001202,A data field which describes the name of the third party company or laboratory that provided services.,"Beacon v2,RD3"
+Sequencing runs,,Sequencing centre,ref,,,,Organisations,,,,http://purl.obolibrary.org/obo/GENEPIO_0001202,A data field which describes the name of the third party company or laboratory that provided services.,"Beacon v2,RD3"
 Sequencing runs,,librarySource,ontology,,,,LibrarySource,,,,http://purl.obolibrary.org/obo/GENEPIO_0001965,E.g. genomic source,"Beacon v2,RD3"
 Sequencing runs,,librarySelection,string,,,,,,,,http://purl.obolibrary.org/obo/GENEPIO_0001940,Edat.g. RANDOM method,"Beacon v2,RD3"
 Sequencing runs,,libraryStrategy,ontology,,,,SequencingMethods,,,,http://purl.obolibrary.org/obo/FIX_0000704,Method used to determine the order of bases in a nucleic acid sequence. In FAIR Genomes: SequencingMethod.,"Beacon v2, FAIR Genomes,RD3"