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 ++++++++++++++++++++++--- bh20sequploader/bh20seq-schema.yml | 8 +---- bh20sequploader/supporting_webuploader.yml | 48 ------------------------------ 3 files changed, 38 insertions(+), 59 deletions(-) delete mode 100644 bh20sequploader/supporting_webuploader.yml (limited to 'bh20sequploader') 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 -- cgit v1.2.3