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-rw-r--r--bh20sequploader/bh20seq-options.yml41
-rw-r--r--bh20sequploader/bh20seq-schema.yml8
-rw-r--r--bh20sequploader/supporting_webuploader.yml48
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