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-rw-r--r--bh20sequploader/bh20seq-shex.rdf73
1 files changed, 38 insertions, 35 deletions
diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf
index 11eb75e..6e2493b 100644
--- a/bh20sequploader/bh20seq-shex.rdf
+++ b/bh20sequploader/bh20seq-shex.rdf
@@ -21,54 +21,57 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
MainSchema:license @:licenseShape ?;
}
+## documentation: #(name of option in yaml), ontology label, mandatory|optional, type
+## entries marked with ?????? need review
+
:hostShape {
- efo:EFO_0000532 [ obo:NCBITaxon_~ ] ;
- sio:SIO_000115 xsd:string ?;
- obo:PATO_0000047 [ obo:PATO_0000384 obo:PATO_0000383 obo:PATO_0001340] ?;
- obo:PATO_0000011 xsd:integer ?;
- obo:NCIT_C42574 [ obo:UO_~ ] ?;
- obo:NCIT_C25688 [obo:NCIT_C115935 obo:NCIT_C3833 obo:NCIT_C25269 obo:GENEPIO_0002020 obo:GENEPIO_0001849 obo:NCIT_C28554 obo:NCIT_C37987 ] ? ;
- efo:EFO_0000727 xsd:string ?;
- obo:VO_0000002 xsd:string {0,10};
- sio:SIO_001167 xsd:string ?;
- sio:SIO_001014 [ obo:HANCESTRO_~ ] ? ; #ethnicity from obo:HANCESTRO
+ efo:EFO_0000532 [ obo:NCBITaxon_~ ] ; #(host_species host), mandatory field, from namespace obo:NCBITaxon
+ sio:SIO_000115 xsd:string ?; #(host_id), identifier, optional string
+ obo:PATO_0000047 [ obo:PATO_0000384 obo:PATO_0000383 obo:PATO_0001340] ?; #(host_sex) biological sex, optional, one selected value
+ obo:PATO_0000011 xsd:integer ?; #(host_age) age, optional integer
+ obo:NCIT_C42574 [ obo:UO_~ ] ?; #host_age_unit, optional from namespace obo:UO
+ obo:NCIT_C25688 [obo:NCIT_C115935 obo:NCIT_C3833 obo:NCIT_C25269 obo:GENEPIO_0002020 obo:GENEPIO_0001849 obo:NCIT_C28554 obo:NCIT_C37987 ] ? ; #(host_health_status) status, optional, one selected value
+ efo:EFO_0000727 xsd:string ?; #(host_treatment), treatment, optional
+ obo:VO_0000002 xsd:string {0,10}; #(host_vaccination), vaccination, optional list of String 0-10
+ sio:SIO_001014 [ obo:HANCESTRO_~ ] ? ; #(ethnicity), ethnicity from obo:HANCESTRO
+ sio:SIO_001167 xsd:string ?; #(additional_host_information), comment, optional, string
}
:sampleShape {
- sio:SIO_000115 xsd:string;
- evs:C25164 xsd:string;
- obo:GAZ_00000448 [wikidata:~] ;
- obo:OBI_0001895 xsd:string ?;
- obo:NCIT_C41206 xsd:string ?;
- obo:OBI_000147 [ obo:NCIT_~ ] ? ; #specimen source from obo:NCIT
- obo:OBI_0001472 xsd:string ?;
- sio:SIO_001167 xsd:string ?;
- edam:data_2091 IRI {0,3};
+ sio:SIO_000115 xsd:string; #(sampleId), identifier, mandatory string
+ evs:C25164 xsd:string; #(collection_date), date, mandatory, string but should be date
+ obo:GAZ_00000448 [wikidata:~] ; #(collection_location), geographic location, mandatory, from wikidata namespace
+ obo:OBI_0001895 xsd:string ?; #(collector_name), specimen collector, optional string
+ obo:NCIT_C41206 xsd:string ?; #(collecting_institution) Institute, optional string
+ obo:OBI_0001479 [ obo:NCIT_~ ] ? ; #(specimen_source), specimen from organism, optional, from obo:NCIT
+ obo:OBI_0001472 xsd:string ?; #(sample_storage_conditions), specimen with known storage state, optional string
+ sio:SIO_001167 xsd:string ?; #(additional_collection_information), comment, optional, string
+ edam:data_2091 IRI {0,3}; #(source_database_accession), Accession, optional, IRI 0-3
}
:submitterShape {
- obo:NCIT_C42781 xsd:string + ;
- sio:SIO_000116 xsd:string *;
- sio:SIO_000172 xsd:string ?;
- obo:NCIT_C37984 xsd:string ?;
- obo:NCIT_C37900 xsd:string ?;
- efo:EFO_0001741 xsd:string ?;
- obo:NCIT_C42781 xsd:string ?;
- obo:NCIT_C19026 xsd:string ?;
- sio:SIO_000115 /https:\u002F\u002Forcid.org\u002F.{4}-.{4}-.{4}-.{4}/ {0,10};
- sio:SIO_001167 xsd:string ?;
+ obo:NCIT_C42781 xsd:string + ; #(authors), Author, mandatory, list 1-*
+ sio:SIO_000116 xsd:string *; #(submitter_name), name, optional 0-*
+ sio:SIO_000172 xsd:string ?; #(submitter_address), address, optional, string
+ obo:NCIT_C37984 xsd:string ?; #(originating_lab) Laboratory, optional, string
+ obo:NCIT_C37900 xsd:string ?; #(lab address), Provider, optional, string
+ efo:EFO_0001741 xsd:string ?; #(provider_sample_id), submitter, optional ????????????????????
+ obo:NCIT_C42781 xsd:string ?; #(submitter_sample_id), Author, optional string ????????????????????
+ obo:NCIT_C19026 xsd:string ?; #(publication), Scientific Publication, optional string
+ sio:SIO_000115 /https:\u002F\u002Forcid.org\u002F.{4}-.{4}-.{4}-.{4}/ {0,10}; #(submitter_orcid) identifier, optional but given regular expression
+ sio:SIO_001167 xsd:string ?; #(additional_submitter_information), comment, optional string
}
:technologyShape {
- obo:OBI_0600047 IRI {0,3} ;
- efo:EFO_0002699 xsd:string ?;
- obo:FLU_0000848 xsd:double OR xsd:integer {0,3};
- sio:SIO_001167 xsd:string ?;
+ obo:OBI_0600047 IRI {0,3} ; #(sample_sequencing_technology) sequencing assay, optional ????????????
+ efo:EFO_0002699 xsd:string ?; #(sequence_assembly_method) high throughput sequencer, optional ?????????????
+ obo:FLU_0000848 xsd:double OR xsd:integer {0,3}; #(sequence coverage) sequence coverage, optional
+ sio:SIO_001167 xsd:string ?; #(additional_technology_information), comment, optional, string
}
:virusShape{
- edam:data_1875 [ obo:NCBITaxon_~ ] ;
- sio:SIO_010055 xsd:string ?;
+ edam:data_1875 [ obo:NCBITaxon_~ ] ; # (virus_species) NCBI taxon, mandatory, from namespace obo:NCBITaxon_
+ sio:SIO_010055 xsd:string ?; # (virus_strain) strain, optional string
}
:licenseShape{