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-rw-r--r--bh20sequploader/bh20seq-schema.yml15
-rw-r--r--bh20sequploader/supporting_webuploader.yml20
-rw-r--r--bh20sequploader/validation_shape.rdf59
3 files changed, 87 insertions, 7 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 2d2e4c9..a901be0 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -23,11 +23,12 @@ $graph:
type: string
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000115
- host_common_name:
- doc: Text label for the host species (e.g. homo sapiens)
- type: string?
- jsonldPredicate:
- _id: http://purl.obolibrary.org/obo/NOMEN_0000037
+# Removed_common_name. Not necessary since we turned species into IRI
+# host_common_name:
+# doc: Text label for the host species (e.g. homo sapiens)
+# type: string?
+# jsonldPredicate:
+# _id: http://purl.obolibrary.org/obo/NOMEN_0000037
host_sex:
doc: Sex of the host as define in NCIT, IRI expected (http://purl.obolibrary.org/obo/C20197 (Male), http://purl.obolibrary.org/obo/NCIT_C27993 (Female) or unkown (http://purl.obolibrary.org/obo/NCIT_C17998))
type: string
@@ -120,7 +121,7 @@ $graph:
fields:
virus_species:
doc: The name of a taxon from the NCBI taxonomy database
- type: string?
+ type: string
jsonldPredicate:
_id: http://edamontology.org/data_1875
_type: "@id"
@@ -145,7 +146,7 @@ $graph:
_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: string?
+ type: int?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/FLU_0000848
diff --git a/bh20sequploader/supporting_webuploader.yml b/bh20sequploader/supporting_webuploader.yml
new file mode 100644
index 0000000..5ad8f6c
--- /dev/null
+++ b/bh20sequploader/supporting_webuploader.yml
@@ -0,0 +1,20 @@
+host_age_unit:
+ year: http://purl.obolibrary.org/obo/UO_0000036
+ month: http://purl.obolibrary.org/obo/UO_0000035
+ week: http://purl.obolibrary.org/obo/UO_0000035
+ day: http://purl.obolibrary.org/obo/UO_0000034
+ hour: http://purl.obolibrary.org/obo/UO_0000032
+
+host_sex:
+ Male: http://purl.obolibrary.org/obo/C20197
+ Female: http://purl.obolibrary.org/obo/NCIT_C27993
+ unknown: http://purl.obolibrary.org/obo/NCIT_C17998
+
+host_species:
+ OLS-ontology: ncbitaxon
+
+virus_species:
+ OLS-ontology: ncbitaxon
+
+collection_location:
+ OLS-ontology: gaz \ No newline at end of file
diff --git a/bh20sequploader/validation_shape.rdf b/bh20sequploader/validation_shape.rdf
new file mode 100644
index 0000000..1d1e7d2
--- /dev/null
+++ b/bh20sequploader/validation_shape.rdf
@@ -0,0 +1,59 @@
+PREFIX : <http://whatever/>
+PREFIX MainSchema: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
+PREFIX hostSchema: <http://biohackathon.org/bh20-seq-schema#hostSchema/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+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/>
+
+:submissionShape {
+ MainSchema:host @:hostShape ;
+ MainSchema:sample @:sampleShape ;
+ MainSchema:submitter @:submitterShape ;
+ MainSchema:technology @:technologyShape ;
+ MainSchema:virus @:virusShape;
+}
+
+:hostShape {
+ efo:EFO_0000532 [ obo:NCBITaxon_~ ] ;
+ obo:PATO_0000047 [ obo:NCIT_C20197 obo:NCIT_C27993 obo:NCIT_C17998 ] ;
+ sio:SIO_000115 xsd:string ;
+ obo:PATO_0000011 xsd:integer ?;
+ obo:NCIT_C42574 [ obo:UO_~ ] ?;
+ sio:SIO_001167 xsd:string ?;
+ efo:EFO_0000727 xsd:string ?;
+}
+
+: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_~] ?;
+ obo:OBI_0001472 xsd:string ?;
+ obo:OBI_0001479 xsd:string ?;
+}
+
+:submitterShape {
+ sio:SIO_000116 xsd:string ;
+ obo:NCIT_C37984 xsd:string ;
+ obo:NCIT_C37900 xsd:string ?;
+ obo:NCIT_C42781 xsd:string ?;
+ obo:OBI_0600047 xsd:string ?;
+ sio:SIO_000115 /https:\u002F\u002Forcid.org\u002F[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}/?;
+ sio:SIO_000172 xsd:string ?;
+ efo:EFO_0001741 xsd:string ?;
+}
+
+:technologyShape {
+ obo:OBI_0600047 xsd:string ;
+ obo:FLU_0000848 xsd:integer ?;
+ efo:EFO_0002699 xsd:string ?;
+}
+
+:virusShape{
+ edam:data_1875 [ obo:NCBITaxon_~ ] ;
+ sio:SIO_010055 xsd:string ?;
+} \ No newline at end of file