Johan van Soest jvsoest
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| prefix dcterm: <http://purl.org/dc/terms/> | |
| prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | |
| prefix ctvoc: <http://bio2rdf.org/clinicaltrials_vocabulary:> | |
| prefix ctres: <http://bio2rdf.org/clinicaltrials_resource:> | |
| prefix ct: <http://bio2rdf.org/clinicaltrials:> | |
| select ?trial ?location ?cityName ?countryName | |
| where { | |
| BIND(ct:NCT00005636 AS ?trial). |
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| com.bigdata.rwstore.RWStore.readBlobsAsync=false | |
| com.bigdata.journal.AbstractJournal.file=blazegraph.jnl | |
| # The persistence engine. Use 'Disk' for the WORM or 'DiskRW' for the RWStore. | |
| com.bigdata.journal.AbstractJournal.bufferMode=DiskRW | |
| # Setup for the RWStore recycler rather than session protection. | |
| com.bigdata.service.AbstractTransactionService.minReleaseAge=1 |
jvsoest
/ sedi_mr.sparql
Last active
June 7, 2017 14:03
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| prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | |
| prefix icd: <http://purl.bioontology.org/ontology/ICD10/> | |
| prefix uo: <http://purl.obolibrary.org/obo/UO_> | |
| prefix sedi: <http://semantic-dicom.org/dcm#> | |
| prefix seq: <http://semantic-dicom.org/seq#> | |
| SELECT ?dicom_series ?institute ?machine ?anatomicRegionSeq | |
| WHERE { | |
| ?patient sedi:hasStudy ?dicom_study. | |
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| ###### login to XNAT and search/get files ######## | |
| import xnat | |
| session = xnat.connect('https://xnat.bmia.nl', user='bla') | |
| session.projects | |
| project = session.projects['STW_STRATEGY_HN_VELLORE'] | |
| subject = project.subjects['BMIAXNAT_S08453'] | |
| experiment = subject.experiments['BMIAXNAT_E28844'] |
jvsoest
/ patient_protocol_trial_publications.sparql
Last active
October 15, 2017 16:42
One query to retrieve patient information, disease and treatment characteristics, trials matching the treatment characteristics, and the link to publications linked to these trials. Hence, we can find publications related to the disease and treatment of specific patients (via the treatment protocols and clinical trials).
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| prefix roo: <http://www.cancerdata.org/roo/> | |
| prefix ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#> | |
| prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | |
| prefix icd: <http://purl.bioontology.org/ontology/ICD10/> | |
| prefix uo: <http://purl.obolibrary.org/obo/UO_> | |
| prefix dcterm: <http://purl.org/dc/terms/> | |
| prefix ctvoc: <http://bio2rdf.org/clinicaltrials_vocabulary:> | |
| prefix ctres: <http://bio2rdf.org/clinicaltrials_resource:> | |
| prefix ct: <http://bio2rdf.org/clinicaltrials:> |
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| prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | |
| prefix fhir: <http://hl7.org/fhir/> | |
| SELECT ?subject ?givenName ?prefixName ?familyName ?procedure ?codeValue ?systemValue ?uriTerm ?uriLabel ?superTerm ?superLabel | |
| WHERE { | |
| #get the procedure | |
| ?procedure rdf:type fhir:Procedure; | |
| fhir:Procedure.code ?pCode; | |
| fhir:Procedure.subject ?bnode_subject. |
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| prefix roo: <http://www.cancerdata.org/roo/> | |
| prefix ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#> | |
| prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | |
| prefix icd: <http://purl.bioontology.org/ontology/ICD10/> | |
| prefix uo: <http://purl.obolibrary.org/obo/UO_> | |
| SELECT * | |
| WHERE { | |
| ?patient rdf:type ncit:C16960. |
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| from flask import Flask, render_template, request, url_for | |
| import os | |
| if not os.path.exists("static"): | |
| os.makedirs("static") | |
| app = Flask('ImageShow', template_folder='') | |
| @app.route('/', methods=['GET', 'POST']) | |
| def index(): |
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| # retrieve as reference text | |
| curl -LH "Accept: text/bibliography" http://dx.doi.org/10.1016/j.radonc.2014.04.008 | |
| # retrieve as bibtex | |
| curl -LH "Accept: text/bibliography; style=bibtex" http://dx.doi.org/10.1016/j.radonc.2014.04.008 | |
| # retrieve as bibtex (url-safe) | |
| curl -LH "Accept: application/x-bibtex" http://dx.doi.org/10.1016/j.radonc.2014.04.008 |
jvsoest
/ ct_rtstruct_retrieval.sparql
Last active
January 7, 2020 15:41
SEDI retrieval of CT and RTStruct information
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| PREFIX sedi: <http://semantic-dicom.org/dcm#> | |
| PREFIX seq: <http://semantic-dicom.org/seq#> | |
| prefix owl: <http://www.w3.org/2002/07/owl#> | |
| prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | |
| select DISTINCT ?patientID ?studyUID ?seriesUID ?modality ?manufacturer ?model ?softwareVersion ?sopInstanceUID ?sliceThickness ?contourName ?refSeriesUID | |
| where { | |
| # Get patient & ID | |
| ?patient rdf:type sedi:Patient. |
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