From c5fe5de7e4c77bfb48b1ae2f662c2d9cc120c06e Mon Sep 17 00:00:00 2001
From: lltommy
Date: Wed, 11 Nov 2020 09:54:56 +0100
Subject: restricting specimen_source to obo:NCIT which would have prevented
 the ncbi taxon bug

---
 bh20sequploader/bh20seq-options.yml | 2 ++
 bh20sequploader/bh20seq-shex.rdf    | 4 ++--
 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};
-- 
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