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 [<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/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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