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-rw-r--r--bh20sequploader/bh20seq-schema.yml52
-rw-r--r--bh20sequploader/bh20seq-shex.rdf25
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 ?;
}