jvsoest’s gists

jvsoest / right-censored-to-binary.sparql

Last active January 7, 2022 10:59

SPARQL right-censored to binary

	PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
	PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
	prefix ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
	prefix snomedct: <http://purl.bioontology.org/ontology/SNOMEDCT/>
	prefix roo: <http://www.cancerdata.org/roo/>

	INSERT {
	GRAPH <http://inferred-manually.local/> {
	?patient roo:survival_5_years ?survival_5y.
	}

jvsoest / disableUSBC-PD.sh

Last active March 8, 2023 00:04

Disable USB-C PD on NUC10i5(FNH) to reduce CPU load

	# 2020-11-9: Solved in recent Ubuntu updates, not needed anymore, only for historical purposes available.
	#
	# Script to disable USB-C PD controller with nuc10
	# See: https://community.intel.com/t5/Intel-NUCs/NUC10i3-IRQ-problem/td-p/669863?profile.language=it
	# https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1883511

	processActive=$(pgrep -l irq/65-i2c-INT3 \| wc -l)

	if [ "$processActive" -gt "0" ]; then
	echo "stopping USB-C PD controller"

jvsoest / ct_rtstruct_retrieval.sparql

Last active January 7, 2020 15:41

SEDI retrieval of CT and RTStruct information

	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.

jvsoest / doiRetrieve.sh

Created December 28, 2019 16:02

DOI metadata retrieval

	# 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 / service.py

Created January 17, 2018 20:08

Python image service

	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():

jvsoest / example_sparql.sparql

Last active December 4, 2017 13:34

example_sparql

	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.

jvsoest / fhir_dlra_query.sparql

Last active November 20, 2017 07:11

FHIR query DLRA

	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.

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).

	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:>

jvsoest / xnat.py

Created July 24, 2017 13:12

XNAT python

	###### 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 / sedi_mr.sparql

Last active June 7, 2017 14:03

	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.

Johan van Soest jvsoest