diff options
| -rw-r--r-- | bh20simplewebuploader/main.py | 17 | ||||
| -rw-r--r-- | paper/paper.md | 6 | ||||
| -rw-r--r-- | semantic_enrichment/labels.ttl | 23 |
3 files changed, 37 insertions, 9 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 1a441f0..2aebe80 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -451,8 +451,9 @@ def getDetailsForSeq(): @app.route('/api/getSEQCountbytech', methods=['GET']) def getSEQCountbytech(): query="""SELECT ?tech ?tech_label (count(?fasta) as ?fastaCount) WHERE - {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0600047> ?tech] - BIND (concat(?tech,"_label") as ?tech_label)} + {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0600047> ?tech] . + OPTIONAL {?tech <http://www.w3.org/2000/01/rdf-schema#label> ?tech_tmp_label } . + BIND(IF(BOUND(?tech_tmp_label), ?tech_tmp_label,?tech) as ?tech_label)} GROUP BY ?tech ?tech_label ORDER BY DESC (?fastaCount) """ payload = {'query': query, 'format': 'json'} @@ -505,8 +506,9 @@ def getSEQbyLocation(): @app.route('/api/getSEQCountbyLocation', methods=['GET']) def getSEQCountbyLocation(): query="""SELECT ?geoLocation ?geoLocation_label (count(?fasta) as ?fastaCount) WHERE - {?fasta ?x [<http://purl.obolibrary.org/obo/GAZ_00000448> ?geoLocation] - BIND (concat(?geoLocation,"_label") as ?geoLocation_label)} + {?fasta ?x [<http://purl.obolibrary.org/obo/GAZ_00000448> ?geoLocation] . + Optional {?geoLocation <http://www.w3.org/2000/01/rdf-schema#label> ?geoLocation_tmp_label} + BIND(IF(BOUND(?geoLocation_tmp_label), ?geoLocation_tmp_label, ?geoLocation) as ?geoLocation_label)} GROUP BY ?geoLocation ?geoLocation_label ORDER BY DESC (?fastaCount) """ payload = {'query': query, 'format': 'json'} @@ -521,9 +523,10 @@ def getSEQCountbyLocation(): def getSEQCountbySpecimenSource(): query="""SELECT ?specimen_source ?specimen_source_label (count(?fasta) as ?fastaCount) WHERE {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0001479> ?specimen_source] - BIND (concat(?specimen_source,"_label") as ?specimen_source_label)} - GROUP BY ?specimen_source ?specimen_source_label - ORDER BY DESC (?fastaCount) + Optional { ?specimen_source <http://www.w3.org/2000/01/rdf-schema#label> ?specimen_source_tmp_label} + BIND(IF(BOUND(?specimen_source_tmp_label), ?specimen_source_tmp_label ,?specimen_source) as ?specimen_source_label)} + GROUP BY ?specimen_source ?specimen_source_label + ORDER BY DESC (?fastaCount) """ payload = {'query': query, 'format': 'json'} r = requests.get(baseURL, params=payload) diff --git a/paper/paper.md b/paper/paper.md index 6a5d624..4df267f 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -15,7 +15,7 @@ authors: orcid: 0000 affiliation: 3 - name: Thomas Liener - orcid: 0000 + orcid: https://orcid.org/0000-0003-3257-9937 affiliation: 4 - name: Erik Garrison orcid: 0000 @@ -52,7 +52,9 @@ affiliations: index: 1 - name: Curii, Boston, USA index: 2 - - name: UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA. + - name: Thomas Liener Consultancy + index: 4 + - name: UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA index: 5 - name: Department of Computer Science, Faculty of Sciences, Vrije Universiteit Amsterdam, The Netherlands index: 6 diff --git a/semantic_enrichment/labels.ttl b/semantic_enrichment/labels.ttl index b4e5d1f..cd0464a 100644 --- a/semantic_enrichment/labels.ttl +++ b/semantic_enrichment/labels.ttl @@ -13,6 +13,13 @@ <http://purl.obolibrary.org/obo/OBI_0001895> <http://www.w3.org/2000/01/rdf-schema#label> "specimen collector" . <http://edamontology.org/data_2091> <http://www.w3.org/2000/01/rdf-schema#label> "Accession" . <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> <http://www.w3.org/2000/01/rdf-schema#label> "collection date" . +<http://purl.obolibrary.org/obo/PATO_0000047> <http://www.w3.org/2000/01/rdf-schema#label> "biological sex" . +<http://purl.obolibrary.org/obo/PATO_0000011> <http://www.w3.org/2000/01/rdf-schema#label> "age" . +<http://purl.obolibrary.org/obo/NCIT_C42574> <http://www.w3.org/2000/01/rdf-schema#label> "Unit of Time". +<http://purl.obolibrary.org/obo/NCIT_C25688> <http://www.w3.org/2000/01/rdf-schema#label> "Status" . +<http://www.ebi.ac.uk/efo/EFO_0000727> <http://www.w3.org/2000/01/rdf-schema#label> "treatment" . +<http://purl.obolibrary.org/obo/VO_0000002> <http://www.w3.org/2000/01/rdf-schema#label> "vaccination" . +<http://semanticscience.org/resource/SIO_001014> <http://www.w3.org/2000/01/rdf-schema#label> "ethnicity" . <http://purl.obolibrary.org/obo/NCIT_C3833> <http://www.w3.org/2000/01/rdf-schema#label> "Asymptomatic" . <http://purl.obolibrary.org/obo/NCIT_C25269> <http://www.w3.org/2000/01/rdf-schema#label> "Symptomatic" . <http://purl.obolibrary.org/obo/GENEPIO_0002020> <http://www.w3.org/2000/01/rdf-schema#label> "admitted to hospital" . @@ -22,3 +29,19 @@ <http://purl.obolibrary.org/obo/NCIT_C115935> <http://www.w3.org/2000/01/rdf-schema#label> "Healthy" . <http://purl.obolibrary.org/obo/PATO_0000384> <http://www.w3.org/2000/01/rdf-schema#label> "male". <http://purl.obolibrary.org/obo/PATO_0000383> <http://www.w3.org/2000/01/rdf-schema#label> "female" . +<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_0008632> <http://www.w3.org/2000/01/rdf-schema#label> "ONT MinION" . +<http://purl.obolibrary.org/obo/NCIT_C146818> <http://www.w3.org/2000/01/rdf-schema#label> " Oxford Nanopore Sequencing" . +<http://www.ebi.ac.uk/efo/EFO_0004205> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina MiSeq" . +<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_C19641> <http://www.w3.org/2000/01/rdf-schema#label> "Dideoxy Chain Termination DNA Sequencing" . +<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_C155835> <http://www.w3.org/2000/01/rdf-schema#label> "Oropharyngeal Swab Specimen" . +<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_C13278> <http://www.w3.org/2000/01/rdf-schema#label> "Sputum" . +<http://purl.obolibrary.org/obo/NCIT_C13347> <http://www.w3.org/2000/01/rdf-schema#label> "Aspirate" . +<http://purl.obolibrary.org/obo/NCIT_C13234> <http://www.w3.org/2000/01/rdf-schema#label> "Feces" . +<http://purl.obolibrary.org/obo/NCIT_C13325> <http://www.w3.org/2000/01/rdf-schema#label> "Serum" . +<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" .
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