diff options
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 15 | ||||
| -rw-r--r-- | bh20sequploader/bh20seq-shex.rdf | 5 | ||||
| -rw-r--r-- | example/maximum_metadata_example.yaml | 1 | ||||
| -rw-r--r-- | example/minimal_metadata_example.yaml | 2 |
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: |