From 7b011e540871d49a5719dc25d9941472cacc8fc5 Mon Sep 17 00:00:00 2001 From: lltommy Date: Wed, 13 May 2020 18:22:49 +0200 Subject: Adding some more labels and adjusting some queries --- bh20simplewebuploader/main.py | 17 ++++++++++------- semantic_enrichment/labels.ttl | 23 +++++++++++++++++++++++ 2 files changed, 33 insertions(+), 7 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 [ ?tech] - BIND (concat(?tech,"_label") as ?tech_label)} + {?fasta ?x [ ?tech] . + OPTIONAL {?tech ?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 [ ?geoLocation] - BIND (concat(?geoLocation,"_label") as ?geoLocation_label)} + {?fasta ?x [ ?geoLocation] . + Optional {?geoLocation ?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 [ ?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 ?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/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 @@ "specimen collector" . "Accession" . "collection date" . + "biological sex" . + "age" . + "Unit of Time". + "Status" . + "treatment" . + "vaccination" . + "ethnicity" . "Asymptomatic" . "Symptomatic" . "admitted to hospital" . @@ -22,3 +29,19 @@ "Healthy" . "male". "female" . + "Illumina NextSeq 500" . + "ONT MinION" . + " Oxford Nanopore Sequencing" . + "Illumina MiSeq" . + "Illumina" . + "Ion Semiconductor Sequencing". + "Dideoxy Chain Termination DNA Sequencing" . + "Nasopharyngeal Swab Specimen" . + "Oropharyngeal Swab Specimen" . + "Bronchoalveolar Lavage Fluid" . + "Sputum" . + "Aspirate" . + "Feces" . + "Serum" . + "Saliva" . + "Nasal Swab" . \ No newline at end of file -- cgit v1.2.3 From c44a03772f1fe12bb9a6fe27e242337d14356ff7 Mon Sep 17 00:00:00 2001 From: LLTommy Date: Wed, 13 May 2020 18:29:25 +0200 Subject: Update paper.md --- paper/paper.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) 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 -- cgit v1.2.3