diff options
| -rw-r--r-- | bh20sequploader/bh20seq-options.yml | 2 | ||||
| -rw-r--r-- | bh20sequploader/bh20seq-shex.rdf | 4 | ||||
| -rw-r--r-- | semantic_enrichment/labels.ttl | 25 |
3 files changed, 28 insertions, 3 deletions
diff --git a/bh20sequploader/bh20seq-options.yml b/bh20sequploader/bh20seq-options.yml index d1ea398..02b7377 100644 --- a/bh20sequploader/bh20seq-options.yml +++ b/bh20sequploader/bh20seq-options.yml @@ -44,3 +44,5 @@ specimen_source: 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 + saliva: http://purlobolibrary.org/obo/NCIT_C13275 + aspirate: http://purl.obolibrary.org/obo/NCIT_C13347 diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf index 1b15c58..11eb75e 100644 --- a/bh20sequploader/bh20seq-shex.rdf +++ b/bh20sequploader/bh20seq-shex.rdf @@ -31,7 +31,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/> efo:EFO_0000727 xsd:string ?; obo:VO_0000002 xsd:string {0,10}; sio:SIO_001167 xsd:string ?; - sio:SIO_001014 [ obo:HANCESTRO_~ ] ? ; #ethnicity + sio:SIO_001014 [ obo:HANCESTRO_~ ] ? ; #ethnicity from obo:HANCESTRO } :sampleShape { @@ -40,7 +40,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/> obo:GAZ_00000448 [wikidata:~] ; obo:OBI_0001895 xsd:string ?; obo:NCIT_C41206 xsd:string ?; - obo:OBI_0001479 IRI {0,2}; + obo:OBI_000147 [ obo:NCIT_~ ] ? ; #specimen source from obo:NCIT obo:OBI_0001472 xsd:string ?; sio:SIO_001167 xsd:string ?; edam:data_2091 IRI {0,3}; diff --git a/semantic_enrichment/labels.ttl b/semantic_enrichment/labels.ttl index 42c199e..6d0838f 100644 --- a/semantic_enrichment/labels.ttl +++ b/semantic_enrichment/labels.ttl @@ -31,26 +31,49 @@ <http://purl.obolibrary.org/obo/PATO_0000383> <http://www.w3.org/2000/01/rdf-schema#label> "female" . <http://www.ebi.ac.uk/efo/EFO_0008635> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina iSeq 100". +<http://www.ebi.ac.uk/efo/EFO_0008635> <http://www.w3.org/2000/01/rdf-schema#comment> "The Illumina iSeq 100 is a benchtop sequencing machine developed by Illumina. Its primary applications include small whole-genome sequencing, targeted sequencing of a set of genes or gene regions, gene expression analysis and 16S metagenomic sequencing" . <http://www.ebi.ac.uk/efo/EFO_0009173> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina NextSeq 500" . +<http://www.ebi.ac.uk/efo/EFO_0009173> <http://www.w3.org/2000/01/rdf-schema#comment> "The Illumina NextSeq 500 is a benchtop high-throughput sequencing machine developed by Illumina" . <http://www.ebi.ac.uk/efo/EFO_0008565> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina HiSeq 2500" . +<http://www.ebi.ac.uk/efo/EFO_0008565> <http://www.w3.org/2000/01/rdf-schema#comment> "The Illumina HiSeq 2500 is a sequencing machine developed by Illumina" . <http://www.ebi.ac.uk/efo/EFO_0008566> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina NextSeq 550" . +<http://www.ebi.ac.uk/efo/EFO_0008566> <http://www.w3.org/2000/01/rdf-schema#comment> "The Illumina NextSeq 550 is a benchtop high-throughput sequencing machine developed by Illumina. Its primary applications include exome sequencing, targeted gene sequencing (amplicon, gene panel), whole-transcriptome sequencing and cytogenomic arrays" . <http://www.ebi.ac.uk/efo/EFO_0008636> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina MiniSeq" . +<http://www.ebi.ac.uk/efo/EFO_0008636> <http://www.w3.org/2000/01/rdf-schema#comment> "The Illumina MiniSeq is a benchtop sequencing machine developed by Illumina" . <http://www.ebi.ac.uk/efo/EFO_0008632> <http://www.w3.org/2000/01/rdf-schema#label> "ONT MinION" . +<http://www.ebi.ac.uk/efo/EFO_0008632> <http://www.w3.org/2000/01/rdf-schema#comment> "The ONT MinION is a pocket-sized sequencing machine developed by Oxford Nanopore Technologies" . <http://purl.obolibrary.org/obo/NCIT_C146818> <http://www.w3.org/2000/01/rdf-schema#label> "Oxford Nanopore Sequencing" . +<http://purl.obolibrary.org/obo/NCIT_C146818> <http://www.w3.org/2000/01/rdf-schema#comment> "A proprietary next-generation DNA sequencing technology from Oxford Nanopore Technologies that can directly identify and sequence a DNA molecule as it passes through a nanopore, driven by electrophoresis" . <http://www.ebi.ac.uk/efo/EFO_0004205> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina MiSeq" . +<http://www.ebi.ac.uk/efo/EFO_0004205> <http://www.w3.org/2000/01/rdf-schema#comment> "The Illumina MiSeq is a high-throughput sequencing machine developed by Illumina. Its primary applications include small whole-genome sequencing, targeted sequencing of a set of genes or gene regions and 16S metagenomic sequencing" . <http://www.ebi.ac.uk/efo/EFO_0008567> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina HiSeq X" . +<http://www.ebi.ac.uk/efo/EFO_0008567> <http://www.w3.org/2000/01/rdf-schema#comment> "The Illumina HiSeq X is an ultra-high-throughput sequencing machine developed by Illumina. Sets of 5 or 10 HiSeq X instruments make up the Illumina HiSeq X Five and Illumina HiSeq X Ten systems, respectively" . <http://www.ebi.ac.uk/efo/EFO_0008637> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina NovaSeq 6000" . +<http://www.ebi.ac.uk/efo/EFO_0008637> <http://www.w3.org/2000/01/rdf-schema#comment> "The Illumina NovaSeq 6000 is a high-throughput sequencing machine developed by Illumina" . <http://purl.obolibrary.org/obo/OBI_0000759> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina" . + <http://purl.obolibrary.org/obo/NCIT_C125894> <http://www.w3.org/2000/01/rdf-schema#label> "Ion Semiconductor Sequencing". +<http://purl.obolibrary.org/obo/NCIT_C125894> <http://www.w3.org/2000/01/rdf-schema#comment> "A method of DNA sequencing based on the detection of hydrogen ions that are released during synthesis of a complementary strand polymerized on a template strand. This technology differs from other sequencing technologies in that no modified nucleotides or optics are used. It claims to be simpler, faster, and more cost effective and scalable than any other technology available" . <http://purl.obolibrary.org/obo/NCIT_C19641> <http://www.w3.org/2000/01/rdf-schema#label> "Dideoxy Chain Termination DNA Sequencing" . +<http://purl.obolibrary.org/obo/NCIT_C19641> <http://www.w3.org/2000/01/rdf-schema#comment> "A DNA sequencing technique in which a mixture of deoxynucleosidetriphosphates (dNTPs) and chain-terminating dNTPs, which are radioactively or fluorescently labeled, are combined within the reaction mixture. Once the reaction is complete, the DNA strands are separated by size, and the labeled chain terminating dNTPs can be read in sequence by the investigator or by a machine" . <http://www.ebi.ac.uk/efo/EFO_0008567> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina HiSeq X" . +<http://www.ebi.ac.uk/efo/EFO_0008567> <http://www.w3.org/2000/01/rdf-schema#comment> "The Illumina HiSeq X is an ultra-high-throughput sequencing machine developed by Illumina. Sets of 5 or 10 HiSeq X instruments make up the Illumina HiSeq X Five and Illumina HiSeq X Ten systems, respectively" . <http://purl.obolibrary.org/obo/NCIT_C155831> <http://www.w3.org/2000/01/rdf-schema#label> "Nasopharyngeal Swab Specimen" . +<http://purl.obolibrary.org/obo/NCIT_C155831> <http://www.w3.org/2000/01/rdf-schema#comment> "A biospecimen collected from the back of the throat by swabbing" . <http://purl.obolibrary.org/obo/NCIT_C155835> <http://www.w3.org/2000/01/rdf-schema#label> "Oropharyngeal Swab Specimen" . +<http://purl.obolibrary.org/obo/NCIT_C155835> <http://www.w3.org/2000/01/rdf-schema#comment> "A biospecimen collected from the oropharynx by swabbing" . <http://purl.obolibrary.org/obo/NCIT_C13195> <http://www.w3.org/2000/01/rdf-schema#label> "Bronchoalveolar Lavage Fluid" . +<http://purl.obolibrary.org/obo/NCIT_C13195> <http://www.w3.org/2000/01/rdf-schema#comment> "Fluid introduced into, and collected from, the lungs by a bronchoalveolar lavage procedure" . <http://purl.obolibrary.org/obo/NCIT_C13278> <http://www.w3.org/2000/01/rdf-schema#label> "Sputum" . +<http://purl.obolibrary.org/obo/NCIT_C13278> <http://www.w3.org/2000/01/rdf-schema#comment> "Material containing mucus, cellular debris, microorganisms and sometimes blood or pus. It is ejected through the mouth from the lungs, bronchi, and trachea" . <http://purl.obolibrary.org/obo/NCIT_C13347> <http://www.w3.org/2000/01/rdf-schema#label> "Aspirate" . +<http://purl.obolibrary.org/obo/NCIT_C13347> <http://www.w3.org/2000/01/rdf-schema#comment> "Fluid withdrawn from a body cavity, organ, cyst, or tumor" . <http://purl.obolibrary.org/obo/NCIT_C13234> <http://www.w3.org/2000/01/rdf-schema#label> "Feces" . +<http://purl.obolibrary.org/obo/NCIT_C13234> <http://www.w3.org/2000/01/rdf-schema#comment> "The material discharged from the bowel during defecation. It consists of undigested food, intestinal mucus, epithelial cells, and bacteria" . <http://purl.obolibrary.org/obo/NCIT_C13325> <http://www.w3.org/2000/01/rdf-schema#label> "Serum" . +<http://purl.obolibrary.org/obo/NCIT_C13325> <http://www.w3.org/2000/01/rdf-schema#comment> "The clear portion of the blood that remains after the removal of the blood cells and the clotting proteins" . <http://purl.obolibrary.org/obo/NCIT_C13275> <http://www.w3.org/2000/01/rdf-schema#label> "Saliva" . -<http://purl.obolibrary.org/obo/NCIT_C132119> <http://www.w3.org/2000/01/rdf-schema#label> "Nasal Swab" .
\ No newline at end of file +<http://purl.obolibrary.org/obo/NCIT_C13275> <http://www.w3.org/2000/01/rdf-schema#comment> "The watery fluid in the mouth made by the salivary glands. Saliva moistens food to help digestion and it helps protect the mouth against infections" . +<http://purl.obolibrary.org/obo/NCIT_C132119> <http://www.w3.org/2000/01/rdf-schema#label> "Nasal Swab" . +<http://purl.obolibrary.org/obo/NCIT_C132119> <http://www.w3.org/2000/01/rdf-schema#comment> "A method used to collect biological material from within the nasal passages. A cotton swab is inserted into the nasal opening and rotated against the anterior nasal mucosa and them withdrawn" . |