Updating NCBI dictonaries, adding UI options, small yaml schema changes

3 files changed, 38 insertions, 59 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
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 4cd0865..fc80080 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -23,15 +23,9 @@ $graph:
         type: string
         jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_000115
-# Removed_common_name. Not necessary since we turned species into IRI
-#    host_common_name:
-#        doc: Text label for the host species (e.g. homo sapiens)
-#        type: string?
-#        jsonldPredicate:
-#          _id: http://purl.obolibrary.org/obo/NOMEN_0000037
     host_sex:
         doc: Sex of the host as defined in NCIT, IRI expected (http://purl.obolibrary.org/obo/NCIT_C20197 (Male), http://purl.obolibrary.org/obo/NCIT_C27993 (Female), http://purl.obolibrary.org/obo/NCIT_C45908 (Intersex), or http://purl.obolibrary.org/obo/NCIT_C17998 (Unknown))
-        type: string
+        type: string?
         jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/PATO_0000047
           _type: "@id"
diff --git a/bh20sequploader/supporting_webuploader.yml b/bh20sequploader/supporting_webuploader.yml
deleted file mode 100644
index 3650526..0000000
--- a/bh20sequploader/supporting_webuploader.yml
+++ /dev/null
@@ -1,48 +0,0 @@
-host_age_unit:
-  year: http://purl.obolibrary.org/obo/UO_0000036
-  month: http://purl.obolibrary.org/obo/UO_0000035
-  week: http://purl.obolibrary.org/obo/UO_0000035
-  day: http://purl.obolibrary.org/obo/UO_0000034
-  hour: 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
-  unknown: http://purl.obolibrary.org/obo/NCIT_C17998
-
-sample_sequencing_technology:
-  Illumina NextSeq 500: http://www.ebi.ac.uk/efo/EFO_0009173
-  Oxford Nanopore MinION: http://www.ebi.ac.uk/efo/EFO_0008632
-  Illumina MiSeq: http://www.ebi.ac.uk/efo/EFO_0004205
-  IonTorrent: http://purl.obolibrary.org/obo/NCIT_C125894
-  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
-  Oxford Nanopore MinION: http://www.ebi.ac.uk/efo/EFO_0008632
-  Illumina MiSeq: http://www.ebi.ac.uk/efo/EFO_0004205
-  IonTorrent: http://purl.obolibrary.org/obo/NCIT_C125894
-  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
-
-host_species:
-  OLS-ontology: ncbitaxon
-
-virus_species:
-  OLS-ontology: ncbitaxon
-
-collection_location:
-  OLS-ontology: gaz
\ No newline at end of file