SPARQL examples testing and conversion utilities

This is a set of tools to convert, test and help maintain SPARQL query examples.

The code comes from the SIB SPARQL Examples project.

For this code to work each query should be in a turtle file.

Each SPARQL query is itself in a turtle file. We use the following ontologies for the basic concepts.

• ShACL for the relation to the text of the Select/Ask queries, and declaring prefixes
• RDFS for comments and labels as shown in the user interfaces
• RDF for basic type relations
• schema.org for the target SPARQL endpoint and tagging relevant keywords

The following illustrates an example to retrieve all taxa from the UniProt SPARQL endpoint.

prefix ex: <https://sparql.uniprot.org/.well-known/sparql-examples/>  # <!-- change per dataset
prefix sh: <http://www.w3.org/ns/shacl#>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#>
ex:1  # <!-- UniProt, Rhea and Swiss-Lipids are numbered but this can be anything.
    a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ;
    sh:prefixes _:sparql_examples_prefixes ; # <!-- required for the import of the prefix declarations. Note the blank node
    rdfs:comment """A comment <em>May have HTML in them</em>. Example: Select all taxa from the <a href=\"https://www.uniprot.org/taxonomy/\">UniProt taxonomy</a>"""^^rdf:HTML ;
    sh:select """PREFIX up: <http://purl.uniprot.org/core/>

SELECT ?taxon
FROM <http://sparql.uniprot.org/taxonomy>
WHERE
{
    ?taxon a up:Taxon .
}""" ;
    schema:target <https://sparql.uniprot.org/sparql/> ;
    schema:keywords "taxa".

If you want to add a label to a query please use the schema.org keywords.

Running the code

If using a release:

mkdir target
wget "https://github.com/sib-swiss/sparql-examples-utils/releases/download/v2.0.10/sparql-examples-utils-2.0.10-uber.jar"
mv sparql-examples-utils-2.0.10-uber.jar target

# This target directory is only so that the commands in the examples match as if the code was build locally.
# basically target/ can be remove from all examples below

If building locally in this git repository:

mvn package

Quality Assurance (QA)

To test your examples pass the folder/directory containing your examples as an argument (--input-directory to the test subcommand, e.g.:

java -jar target/sparql-examples-utils-*-uber.jar test --input-directory=../sparql-examples/examples

The queries can be executed automatically on all endpoints they apply to using an extra argument for the test --also-run-slow-tests. This does change the queries to add a LIMIT 1 if no limit was set in the query.

java -jar target/sparql-examples-utils-*-uber.jar test --input-directory=../sparql-examples/examples -p MetaNetX --also-run-slow-tests

Note

All CLI commands provided in this readme expects you have the sparql-examples folder cloned in the same directory alongside this sparql-examples-utils project folder. Feel free to change them for your own example folder and path.

Conversion for upload in SPARQL endpoint

Before loading the examples into a SPARQL endpoint they should be concatenated into one file, including the prefixes/namespaces definitions.

Compile all query files for a specific example subfolder, into a local turtle file:

java -jar target/sparql-examples-utils-*-uber.jar convert -i ../sparql-examples/examples -p Bgee -f ttl > examples_Bgee.ttl

Or compile all subfolders as JSON-LD to the standard output:

java -jar target/sparql-examples-utils-*-uber.jar convert -i ../sparql-examples/examples -p all -f jsonld

Conversion to RQ files

For easier use by other tools we can also generate .rq files. Following the syntax of grlc.io allowing to use these queries as HTTP APIs.

java -jar target/sparql-examples-utils-*-uber.jar convert -i ../sparql-examples/examples -p all -r

Generate markdown file

Generate markdown files with the query and a mermaid diagram of the queries, to be used to deploy a static website for the query examples.

java -jar target/sparql-examples-utils-*-uber.jar convert -i ../sparql-examples/examples -m

Querying for queries

As the SPARQL examples are themselves RDF, they can be queried for as soon as they are loaded in a SPARQL endpoint.

PREFIX sh: <http://www.w3.org/ns/shacl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX spex: <https://purl.expasy.org/sparql-examples/ontology#>
SELECT DISTINCT ?sq ?comment ?query
WHERE {
    ?sq a sh:SPARQLExecutable ;
        rdfs:comment ?comment ;
        sh:select|sh:ask|sh:construct|spex:describe ?query .
} ORDER BY ?sq

Finding queries that run on more than one endpoint

java -jar target/sparql-examples-utils-*-uber.jar convert --input-directory ../sparql-examples/examples > examples_all.ttl

sparql --data examples_all.ttl "SELECT ?query (GROUP_CONCAT(?target ; separator=', ') AS ?targets) WHERE { ?query <https://schema.org/target> ?target } GROUP BY ?query HAVING (COUNT(DISTINCT ?target) > 1) "

Native executable

The project is ready to be compiled by the native-image tool of the GraalVM project.

To do so set your JAVA_HOME to the graalvm location and user maven package -Pnative

e.g. on linux with graalvm installed in your $HOME/bin directory:

export JAVA_HOME=$HOME/bin/graalvm-jdk-${GRAALVM_VERSION}
mvn package -Pnative

# Then there is now a local native binary that you can use to convert all entries
./target/sparql-examples-utils converter -i ${DIRECTORY_WITH_EXAMPLES}

How to cite this work

If you reuse any part of this work, please cite the arXiv paper:

@misc{largecollectionsparqlquestionquery,
      title={A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications},
      author={Jerven Bolleman and Vincent Emonet and Adrian Altenhoff and Amos Bairoch and Marie-Claude Blatter and Alan Bridge and Severine Duvaud and Elisabeth Gasteiger and Dmitry Kuznetsov and Sebastien Moretti and Pierre-Andre Michel and Anne Morgat and Marco Pagni and Nicole Redaschi and Monique Zahn-Zabal and Tarcisio Mendes de Farias and Ana Claudia Sima},
      year={2024},
      doi={10.48550/arXiv.2410.06010},
      eprint={2410.06010},
      archivePrefix={arXiv},
      primaryClass={cs.DB},
      url={https://arxiv.org/abs/2410.06010},
}

Extracting queries from wikibase

These utils have a mode to extract queries from wikibase instances.

For example to extract the queries from factgrid into a separate example directory.

java -jar target/sparql-examples-utils-*-uber.jar \
    wikibase \
    -e [email protected] \
    -o $HOME/git/wikibase-sparql-examples/examples/FactGrid \
    -s https://database.factgrid.de/sparql \
    -u https://database.factgrid.de/