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Other SPARQL interfaces

Here is a list of SPARQL endpoints - integrated in the ReconXKG RDF - that can be useful to query individually.

Note that they may rely on different RDF engines (i.e. GraphDB is not used everywhere).

The Virtuoso engine is often used because it can manage larger amount of data, and is also freely available.

UniProt

The UniProt SPARQL endpoint is available at https://sparql.uniprot.org/

UniProt SPARQL endpoint

Rhea

The Rhea SPARQL endpoint is available at https://sparql.rhea-db.org/

Rhea SPARQL endpoint

MetaNetX

The MetaNetX SPARQL endpoint is available at https://rdf.metanetx.org/

MetaNetX SPARQL endpoint

Remote queries with SERVICE

One of the strength of SPARQL queries is they can be remotely executed, opening the federated query way of querying.

Exercise: Take an example query found in Rhea, and execute it from the reconx.vital-it.ch SPARQL interface.

E.g.: 

PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>
# Query 2
# Select all Rhea reactions annotated with a given Pubmed identifier (PMID = 29867142)
#
SELECT ?pubmed ?rhea ?accession ?isTransport ?equation
WHERE {
    ?rhea rdfs:subClassOf rh:Reaction .
    ?rhea rh:accession ?accession .
    ?rhea rh:citation ?pubmed .
    VALUES (?pubmed) { (pubmed:29867142) }
    ?rhea rh:isTransport ?isTransport .
    ?rhea rh:equation ?equation .
} ORDER BY ?rhea

NB: The Rhea SPARQL endpoint URL is https://sparql.rhea-db.org/.

Answer 
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>
# Query 2
# Select all Rhea reactions annotated with a given Pubmed identifier (PMID = 29867142)
#
SELECT ?pubmed ?rhea ?accession ?isTransport ?equation
WHERE {
    SERVICE <https://sparql.rhea-db.org/> {                  # <--------------------
        ?rhea rdfs:subClassOf rh:Reaction .
        ?rhea rh:accession ?accession .
        ?rhea rh:citation ?pubmed .
        VALUES (?pubmed) { (pubmed:29867142) }
        ?rhea rh:isTransport ?isTransport .
        ?rhea rh:equation ?equation .
    }                                                        # <--------------------
} ORDER BY ?rhea