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-rw-r--r--bh20sequploader/bh20seq-schema.yml15
-rw-r--r--bh20sequploader/bh20seq-shex.rdf5
-rw-r--r--example/maximum_metadata_example.yaml1
-rw-r--r--example/minimal_metadata_example.yaml2
4 files changed, 17 insertions, 6 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index d3e992a..99e1a11 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -49,6 +49,7 @@ $graph:
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C25688
_type: "@id"
+ noLinkCheck: true
host_treatment:
doc: Process in which the act is intended to modify or alter host status
type: string?
@@ -59,6 +60,13 @@ $graph:
type: string[]?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/VO_0000002
+ ethnicity:
+ doc: Ethinicity of the host e.g. http://purl.obolibrary.org/obo/HANCESTRO_0010
+ type: string?
+ jsonldPredicate:
+ _id: http://semanticscience.org/resource/SIO_001014
+ _type: "@id"
+ noLinkCheck: true
additional_host_information:
doc: Field for additional host information
type: string?
@@ -91,7 +99,7 @@ $graph:
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0001895
collecting_institution:
- doc: Institute that was responsible of sampeling
+ doc: Institute that was responsible for sampeling
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C41206
@@ -118,12 +126,13 @@ $graph:
jsonldPredicate:
_id: http://edamontology.org/data_2091
_type: "@id"
+ noLinkCheck: true
- name: virusSchema
type: record
fields:
virus_species:
- doc: The name of a taxon from the NCBI taxonomy database
+ doc: The name of virus species from the NCBI taxonomy database, e.g. http://purl.obolibrary.org/obo/NCBITaxon_2697049 for Severe acute respiratory syndrome coronavirus 2
type: string
jsonldPredicate:
_id: http://edamontology.org/data_1875
@@ -152,7 +161,7 @@ $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. [100]) - if multiple technologies were used multiple float values can be submitted e.g. [100, 20]
- type: float[]?
+ type: double[]?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/FLU_0000848
additional_technology_information:
diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf
index fe6deee..cdf2296 100644
--- a/bh20sequploader/bh20seq-shex.rdf
+++ b/bh20sequploader/bh20seq-shex.rdf
@@ -27,6 +27,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
efo:EFO_0000727 xsd:string ?;
obo:VO_0000002 xsd:string {0,10};
sio:SIO_001167 xsd:string ?;
+ sio:SIO_001014 [ obo:HANCESTRO_~ ] ? ; #ethnicity
}
:sampleShape {
@@ -42,7 +43,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
}
:submitterShape {
- obo:NCIT_C42781 xsd:string * ;
+ obo:NCIT_C42781 xsd:string + ;
sio:SIO_000116 xsd:string *;
sio:SIO_000172 xsd:string ?;
obo:NCIT_C37984 xsd:string ?;
@@ -57,7 +58,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
:technologyShape {
obo:OBI_0600047 IRI {0,3} ;
efo:EFO_0002699 xsd:string ?;
- obo:FLU_0000848 xsd:float {0,3};
+ obo:FLU_0000848 xsd:double OR xsd:integer {0,3};
sio:SIO_001167 xsd:string ?;
}
diff --git a/example/maximum_metadata_example.yaml b/example/maximum_metadata_example.yaml
index 0ba9ada..1bc70d7 100644
--- a/example/maximum_metadata_example.yaml
+++ b/example/maximum_metadata_example.yaml
@@ -9,6 +9,7 @@ host:
host_health_status: http://purl.obolibrary.org/obo/NCIT_C25269
host_treatment: Process in which the act is intended to modify or alter host status (Compounds)
host_vaccination: [vaccines1,vaccine2]
+ ethnicity: http://purl.obolibrary.org/obo/HANCESTRO_0010
additional_host_information: Optional free text field for addtional information
sample:
diff --git a/example/minimal_metadata_example.yaml b/example/minimal_metadata_example.yaml
index 1e8d3f5..51f8a87 100644
--- a/example/minimal_metadata_example.yaml
+++ b/example/minimal_metadata_example.yaml
@@ -5,7 +5,7 @@ host:
sample:
sample_id: XX
- collection_date: 2020-01
+ collection_date: "2020-01-01"
collection_location: http://www.wikidata.org/entity/Q148
virus: