Schema changes from @LLTommy

2 files changed, 38 insertions, 39 deletions

diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 982447c..3d8604a 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -21,7 +21,7 @@ $graph:
           identity: true
     host_id:
         doc: Identifer for the host. If you submit multiple samples from the same host, use the same host_id for those samples
-        type: string
+        type: string?
         jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_000115
     host_sex:
@@ -66,16 +66,27 @@ $graph:
 - name: sampleSchema
   type: record
   fields:
+    collection_date:
+      doc: Date when the sample was taken
+      type: string
+      jsonldPredicate:
+        _id: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164
+    collection_location:
+      doc: Geographical location where the sample was collected as wikidata reference, e.g. http://www.wikidata.org/entity/Q148 (China)
+      type: string
+      jsonldPredicate:
+        _id: http://purl.obolibrary.org/obo/GAZ_00000448
+        _type: "@id"
     collector_name:
       doc: Name of the person that took the sample
-      type: string
+      type: string?
       jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/OBI_0001895
     collecting_institution:
       doc: Institute that was responsible of sampeling
-      type: string
+      type: string?
       jsonldPredicate:
-          _id: http://semanticscience.org/resource/SIO_001167
+          _id: http://purl.obolibrary.org/obo/NCIT_C41206
     specimen_source:
       doc: Method how the specimen was derived as NCIT IRI, e.g. http://purl.obolibrary.org/obo/NCIT_C155831 (=nasopharyngeal swab)
       type: string?
@@ -89,19 +100,6 @@ $graph:
       jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/OBI_0001479
           _type: "@id"
-          identity: true
-    collection_date:
-      doc: Date when the sample was taken
-      type: string
-      jsonldPredicate:
-          _id: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164
-    collection_location:
-      doc: Geographical location where the sample was collected as wikidata reference, e.g. http://www.wikidata.org/entity/Q148 (China)
-      type: string
-      jsonldPredicate:
-        _id: http://purl.obolibrary.org/obo/GAZ_00000448
-        _type: "@id"
-        identity: true
     sample_storage_conditions:
       doc: Information about storage of a specified type, e.g.  frozen specimen, paraffin, fresh ....
       type: string?
@@ -114,7 +112,7 @@ $graph:
           _id: http://semanticscience.org/resource/SIO_001167
     sample_id:
       doc: Id of the sample as defined by the submitter
-      type: string
+      type: string?
       jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_000115
     source_database_accession:
@@ -167,7 +165,7 @@ $graph:
       jsonldPredicate:
         _id: http://purl.obolibrary.org/obo/FLU_0000848
     sequencing_coverage2:
-      doc: If a second sequence technology was use you can submit its coverage here
+      doc: If a second sequence technology was used you can submit its coverage here
       type: float?
       jsonldPredicate:
         _id: http://purl.obolibrary.org/obo/FLU_0000848
@@ -180,9 +178,14 @@ $graph:
 - name: submitterSchema
   type: record
   fields:
+    authors:
+      doc: Name of the author(s)
+      type: string
+      jsonldPredicate:
+          _id: http://purl.obolibrary.org/obo/NCIT_C42781
     submitter_name:
       doc: Name of the submitter
-      type: string
+      type: string?
       jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_000116
     submitter_address:
@@ -192,7 +195,7 @@ $graph:
           _id: http://semanticscience.org/resource/SIO_000172
     originating_lab:
       doc: Name of the laboratory that took the sample
-      type: string
+      type: string?
       jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/NCIT_C37984
     lab_address:
@@ -208,11 +211,6 @@ $graph:
       type: string?
       jsonldPredicate:
           _id: http://www.ebi.ac.uk/efo/EFO_0001741
-    authors:
-      doc: Name of the author(s)
-      type: string?
-      jsonldPredicate:
-          _id: http://purl.obolibrary.org/obo/NCIT_C42781
     publication:
       doc: Reference to publication of this sample (e.g. DOI, pubmed ID, ...)
       type: string?
@@ -232,7 +230,7 @@ $graph:
   fields:
     host: hostSchema
     sample: sampleSchema
-    virus: virusSchema?
+    virus: virusSchema
     technology: technologySchema
     submitter: submitterSchema
     id:
diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf
index 8d3f5fc..6e646c7 100644
--- a/bh20sequploader/bh20seq-shex.rdf
+++ b/bh20sequploader/bh20seq-shex.rdf
@@ -7,6 +7,7 @@ PREFIX sio: <http://semanticscience.org/resource/>
 PREFIX efo: <http://www.ebi.ac.uk/efo/>
 PREFIX evs: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
 PREFIX edam: <http://edamontology.org/>
+PREFIX wikidata: <http://www.wikidata.org/entity/>
 
 :submissionShape {
   MainSchema:host   @:hostShape ;
@@ -18,8 +19,8 @@ PREFIX edam: <http://edamontology.org/>
 
 :hostShape  {
   	efo:EFO_0000532 [ obo:NCBITaxon_~ ] ;
-    obo:PATO_0000047 [ obo:NCIT_C20197  obo:NCIT_C27993  obo:NCIT_C17998 ] ;
-    sio:SIO_000115 xsd:string ;
+    sio:SIO_000115 xsd:string ?;
+    obo:PATO_0000047 [ obo:PATO_0000384 obo:PATO_0000383 ] ?;
     obo:PATO_0000011 xsd:integer ?;
     obo:NCIT_C42574 [ obo:UO_~ ] ?;
     sio:SIO_001167 xsd:string ?;
@@ -27,20 +28,20 @@ PREFIX edam: <http://edamontology.org/>
 }
 
 :sampleShape  {
-    obo:OBI_0001895 xsd:string ;
-    sio:SIO_000115 xsd:string ;
-    sio:SIO_001167 xsd:string ;
-	evs:C25164 xsd:string ?;
-    obo:GAZ_00000448 [obo:GAZ_~] ?;
+	evs:C25164 xsd:string?;
+    obo:GAZ_00000448 [wikidata:~] ;
+    obo:OBI_0001895 xsd:string ?;
+    sio:SIO_001167 xsd:string ?;
+    sio:SIO_000115 xsd:string ?;
     obo:OBI_0001472 xsd:string ?;
-    obo:OBI_0001479 xsd:string ?;
+    obo:OBI_0001479 IRI {0,2};
 }
 
 :submitterShape {
-    sio:SIO_000116 xsd:string ;
-	obo:NCIT_C37984 xsd:string ;
+    obo:NCIT_C42781 xsd:string ;
+	obo:NCIT_C37984 xsd:string ?;
 	obo:NCIT_C37900 xsd:string ?;
-    obo:NCIT_C42781 xsd:string ?;
+    sio:SIO_000116 xsd:string ?;
     obo:OBI_0600047 xsd:string ?;
     sio:SIO_000115 /https:\u002F\u002Forcid.org\u002F.{4}-.{4}-.{4}-.{4}/?;
     sio:SIO_000172 xsd:string ?;
@@ -48,7 +49,7 @@ PREFIX edam: <http://edamontology.org/>
 }
 
 :technologyShape {
-    obo:OBI_0600047 xsd:string ;
+    obo:OBI_0600047 IRI {0,2} ;
     obo:FLU_0000848 xsd:integer ?;
     efo:EFO_0002699 xsd:string ?;
 }