Merge branch 'master' into patch-3

1 files changed, 43 insertions, 33 deletions

diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index bbcafc8..9a89979 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -18,17 +18,19 @@ $graph:
         jsonldPredicate:
           _id: http://www.ebi.ac.uk/efo/EFO_0000532
           _type: "@id"
+          noLinkCheck: 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:
-        doc: Sex of the host, IRI expected
+        doc: Sex of the host as defined in PATO, expect male () or female ()
         type: string?
         jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/PATO_0000047
           _type: "@id"
+          noLinkCheck: true
     host_age:
         doc: Age of the host as number (e.g. 50)
         type: int?
@@ -40,10 +42,12 @@ $graph:
         jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/NCIT_C42574
           _type: "@id"
+          noLinkCheck: true
     host_health_status:
-        doc: A condition or state at a particular time
+        doc: A condition or state at a particular time, must be one of the following (obo:NCIT_C115935 obo:NCIT_C3833 obo:NCIT_C25269 obo:GENEPIO_0002020 obo:GENEPIO_0001849 obo:NCIT_C28554 obo:NCIT_C37987)
         type: string?
-        jsonldPredicate: http://purl.obolibrary.org/obo/NCIT_C25688
+        jsonldPredicate:
+          _id: http://purl.obolibrary.org/obo/NCIT_C25688
     host_treatment:
       doc: Process in which the act is intended to modify or alter host status
       type: string?
@@ -63,39 +67,47 @@ $graph:
 - name: sampleSchema
   type: record
   fields:
+    sample_id:
+      doc: Id of the sample as defined by the submitter
+      type: string
+      jsonldPredicate:
+        _id: http://semanticscience.org/resource/SIO_000115
+    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"
+        noLinkCheck: true
     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?
       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?
       jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/OBI_0001479
           _type: "@id"
-    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"
+          noLinkCheck: true
     sample_storage_conditions:
       doc: Information about storage of a specified type, e.g.  frozen specimen, paraffin, fresh ....
       type: string?
@@ -106,11 +118,6 @@ $graph:
       type: string?
       jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_001167
-    sample_id:
-      doc: Id of the sample as defined by the submitter
-      type: string
-      jsonldPredicate:
-          _id: http://semanticscience.org/resource/SIO_000115
     source_database_accession:
       doc: If data is deposit at a public resource (e.g. Genbank, ENA) enter the Accession Id here
       type: string?
@@ -126,6 +133,7 @@ $graph:
       jsonldPredicate:
           _id: http://edamontology.org/data_1875
           _type: "@id"
+          noLinkCheck: true
     virus_strain:
       doc: Name of the virus strain
       type: string?
@@ -137,16 +145,18 @@ $graph:
   fields:
     sample_sequencing_technology:
       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"
+        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
     sequence_assembly_method:
       doc: Protocol which provides instructions on the alignment of sequencing reads to reference genome
       type: string?
@@ -158,7 +168,7 @@ $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
@@ -171,9 +181,14 @@ $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:
@@ -183,7 +198,7 @@ $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:
@@ -199,11 +214,6 @@ $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?
@@ -223,7 +233,7 @@ $graph:
   fields:
     host: hostSchema
     sample: sampleSchema
-    virus: virusSchema?
+    virus: virusSchema
     technology: technologySchema
     submitter: submitterSchema
     id: