diff options
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 24 | ||||
| -rw-r--r-- | bh20sequploader/bh20seq-shex.rdf | 10 |
2 files changed, 18 insertions, 16 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index 2b36e99..bc652a6 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -191,16 +191,16 @@ $graph: _id: http://purl.obolibrary.org/obo/OBI_0600047 _type: "@id" noLinkCheck: true + assembly_method: + doc: Assembly method refers to how the reads were assembled into contigs for which either a de novo (http://purl.obolibrary.org/obo/GENEPIO_0001628) or mapping/reference based (http://purl.obolibrary.org/obo/GENEPIO_0002028) strategy is used. + type: string + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/GENEPIO_0000090 alignment_protocol: doc: Field for additional information on the pipeline applied to obtain the assembly type: string? jsonldPredicate: _id: http://www.ebi.ac.uk/efo/EFO_0004917 - assembly_method: - doc: Assembly method refers to how the reads were assembled into contigs for which either a de novo (http://purl.obolibrary.org/obo/GENEPIO_0001628) or mapping/reference based (http://purl.obolibrary.org/obo/GENEPIO_0002028) strategy is used. - type: string? - jsonldPredicate: - _id: http://purl.obolibrary.org/obo/GENEPIO_0000090 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: double[]? @@ -231,23 +231,25 @@ $graph: jsonldPredicate: _id: http://semanticscience.org/resource/SIO_000172 originating_lab: - doc: Name of the laboratory that took the sample + doc: Laboratory where the sample originates from sample type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/NCIT_C37984 lab_address: - doc: Address of the laboratory where the sample was taken + doc: Address of the laboratory type: string? jsonldPredicate: - _id: http://purl.obolibrary.org/obo/NCIT_C37900 - provider_sample_id: + _id: http://purl.obolibrary.org/obo/NCIT_C25407 + provider: + doc: Provider of the sample type: string? jsonldPredicate: - _id: http://www.ebi.ac.uk/efo/EFO_0001741 + _id: http://purl.obolibrary.org/obo/NCIT_C37900 submitter_sample_id: + doc: Identifer given to the sample by the submitter type: string? jsonldPredicate: - _id: http://purl.obolibrary.org/obo/NCIT_C42781 + _id: http://purl.obolibrary.org/obo/NCIT_C25364 publication: doc: Reference to publication of this sample (e.g. DOI, pubmed ID, ...) type: string? diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf index 602f6a0..365a6e6 100644 --- a/bh20sequploader/bh20seq-shex.rdf +++ b/bh20sequploader/bh20seq-shex.rdf @@ -54,9 +54,9 @@ PREFIX wikidata: <http://www.wikidata.org/entity/> 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_C25407 xsd:string ?; #(lab address), Address, optional, string + obo:NCIT_C37900 xsd:string ?; #(provider), Provider, optional, string + obo:NCIT_C25364 xsd:string ?; #(submitter_sample_id), identifier, 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 @@ -64,8 +64,8 @@ PREFIX wikidata: <http://www.wikidata.org/entity/> :technologyShape { obo:OBI_0600047 IRI {1,3} ; #(sample_sequencing_technology), sequencing assay, optional - efo:EFO_0004917 xsd:string ; #(alignment_protocol), high throughput sequence alignment protocol, optional - obo:GENEPIO_0000090 [obo:GENEPIO_0001628 obo:GENEPIO_0002028 ] ? ; #(assembly method), assembly method, optional, one of the two + obo:GENEPIO_0000090 [obo:GENEPIO_0001628 obo:GENEPIO_0002028 ] ; #(assembly method), assembly method, mandatory, one of the two + efo:EFO_0004917 xsd:string ?; #(alignment_protocol), high throughput sequence alignment protocol, 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 } |