Changes to the structure - we use lists now instead of strings where it makes sense. This allows us to have multiple values where in makes sense

3 files changed, 20 insertions, 73 deletions

diff --git a/bh20sequploader/bh20seq-options.yml b/bh20sequploader/bh20seq-options.yml
index 104ed6c..c553f41 100644
--- a/bh20sequploader/bh20seq-options.yml
+++ b/bh20sequploader/bh20seq-options.yml
@@ -35,38 +35,8 @@ sample_sequencing_technology:
   Oxford Nanopore Sequencing: http://purl.obolibrary.org/obo/NCIT_C146818
   Sanger dideoxy sequencing: http://purl.obolibrary.org/obo/NCIT_C19641
 
-sample_sequencing_technology2:
-  Illumina NextSeq 500: http://www.ebi.ac.uk/efo/EFO_0009173
-  Illumina NextSeq 550: http://www.ebi.ac.uk/efo/EFO_0008566
-  Illumina HiSeq X: http://www.ebi.ac.uk/efo/EFO_0008567
-  Illumina MiSeq: http://www.ebi.ac.uk/efo/EFO_0004205
-  Illumina: http://purl.obolibrary.org/obo/OBI_0000759
-  IonTorrent: http://purl.obolibrary.org/obo/NCIT_C125894
-  Ion Semiconductor Sequencing: http://purl.obolibraryorg/obo/NCIT_C125894
-  Oxford Nanopore MinION: http://www.ebi.ac.uk/efo/EFO_0008632
-  Oxford Nanopore Sequencing: http://purl.obolibrary.org/obo/NCIT_C146818
-  Sanger dideoxy sequencing: http://purl.obolibrary.org/obo/NCIT_C19641
-
-sample_sequencing_technology3:
-  Illumina NextSeq 500: http://www.ebi.ac.uk/efo/EFO_0009173
-  Illumina NextSeq 550: http://www.ebi.ac.uk/efo/EFO_0008566
-  Illumina HiSeq X: http://www.ebi.ac.uk/efo/EFO_0008567
-  Illumina MiSeq: http://www.ebi.ac.uk/efo/EFO_0004205
-  Illumina: http://purl.obolibrary.org/obo/OBI_0000759
-  IonTorrent: http://purl.obolibrary.org/obo/NCIT_C125894
-  Ion Semiconductor Sequencing: http://purl.obolibraryorg/obo/NCIT_C125894
-  Oxford Nanopore MinION: http://www.ebi.ac.uk/efo/EFO_0008632
-  Oxford Nanopore Sequencing: http://purl.obolibrary.org/obo/NCIT_C146818
-  Sanger dideoxy sequencing: http://purl.obolibrary.org/obo/NCIT_C19641
-
 specimen_source:
   nasopharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155831
   oropharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155835
   sputum: http://purl.obolibrary.org/obo/NCIT_C13278
   bronchoalveolar lavage fluid: http://purl.obolibrary.org/obo/NCIT_C13195
-
-specimen_source2:
-  nasopharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155831
-  oropharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155835
-  sputum: http://purl.obolibrary.org/obo/NCIT_C13278
-  bronchoalveolar lavage fluid: http://purl.obolibrary.org/obo/NCIT_C13195
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index ea813a0..f36a6e6 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -48,6 +48,7 @@ $graph:
         type: string?
         jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/NCIT_C25688
+          _type: "@id"
     host_treatment:
       doc: Process in which the act is intended to modify or alter host status
       type: string?
@@ -55,7 +56,7 @@ $graph:
           _id: http://www.ebi.ac.uk/efo/EFO_0000727
     host_vaccination:
       doc: List of vaccines given to the host
-      type: string?
+      type: string[]?
       jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/VO_0000002
     additional_host_information:
@@ -96,14 +97,7 @@ $graph:
           _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?
-      jsonldPredicate:
-          _id: http://purl.obolibrary.org/obo/OBI_0001479
-          _type: "@id"
-          noLinkCheck: true
-    specimen_source2:
-      doc: Method how the specimen was derived as NCIT IRI, e.g. http://purl.obolibrary.org/obo/NCIT_C155835 (=throat swabb)
-      type: string?
+      type: string[]?
       jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/OBI_0001479
           _type: "@id"
@@ -119,10 +113,11 @@ $graph:
       jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_001167
     source_database_accession:
-      doc: If data is deposit at a public resource (e.g. Genbank, ENA) enter the Accession Id here
-      type: string?
+      doc: If data is deposit at a public resource (e.g. Genbank, ENA) enter the Accession Id here. Please use a resolveable URL (e.g. http://identifiers.org/insdc/LC522350.1#sequence)
+      type: string[]?
       jsonldPredicate:
           _id: http://edamontology.org/data_2091
+          _type: "@id"
 
 - name: virusSchema
   type: record
@@ -145,21 +140,7 @@ $graph:
   fields:
     sample_sequencing_technology:
       doc: Technology that was used to sequence this sample (e.g Sanger, Nanopor MiniION)
-      type: string?
-      jsonldPredicate:
-        _id: http://purl.obolibrary.org/obo/OBI_0600047
-        _type: "@id"
-        noLinkCheck: true
-    sample_sequencing_technology2:
-      doc: Technology that was used to sequence this sample (e.g Sanger, Nanopor MiniION)
-      type: string?
-      jsonldPredicate:
-        _id: http://purl.obolibrary.org/obo/OBI_0600047
-        _type: "@id"
-        noLinkCheck: true
-    sample_sequencing_technology3:
-      doc: Technology that was used to sequence this sample (e.g Sanger, Nanopor MiniION)
-      type: string?
+      type: string[]?
       jsonldPredicate:
         _id: http://purl.obolibrary.org/obo/OBI_0600047
         _type: "@id"
@@ -170,13 +151,8 @@ $graph:
       jsonldPredicate:
         _id: http://www.ebi.ac.uk/efo/EFO_0002699
     sequencing_coverage:
-      doc: Sequence coverage defined as the average number of reads representing a given nucleotide (e.g. 100x)
-      type: float?
-      jsonldPredicate:
-        _id: http://purl.obolibrary.org/obo/FLU_0000848
-    sequencing_coverage2:
-      doc: If a second sequence technology was used you can submit its coverage here
-      type: float?
+      doc: Sequence coverage defined as the average number of reads representing a given nucleotide (e.g. [100]) - if multiple technologies were used multiple float values can be submitted e.g. [100, 20]
+      type: int[]?
       jsonldPredicate:
         _id: http://purl.obolibrary.org/obo/FLU_0000848
     additional_technology_information:
@@ -189,13 +165,13 @@ $graph:
   type: record
   fields:
     authors:
-      doc: Name of the author(s)
-      type: string
+      doc: Name(s) of the author(s)
+      type: string[]
       jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/NCIT_C42781
     submitter_name:
-      doc: Name of the submitter
-      type: string?
+      doc: Name of the submitter(s)
+      type: string[]?
       jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_000116
     submitter_address:
@@ -228,7 +204,7 @@ $graph:
         _id: http://purl.obolibrary.org/obo/NCIT_C19026
     submitter_orcid:
       doc: ORCID of the submitter as a full URI, e.g. https://orcid.org/0000-0002-1825-0097
-      type: string?
+      type: string[]?
       jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_000115
           _type: "@id"
diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf
index c3b0ae1..4ec957d 100644
--- a/bh20sequploader/bh20seq-shex.rdf
+++ b/bh20sequploader/bh20seq-shex.rdf
@@ -25,7 +25,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
     obo:NCIT_C42574 [ obo:UO_~ ] ?;
 	obo:NCIT_C25688 [obo:NCIT_C115935 obo:NCIT_C3833 obo:NCIT_C25269 obo:GENEPIO_0002020 obo:GENEPIO_0001849 obo:NCIT_C28554 obo:NCIT_C37987 ] ? ;
     efo:EFO_0000727 xsd:string ?;
-    obo:VO_0000002 xsd:string ?;
+    obo:VO_0000002 xsd:string {0,10};
     sio:SIO_001167 xsd:string ?;
 }
 
@@ -38,25 +38,26 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
     obo:OBI_0001479 IRI {0,2};
     obo:OBI_0001472 xsd:string ?;
     sio:SIO_001167 xsd:string ?;
+	edam:data_2091 IRI {0,3};
 }
 
 :submitterShape {
-    obo:NCIT_C42781 xsd:string ;
-    sio:SIO_000116 xsd:string ?;
+    obo:NCIT_C42781 xsd:string * ;
+    sio:SIO_000116 xsd:string *;
     sio:SIO_000172 xsd:string ?;
     obo:NCIT_C37984 xsd:string ?;
     obo:OBI_0600047 xsd:string ?;
   	obo:NCIT_C37900 xsd:string ?;
     efo:EFO_0001741 xsd:string ?;
     obo:NCIT_C19026 xsd:string ?;
-    sio:SIO_000115 /https:\u002F\u002Forcid.org\u002F.{4}-.{4}-.{4}-.{4}/?;
+    sio:SIO_000115 /https:\u002F\u002Forcid.org\u002F.{4}-.{4}-.{4}-.{4}/ {0,10};
     sio:SIO_001167 xsd:string ?;
 }
 
 :technologyShape {
     obo:OBI_0600047 IRI {0,3} ;
     efo:EFO_0002699 xsd:string ?;
-    obo:FLU_0000848 xsd:double {0,2};
+    obo:FLU_0000848 xsd:integer {0,2};
     sio:SIO_001167 xsd:string ?;
 }