SPARQL examples

This is a collection of SPARQL examples usable on different SIB related SPARQL endpoints or datasets. The examples are stored one query per file in project specific repositories in the examples folder.

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, annotated with a language tag
• RDF for basic type relations
• schema.org for the target SPARQL endpoint and tagging relevant keywords

The following illustrates an example to retrieve retrieve human enzymes that metabolize sphingolipids from the UniProt SPARQL endpoint, with a service call to Rhea endpoint.

@prefix ex: <https://sparql.uniprot.org/.well-known/sparql-examples/> . # <!-- change per dataset
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix schema: <https://schema.org/> .
@prefix sh: <http://www.w3.org/ns/shacl#> .
@prefix spex:<https://purl.expasy.org/sparql-examples/ontology#> .

ex:040 # <!-- UniProt, Rhea and Swiss-Lipids are numbered but this can be anything.
	a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ;
    rdfs:comment "Retrieve human enzymes that metabolize sphingolipids and are annotated in ChEMBL"@en ;
    sh:prefixes _:sparql_examples_prefixes ; # <!-- required for the import of the prefix declarations. Note the blank node
    sh:select """PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX up: <http://purl.uniprot.org/core/>

SELECT DISTINCT ?protein ?chemblEntry WHERE {
  SERVICE <https://sparql.rhea-db.org/sparql> {
    ?rhea rdfs:subClassOf rh:Reaction ;
      rh:side/rh:contains/rh:compound/rh:chebi/rdfs:subClassOf+ CHEBI:26739 .
  }
  ?protein up:annotation/up:catalyticActivity/up:catalyzedReaction ?rhea ;
    up:organism taxon:9606 ;
    rdfs:seeAlso ?chemblEntry .
  ?chemblEntry up:database <http://purl.uniprot.org/database/ChEMBL> .
}""" ;
    schema:keywords "enzyme" ;
    schema:target <https://sparql.uniprot.org/sparql/> ;
    spex:federatesWith <https://sparql.rhea-db.org/sparql> .

Artifact generation and quality assurance

We use the SIB SPARQL Examples utils for testing and generating artifacts.

First, download the jar file with:

wget -O sparql-examples-utils.jar 'https://github.com/sib-swiss/sparql-examples-utils/releases/download/v2.0.7/sparql-examples-utils-2.0.7-uber.jar'

Compile all query files into one file to upload to your endpoint

Compile all query files for a specific example folder, into a local file including the prefixes/namespaces definitions:

java -jar sparql-examples-utils.jar convert -i examples/ -p UniProt -f ttl > examples_UniProt.ttl

You can then load this file to this project SPARQL endpoint! We recommend to upload it to a named graph: your endpoint URL + /.well-known/sparql-examples

Or compile for all example folders, as JSON-LD, to the standard output:

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

Generate RQ files

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

java -jar sparql-examples-utils.jar convert -i 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 sparql-examples-utils.jar convert -i examples/ -m

Testing the queries

The queries are parsed and validated but not executed with junit using the Tester

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

should return no test failures. RDF4j and Jena are both a lot stricter than virtuoso.

The queries can be executed automatically on all endpoints they apply to using an extra argument --also-run-slow-tests:

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

This does change the queries to add a LIMIT 1 if no limit was set in the query. Then check if there is a result it is fetched.

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

This expects the Jena tools to be available in your $PATH. e.g. export PATH="$JENA_HOME/bin:$PATH"

java -jar sparql-examples-utils.jar convert -i examples/ -p all -f ttl > 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) "

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},
}