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-rw-r--r--bh20sequploader/bh20seq-options.yml9
-rw-r--r--bh20sequploader/bh20seq-schema.yml2
-rw-r--r--bh20sequploader/bh20seq-shex.rdf2
3 files changed, 11 insertions, 2 deletions
diff --git a/bh20sequploader/bh20seq-options.yml b/bh20sequploader/bh20seq-options.yml
index da47e1a..68f6e79 100644
--- a/bh20sequploader/bh20seq-options.yml
+++ b/bh20sequploader/bh20seq-options.yml
@@ -14,6 +14,15 @@ host_sex:
Male: http://purl.obolibrary.org/obo/PATO_0000384
Female: http://purl.obolibrary.org/obo/PATO_0000383
+host_health_status:
+ healthy: http://purl.obolibrary.org/obo/NCIT_C115935
+ asymptomatic: http://purl.obolibrary.org/obo/NCIT_C3833
+ sympotmatic: http://purl.obolibrary.org/obo/NCIT_C25269
+ admitted to hospital: http://purl.obolibrary.org/obo/GENEPIO_0002020
+ discharged from hospital: http://purl.obolibrary.org/obo/GENEPIO_0001849
+ dead: http://purl.obolibrary.org/obo/NCIT_C28554
+ alive: http://purl.obolibrary.org/obo/NCIT_C37987
+
sample_sequencing_technology:
Illumina NextSeq 500: http://www.ebi.ac.uk/efo/EFO_0009173
Illumina NextSeq 550: http://www.ebi.ac.uk/efo/EFO_0008566
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 80013c3..232ccc6 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -44,7 +44,7 @@ $graph:
_type: "@id"
noLinkCheck: true
host_health_status:
- doc: A condition or state at a particular time
+ doc: A condition or state at a particular time, must be one of the following (obo:NCIT_C115935 obo:NCIT_C3833 obo:NCIT_C25269 obo:GENEPIO_0002020 obo:GENEPIO_0001849 obo:NCIT_C28554 obo:NCIT_C37987)
type: string?
jsonldPredicate: http://purl.obolibrary.org/obo/NCIT_C25688
host_treatment:
diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf
index 8d0055e..bb15f91 100644
--- a/bh20sequploader/bh20seq-shex.rdf
+++ b/bh20sequploader/bh20seq-shex.rdf
@@ -23,7 +23,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
obo:PATO_0000047 [ obo:PATO_0000384 obo:PATO_0000383 ] ?;
obo:PATO_0000011 xsd:integer ?;
obo:NCIT_C42574 [ obo:UO_~ ] ?;
- obo:NCIT_C25688 xsd:string ? ;
+ 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 ?;
sio:SIO_001167 xsd:string ?;