From 47666ab547da0c2fbdc2026f955d7d7b615d11fb Mon Sep 17 00:00:00 2001
From: lltommy
Date: Sun, 19 Apr 2020 19:47:39 +0200
Subject: Updating NCBI dictonaries, adding UI options, small yaml schema
 changes

---
 bh20sequploader/bh20seq-options.yml | 41 +++++++++++++++++++++++++++++++++----
 1 file changed, 37 insertions(+), 4 deletions(-)

(limited to 'bh20sequploader/bh20seq-options.yml')

diff --git a/bh20sequploader/bh20seq-options.yml b/bh20sequploader/bh20seq-options.yml
index d05be5a..da47e1a 100644
--- a/bh20sequploader/bh20seq-options.yml
+++ b/bh20sequploader/bh20seq-options.yml
@@ -11,7 +11,40 @@ host_age_unit:
   Hours: http://purl.obolibrary.org/obo/UO_0000032
 
 host_sex:
-  Male: http://purl.obolibrary.org/obo/NCIT_C20197
-  Female: http://purl.obolibrary.org/obo/NCIT_C27993
-  Intersex: http://purl.obolibrary.org/obo/NCIT_C45908
-  Unknown: http://purl.obolibrary.org/obo/NCIT_C17998
+  Male: http://purl.obolibrary.org/obo/PATO_0000384
+  Female: http://purl.obolibrary.org/obo/PATO_0000383
+
+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
+  Illumina HiSeq X: http://www.ebi.ac.uk/efo/EFO_0008567
+  Illumina MiSeq: http://www.ebi.ac.uk/efo/EFO_0004205
+  Illumina: http://purl.obolibrary.org/obo/OBI_0000759
+  IonTorrent: http://purl.obolibrary.org/obo/NCIT_C125894
+  Oxford Nanopore MinION: http://www.ebi.ac.uk/efo/EFO_0008632
+  Oxford Nanopore Sequencing: http://purl.obolibrary.org/obo/NCIT_C146818
+  Sanger dideoxy sequencing: http://purl.obolibrary.org/obo/NCIT_C19641
+
+sample_sequencing_technology2:
+  Illumina NextSeq 500: http://www.ebi.ac.uk/efo/EFO_0009173
+  Illumina NextSeq 550: http://www.ebi.ac.uk/efo/EFO_0008566
+  Illumina HiSeq X: http://www.ebi.ac.uk/efo/EFO_0008567
+  Illumina MiSeq: http://www.ebi.ac.uk/efo/EFO_0004205
+  Illumina: http://purl.obolibrary.org/obo/OBI_0000759
+  IonTorrent: http://purl.obolibrary.org/obo/NCIT_C125894
+  Ion Semiconductor Sequencing: http://purl.obolibraryorg/obo/NCIT_C125894
+  Oxford Nanopore MinION: http://www.ebi.ac.uk/efo/EFO_0008632
+  Oxford Nanopore Sequencing: http://purl.obolibrary.org/obo/NCIT_C146818
+  Sanger dideoxy sequencing: http://purl.obolibrary.org/obo/NCIT_C19641
+
+specimen_source:
+  nasopharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155831
+  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
+
+specimen_source2:
+  nasopharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155831
+  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
-- 
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