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-rw-r--r--bh20sequploader/bh20seq-schema.yml24
-rw-r--r--bh20sequploader/bh20seq-shex.rdf10
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
}