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authorlltommy2020-04-19 19:47:39 +0200
committerlltommy2020-04-19 19:47:39 +0200
commit47666ab547da0c2fbdc2026f955d7d7b615d11fb (patch)
tree337161e1474ee0c80bae1245e4bd6100f65f0654 /bh20sequploader/bh20seq-options.yml
parent6d477eedd556c0adfc16cdd0ecd67a5144362dcf (diff)
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Updating NCBI dictonaries, adding UI options, small yaml schema changes
Diffstat (limited to 'bh20sequploader/bh20seq-options.yml')
-rw-r--r--bh20sequploader/bh20seq-options.yml41
1 files changed, 37 insertions, 4 deletions
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