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| author | lltommy | 2020-04-23 21:48:16 +0200 |
|---|---|---|
| committer | lltommy | 2020-04-23 21:48:16 +0200 |
| commit | 4666ba880def50adef3ea23ad954cb4e7bf2693a (patch) | |
| tree | 979b614443d165473f4ad8c97f58ddea97c8b12d | |
| parent | f6270f29082642458558d77e6edd449f43b15d30 (diff) | |
| download | bh20-seq-resource-4666ba880def50adef3ea23ad954cb4e7bf2693a.tar.gz bh20-seq-resource-4666ba880def50adef3ea23ad954cb4e7bf2693a.tar.lz bh20-seq-resource-4666ba880def50adef3ea23ad954cb4e7bf2693a.zip | |
Adding a third sequence technology option
| -rw-r--r-- | bh20sequploader/bh20seq-options.yml | 22 | ||||
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 7 | ||||
| -rw-r--r-- | bh20sequploader/bh20seq-shex.rdf | 2 | ||||
| -rw-r--r-- | scripts/dict_ontology_standardization/ncbi_host_health_status.csv | 2 |
4 files changed, 26 insertions, 7 deletions
diff --git a/bh20sequploader/bh20seq-options.yml b/bh20sequploader/bh20seq-options.yml index 4c1d15c..104ed6c 100644 --- a/bh20sequploader/bh20seq-options.yml +++ b/bh20sequploader/bh20seq-options.yml @@ -17,11 +17,11 @@ host_sex: host_health_status: healthy: http://purl.obolibrary.org/obo/NCIT_C115935 - asymptomatic: http://purl.obolibrary.org/obo/NCIT_C3833 - sympotmatic: http://purl.obolibrary.org/obo/NCIT_C25269 - admitted to hospital: http://purl.obolibrary.org/obo/GENEPIO_0002020 - discharged from hospital: http://purl.obolibrary.org/obo/GENEPIO_0001849 - dead: http://purl.obolibrary.org/obo/NCIT_C28554 + asymptomatic: http://purl.obolibrary.org/obo/NCIT_C3833 + symptomatic: http://purl.obolibrary.org/obo/NCIT_C25269 + admitted to hospital: http://purl.obolibrary.org/obo/GENEPIO_0002020 + discharged from hospital: http://purl.obolibrary.org/obo/GENEPIO_0001849 + dead: http://purl.obolibrary.org/obo/NCIT_C28554 alive: http://purl.obolibrary.org/obo/NCIT_C37987 sample_sequencing_technology: @@ -47,6 +47,18 @@ sample_sequencing_technology2: Oxford Nanopore Sequencing: http://purl.obolibrary.org/obo/NCIT_C146818 Sanger dideoxy sequencing: http://purl.obolibrary.org/obo/NCIT_C19641 +sample_sequencing_technology3: + 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 diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index 9a89979..a54ddb1 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -157,6 +157,13 @@ $graph: _id: http://purl.obolibrary.org/obo/OBI_0600047 _type: "@id" noLinkCheck: true + sample_sequencing_technology3: + doc: Technology that was used to sequence this sample (e.g Sanger, Nanopor MiniION) + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/OBI_0600047 + _type: "@id" + noLinkCheck: true sequence_assembly_method: doc: Protocol which provides instructions on the alignment of sequencing reads to reference genome type: string? diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf index 246fd57..953e27a 100644 --- a/bh20sequploader/bh20seq-shex.rdf +++ b/bh20sequploader/bh20seq-shex.rdf @@ -53,7 +53,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/> } :technologyShape { - obo:OBI_0600047 IRI {0,2} ; + obo:OBI_0600047 IRI {0,3} ; efo:EFO_0002699 xsd:string ?; obo:FLU_0000848 xsd:double {0,2}; sio:SIO_001167 xsd:string ?; diff --git a/scripts/dict_ontology_standardization/ncbi_host_health_status.csv b/scripts/dict_ontology_standardization/ncbi_host_health_status.csv index bbb9347..2fb95c1 100644 --- a/scripts/dict_ontology_standardization/ncbi_host_health_status.csv +++ b/scripts/dict_ontology_standardization/ncbi_host_health_status.csv @@ -1,6 +1,6 @@ healthy,http://purl.obolibrary.org/obo/NCIT_C115935 asymptomatic,http://purl.obolibrary.org/obo/NCIT_C3833 -sympotmatic,http://purl.obolibrary.org/obo/NCIT_C25269 +symptomatic,http://purl.obolibrary.org/obo/NCIT_C25269 admitted to hospital,http://purl.obolibrary.org/obo/GENEPIO_0002020 hospitalized patient,http://purl.obolibrary.org/obo/GENEPIO_0002020 discharged from hospital,http://purl.obolibrary.org/obo/GENEPIO_0001849 |