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authorlltommy2020-11-11 09:54:56 +0100
committerlltommy2020-11-11 09:54:56 +0100
commitc5fe5de7e4c77bfb48b1ae2f662c2d9cc120c06e (patch)
tree5d2265d266958fe52b7e32e97d6ec0226d0a495e /bh20sequploader
parent7e3509fed5c2824f1eeb6c6d2debfbd5f68f691d (diff)
downloadbh20-seq-resource-c5fe5de7e4c77bfb48b1ae2f662c2d9cc120c06e.tar.gz
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bh20-seq-resource-c5fe5de7e4c77bfb48b1ae2f662c2d9cc120c06e.zip
restricting specimen_source to obo:NCIT which would have prevented the ncbi taxon bug
Diffstat (limited to 'bh20sequploader')
-rw-r--r--bh20sequploader/bh20seq-options.yml2
-rw-r--r--bh20sequploader/bh20seq-shex.rdf4
2 files changed, 4 insertions, 2 deletions
diff --git a/bh20sequploader/bh20seq-options.yml b/bh20sequploader/bh20seq-options.yml
index d1ea398..02b7377 100644
--- a/bh20sequploader/bh20seq-options.yml
+++ b/bh20sequploader/bh20seq-options.yml
@@ -44,3 +44,5 @@ specimen_source:
oropharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155835
sputum: http://purl.obolibrary.org/obo/NCIT_C13278
bronchoalveolar lavage fluid: http://purl.obolibrary.org/obo/NCIT_C13195
+ saliva: http://purlobolibrary.org/obo/NCIT_C13275
+ aspirate: http://purl.obolibrary.org/obo/NCIT_C13347
diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf
index 89ecd00..6139e55 100644
--- a/bh20sequploader/bh20seq-shex.rdf
+++ b/bh20sequploader/bh20seq-shex.rdf
@@ -30,7 +30,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
efo:EFO_0000727 xsd:string ?;
obo:VO_0000002 xsd:string {0,10};
sio:SIO_001167 xsd:string ?;
- sio:SIO_001014 [ obo:HANCESTRO_~ ] ? ; #ethnicity
+ sio:SIO_001014 [ obo:HANCESTRO_~ ] ? ; #ethnicity from obo:HANCESTRO
}
:sampleShape {
@@ -39,7 +39,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
obo:GAZ_00000448 [wikidata:~] ;
obo:OBI_0001895 xsd:string ?;
obo:NCIT_C41206 xsd:string ?;
- obo:OBI_0001479 IRI {0,2};
+ 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};