MassBank-RDF

Installing Qlever RDF engine + loading MassBank-RDF ttl file

# install qlever
pip install qlever
# check qlever command
qlever
# enable bash completion
eval "$(register-python-argcomplete qlever)" && export QLEVER_ARGCOMPLETE_ENABLED=1 #
# create working directory for QLever
mkdir test
cd test
wget https://github.com/systemsomicslab/MassBank-RDF/raw/main/Qleverfile
wget DOWNLOAD_YOUR_TTLFILES.ttl
qlever index
qlever start
qlever ui

If you want to start new QLever service

mkdir test2
cd test2
wget https://github.com/systemsomicslab/MassBank-RDF/raw/main/Qleverfile
wget DOWNLOAD_YOUR_TTLFILES.ttl
qlever index
qlever start --kill-existing-with-same-port
qlever ui

How to send a SPARQL query from Jupyter to QLever

Install the Python packages

pip install jupyterlab
pip install sparqlwrapper

Running JupyterLab

jupyter-lab

Jupyter cell example

from SPARQLWrapper import SPARQLWrapper, JSON
URL4SPARQLENDPIOINT = "YOUR_QLEVER_SPARQL_ENDPOINT"
sparql = SPARQLWrapper(URL4SPARQLENDPIOINT)
sparql.setQuery(query)
sparql.setReturnFormat(JSON)
results = sparql.query().convert()
for result in results["results"]["bindings"]:
    print(result)

How to check QLever SPARQL endpoint URL

1. Click Backend Information in your QLever UI.
2. Check the red box in the attached image.