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authorlltommy2020-11-12 14:22:08 +0100
committerlltommy2020-11-12 14:22:08 +0100
commit1b5df01d2047ab5c591f2e0400a5c46cb2dc86ea (patch)
tree440c0dfab57cd184caad25542e42aa7bcbe1a9e5 /bh20sequploader
parent2cb5faa2b088cf36c8c41633db137fc020a34529 (diff)
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Proposed new technology shape/yaml structure
Diffstat (limited to 'bh20sequploader')
-rw-r--r--bh20sequploader/bh20seq-schema.yml9
-rw-r--r--bh20sequploader/bh20seq-shex.rdf7
2 files changed, 11 insertions, 5 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 645be5e..2b36e99 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -191,11 +191,16 @@ $graph:
_id: http://purl.obolibrary.org/obo/OBI_0600047
_type: "@id"
noLinkCheck: true
- sequence_assembly_method:
+ 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_0002699
+ _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[]?
diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf
index 6e2493b..602f6a0 100644
--- a/bh20sequploader/bh20seq-shex.rdf
+++ b/bh20sequploader/bh20seq-shex.rdf
@@ -63,10 +63,11 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
}
:technologyShape {
- 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: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: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
+ sio:SIO_001167 xsd:string ?; #(additional_technology_information), comment, optional, string
}
:virusShape{