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Rhea metabolism tutorial

A hands-on introduction to querying metabolism-related data across multiple resources with SPARQL.

Source	Description	Web site	SPARQL endpoint
Rhea	chemical reactions	https://www.rhea-db.org/	https://sparql.rhea-db.org/sparql
UniProt	protein sequences and annotations	https://www.uniprot.org/	https://sparql.uniprot.org/sparql
Bgee	expression data	https://bgee.org/	https://www.bgee.org/sparql/
MetaNetX	reconciled metabolic networks	https://www.metanetx.org/	https://rdf.metanetx.org/

Several of the original queries in this tutorial combine two or three of these endpoints in a single query using SPARQL’s SERVICE keyword - that’s the whole point of a federated query: reach across databases without copying data around. That doesn’t work against a single in-browser example dataset, though (there is nothing to federate with), so for each such query this page shows two versions:

A runnable version against a small combined example dataset, with the SERVICE wrapper removed (since everything already lives in one place, there’s nothing left to federate).
A reference version, unmodified, showing the real query you can paste into the live endpoint listed above to run it for real, across the real databases.

Queries that reach into a third, more specialized service (Bgee expression data, MetaNetX, or the IDSM/Sachem chemical substructure search) aren’t things a small fixture can honestly stand in for, so those stay as reference-only queries with an explanation of why.

Q1: Retrieve all Rhea reactions (approved or preliminary) and their chemical equations

Example data (Turtle) — edit it, then re-run any query below

prefix rh: <http://rdf.rhea-db.org/>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>

rh:11375 rdfs:subClassOf rh:Reaction ;
  rh:status rh:Approved ;
  rh:equation "hexadecanoate + ATP + CoA = hexadecanoyl-CoA + AMP + diphosphate" .

rh:15561 rdfs:subClassOf rh:Reaction ;
  rh:status rh:Preliminary ;
  rh:equation "L-glutamate + NAD+ + H2O = 2-oxoglutarate + NH4+ + NADH + H+" .

rh:20736 rdfs:subClassOf rh:Reaction ;
  rh:status rh:Approved ;
  rh:equation "beta-D-glucose + ATP = beta-D-glucose 6-phosphate + ADP + H+" .

PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT ?reaction ?reactionEquation
WHERE {
  ?reaction rdfs:subClassOf rh:Reaction .
  ?reaction rh:status ?status .
  VALUES ?status { rh:Approved rh:Preliminary }
  ?reaction rh:equation ?reactionEquation .
}
ORDER BY ?reaction

Q2: Retrieve approved reactions using L-glutamate (CHEBI:29985) AND L-glutamine (CHEBI:58359) on opposite sides

Adapted from sparql-examples Rhea/63.

A Rhea reaction is split into two sides; each side contains participants, each participant has a compound, and each compound is cross-referenced to ChEBI. transformableTo links the side a compound starts on to the side it ends up on.

Example data (Turtle) — edit it, then re-run any query below

prefix rh: <http://rdf.rhea-db.org/>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix ch: <http://purl.obolibrary.org/obo/>

rh:15561 rdfs:subClassOf rh:Reaction ;
  rh:status rh:Approved ;
  rh:side rh:15561_L, rh:15561_R .

rh:15561_L rh:contains rh:15561_L_1 ;
  rh:transformableTo rh:15561_R .

rh:15561_R rh:contains rh:15561_R_1 .

rh:15561_L_1 rh:compound rh:Compound_29985 .
rh:15561_R_1 rh:compound rh:Compound_58359 .

rh:Compound_29985 rh:chebi ch:CHEBI_29985 .
rh:Compound_58359 rh:chebi ch:CHEBI_58359 .

PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ch: <http://purl.obolibrary.org/obo/>

SELECT ?reaction WHERE {
  ?reaction rdfs:subClassOf rh:Reaction .
  ?reaction rh:status rh:Approved .

  ?reaction rh:side ?reactionSide1 .
  ?reactionSide1 rh:contains ?participant1 .
  ?participant1 rh:compound ?compound1 .
  ?compound1 rh:chebi ch:CHEBI_29985 .

  ?reaction rh:side ?reactionSide2 .
  ?reactionSide2 rh:contains ?participant2 .
  ?participant2 rh:compound ?compound2 .
  ?compound2 rh:chebi ch:CHEBI_58359 .

  ?reactionSide1 rh:transformableTo ?reactionSide2 .
}

Q3: Select approved reactions with CHEBI:17815 (a 1,2-diacyl-sn-glycerol) or one of its descendants

Adapted from sparql-examples Rhea/92.

ChEBI is itself a hierarchy, so rdfs:subClassOf* (the Kleene-star property path) matches the term itself or any of its descendants, however deep.

Example data (Turtle) — edit it, then re-run any query below

prefix rh: <http://rdf.rhea-db.org/>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix ch: <http://purl.obolibrary.org/obo/>
prefix up: <http://purl.uniprot.org/core/>

ch:CHEBI_17815 up:name "1,2-diacyl-sn-glycerol" .
ch:CHEBI_75542 rdfs:subClassOf ch:CHEBI_17815 ;
  up:name "1,2-dioleoyl-sn-glycerol" .

rh:32964 rdfs:subClassOf rh:Reaction ;
  rh:status rh:Approved ;
  rh:equation "1,2-dioleoyl-sn-glycerol + H2O = oleate + 2-oleoyl-sn-glycerol + H+" ;
  rh:side rh:32964_L .

rh:32964_L rh:contains rh:32964_L_1 .
rh:32964_L_1 rh:compound rh:Compound_75542 .
rh:Compound_75542 rh:chebi ch:CHEBI_75542 .

PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ch: <http://purl.obolibrary.org/obo/>
PREFIX up: <http://purl.uniprot.org/core/>

SELECT DISTINCT ?chebi ?chebiUniprotName ?reaction ?reactionEquation
WHERE {
  ?reaction rdfs:subClassOf rh:Reaction .
  ?reaction rh:status rh:Approved .
  ?reaction rh:equation ?reactionEquation .
  ?reaction rh:side ?reactionSide .
  ?reactionSide rh:contains ?participant .
  ?participant rh:compound ?compound .
  ?compound rh:chebi ?chebi .
  ?chebi rdfs:subClassOf* ch:CHEBI_17815 .
  ?chebi up:name ?chebiUniprotName .
}
ORDER BY ?chebi

Q4: Retrieve Rhea reactions that involve cholesterol using its InChIKey

Chemical compounds can also be looked up by an exact structural identifier, such as an InChIKey, rather than by ChEBI accession.

Example data (Turtle) — edit it, then re-run any query below

prefix rh: <http://rdf.rhea-db.org/>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix ch3: <http://purl.obolibrary.org/obo/chebi/>
prefix ch: <http://purl.obolibrary.org/obo/>
prefix up: <http://purl.uniprot.org/core/>

ch:CHEBI_16113 up:name "cholesterol" ;
  ch3:inchikey "HVYWMOMLDIMFJA-DPAQBDIFSA-N" .

rh:10743 rdfs:subClassOf rh:Reaction ;
  rh:status rh:Approved ;
  rh:equation "cholesterol + O2 + 2 reduced [adrenodoxin] + 2 H+ = pregnenolone + 4-methylpentanal + 2 oxidized [adrenodoxin] + H2O" ;
  rh:side rh:10743_L .

rh:10743_L rh:contains rh:10743_L_1 .
rh:10743_L_1 rh:compound rh:Compound_16113 .
rh:Compound_16113 rh:chebi ch:CHEBI_16113 .

PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ch3: <http://purl.obolibrary.org/obo/chebi/>
PREFIX up: <http://purl.uniprot.org/core/>

SELECT DISTINCT ?chebi ?chebiUniprotName ?reaction ?reactionEquation
WHERE {
  ?reaction rdfs:subClassOf rh:Reaction .
  ?reaction rh:status ?status .
  VALUES ?status { rh:Approved rh:Preliminary }
  ?reaction rh:equation ?reactionEquation .
  ?reaction rh:side ?reactionSide .
  ?reactionSide rh:contains ?participant .
  ?participant rh:compound ?compound .
  ?compound rh:chebi ?chebi .
  ?chebi up:name ?chebiUniprotName .
  ?chebi ch3:inchikey ?inchikey .
  VALUES ?inchikey { "HVYWMOMLDIMFJA-DPAQBDIFSA-N" }
}
ORDER BY ?reaction

Q5: Distribution of Rhea reactions by top-level IUBMB enzyme classification

Adapted from sparql-examples Rhea/109.

Rhea links reactions to enzyme (EC) numbers; the enzyme classification hierarchy (which EC number rolls up to which top-level class) is UniProt data. On the live endpoints this is one federated query; combined into a single example dataset, the SERVICE wrapper simply disappears.

Example data (Turtle) — edit it, then re-run any query below

prefix rh: <http://rdf.rhea-db.org/>
prefix ec: <http://purl.uniprot.org/enzyme/>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix skos: <http://www.w3.org/2004/02/skos/core#>

ec:1.-.-.- skos:prefLabel "Oxidoreductases" .
ec:2.-.-.- skos:prefLabel "Transferases" .
ec:3.-.-.- skos:prefLabel "Hydrolases" .

ec:1.1.1.1 rdfs:subClassOf ec:1.-.-.- .
ec:2.7.1.1 rdfs:subClassOf ec:2.-.-.- .
ec:3.1.3.1 rdfs:subClassOf ec:3.-.-.- .

rh:11372 rh:ec ec:1.1.1.1 .
rh:11376 rh:ec ec:1.1.1.1 .
rh:14709 rh:ec ec:2.7.1.1 .
rh:10736 rh:ec ec:3.1.3.1 .

PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX ec: <http://purl.uniprot.org/enzyme/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>

SELECT ?ecClass ?ecClassName (COUNT(?reaction) AS ?reactionCount)
WHERE {
  ?ec rdfs:subClassOf ?ecClass .
  ?ecClass skos:prefLabel ?ecClassName .
  VALUES ?ecClass { ec:1.-.-.- ec:2.-.-.- ec:3.-.-.- }
  ?reaction rh:ec ?ec .
}
GROUP BY ?ecClass ?ecClassName
ORDER BY ?ecClass

Reference only — not runnable on this page: Real federated version to run at https://sparql.rhea-db.org/sparql

PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX ec: <http://purl.uniprot.org/enzyme/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>

SELECT ?ecClass ?ecClassName (count(?reaction) as ?reactionCount)
WHERE
{
  SERVICE <http://sparql.uniprot.org/sparql> {
    ?ec rdfs:subClassOf ?ecClass .
    ?ecClass skos:prefLabel ?ecClassName .
    VALUES (?ecClass) { (ec:1.-.-.-) (ec:2.-.-.-) (ec:3.-.-.-)
                        (ec:4.-.-.-) (ec:5.-.-.-) (ec:6.-.-.-)
                        (ec:7.-.-.-) }
  }
  ?reaction rh:ec ?ec .
}
ORDER BY ?ecClass

Q6: Retrieve human enzymes metabolizing cholesterol and the reactions they catalyze

Example data (Turtle) — edit it, then re-run any query below

base <http://purl.uniprot.org/uniprot/>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix up: <http://purl.uniprot.org/core/>
prefix taxon: <http://purl.uniprot.org/taxonomy/>
prefix rh: <http://rdf.rhea-db.org/>
prefix ch: <http://purl.obolibrary.org/obo/>

rh:10743 rdfs:subClassOf rh:Reaction ;
  rh:equation "cholesterol + O2 + 2 reduced [adrenodoxin] + 2 H+ = pregnenolone + 4-methylpentanal + 2 oxidized [adrenodoxin] + H2O" ;
  rh:side rh:10743_L .
rh:10743_L rh:contains rh:10743_L_1 .
rh:10743_L_1 rh:compound rh:Compound_16113 .
rh:Compound_16113 rh:chebi ch:CHEBI_16113 .

<Q07973> up:mnemonic "CP7A1_HUMAN" ;
  up:organism taxon:9606 ;
  up:recommendedName <Q07973#RN> ;
  up:annotation <Q07973#CA> .
<Q07973#RN> up:fullName "Cholesterol 7-alpha-monooxygenase" .
<Q07973#CA> a up:Catalytic_Activity_Annotation ;
  up:catalyticActivity <Q07973#CAca> .
<Q07973#CAca> up:catalyzedReaction rh:10743 .

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX ch: <http://purl.obolibrary.org/obo/>

SELECT DISTINCT ?protein ?proteinId ?proteinName ?reaction ?reactionEquation
WHERE {
  ?reaction rdfs:subClassOf rh:Reaction .
  ?reaction rh:side ?reactionSide .
  ?reactionSide rh:contains ?participant .
  ?participant rh:compound ?compound .
  ?compound rh:chebi ch:CHEBI_16113 .
  ?reaction rh:equation ?reactionEquation .

  ?protein up:mnemonic ?proteinId .
  ?protein up:recommendedName ?rn .
  ?rn up:fullName ?proteinName .
  ?protein up:organism taxon:9606 .
  ?protein up:annotation ?a1 .
  ?a1 a up:Catalytic_Activity_Annotation .
  ?a1 up:catalyticActivity ?ca .
  ?ca up:catalyzedReaction ?reaction .
}
ORDER BY ?proteinName

Reference only — not runnable on this page: Real federated version to run at https://sparql.rhea-db.org/sparql

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX ch: <http://purl.obolibrary.org/obo/>

SELECT DISTINCT ?protein ?proteinId ?proteinName ?reaction ?reactionEquation
WHERE {
  ?reaction rdfs:subClassOf rh:Reaction .
  ?reaction rh:side ?reactionSide .
  ?reactionSide rh:contains ?participant .
  ?participant rh:compound ?compound .
  ?compound rh:chebi ch:CHEBI_16113 .
  ?reaction rh:equation ?reactionEquation .

  SERVICE <https://sparql.uniprot.org/sparql/> {
    ?protein up:mnemonic ?proteinId .
    ?protein up:recommendedName ?rn .
    ?rn up:fullName ?proteinName .
    ?protein up:organism taxon:9606 .
    ?protein up:annotation ?a1 .
    ?a1 a up:Catalytic_Activity_Annotation .
    ?a1 up:catalyticActivity ?ca .
    ?ca up:catalyzedReaction ?reaction .
  }
}
ORDER BY ?proteinName

Q7: Ask whether there is a fungal UniProtKB/Swiss-Prot protein metabolizing cholesterol

ASK queries return a plain boolean: whether the pattern matches at all, without listing bindings. This is handy as a fast quality-control check.

Example data (Turtle) — edit it, then re-run any query below

base <http://purl.uniprot.org/uniprot/>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix up: <http://purl.uniprot.org/core/>
prefix taxon: <http://purl.uniprot.org/taxonomy/>
prefix rh: <http://rdf.rhea-db.org/>
prefix ch: <http://purl.obolibrary.org/obo/>

taxon:5062 rdfs:subClassOf taxon:4751 .

rh:10743 rdfs:subClassOf rh:Reaction ;
  rh:status rh:Approved ;
  rh:side rh:10743_L .
rh:10743_L rh:contains rh:10743_L_1 .
rh:10743_L_1 rh:compound rh:Compound_16113 .
rh:Compound_16113 rh:chebi ch:CHEBI_16113 .

<Q9Y7X1> up:organism taxon:5062 ;
  up:annotation <Q9Y7X1#CA> .
<Q9Y7X1#CA> up:catalyticActivity <Q9Y7X1#CAca> .
<Q9Y7X1#CAca> up:catalyzedReaction rh:10743 .

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX ch: <http://purl.obolibrary.org/obo/>

ASK {
  ?reaction rdfs:subClassOf rh:Reaction .
  ?reaction rh:status ?status .
  VALUES ?status { rh:Approved rh:Preliminary }
  ?reaction rh:side ?reactionSide .
  ?reactionSide rh:contains ?participant .
  ?participant rh:compound ?compound .
  ?compound rh:chebi ch:CHEBI_16113 .

  ?protein up:annotation/up:catalyticActivity/up:catalyzedReaction ?reaction .
  ?protein up:organism/rdfs:subClassOf taxon:4751 .
}

Reference only — not runnable on this page: Real federated version to run at https://sparql.uniprot.org/sparql

PREFIX up: <http://purl.uniprot.org/core/>
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX ch: <http://purl.obolibrary.org/obo/>

ASK {
  SERVICE <https://sparql.rhea-db.org/sparql> {
    ?reaction rdfs:subClassOf rh:Reaction .
    ?reaction rh:status ?status .
    VALUES (?status) {(rh:Approved) (rh:Preliminary)}
    ?reaction rh:side ?reactionSide .
    ?reactionSide rh:contains ?participant .
    ?participant rh:compound ?compound .
    ?compound rh:chebi ch:CHEBI_16113 .
  }
  ?protein up:annotation/up:catalyticActivity/up:catalyzedReaction ?reaction .
  ?protein up:organism/rdfs:subClassOf taxon:4751 .
}

Q8: Where are the human enzymes metabolizing cholesterol located in the cell?

Retrieve the UniProt proteins, their catalyzed reactions, and their subcellular location(s), both as a UniProt location term and as the equivalent Gene Ontology Cellular Component ID.

Example data (Turtle) — edit it, then re-run any query below

base <http://purl.uniprot.org/uniprot/>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix up: <http://purl.uniprot.org/core/>
prefix taxon: <http://purl.uniprot.org/taxonomy/>
prefix rh: <http://rdf.rhea-db.org/>
prefix ch: <http://purl.obolibrary.org/obo/>
prefix skos: <http://www.w3.org/2004/02/skos/core#>
prefix location: <http://purl.uniprot.org/locations/>

rh:10743 rdfs:subClassOf rh:Reaction ;
  rh:status rh:Approved ;
  rh:equation "cholesterol + O2 + 2 reduced [adrenodoxin] + 2 H+ = pregnenolone + 4-methylpentanal + 2 oxidized [adrenodoxin] + H2O" ;
  rh:side rh:10743_L .
rh:10743_L rh:contains rh:10743_L_1 .
rh:10743_L_1 rh:compound rh:Compound_16113 .
rh:Compound_16113 rh:chebi ch:CHEBI_16113 .

<Q07973> up:organism taxon:9606 ;
  up:annotation <Q07973#CA>, <Q07973#SL> .
<Q07973#CA> a up:Catalytic_Activity_Annotation ;
  up:catalyticActivity <Q07973#CAca> .
<Q07973#CAca> up:catalyzedReaction rh:10743 .
<Q07973#SL> a up:Subcellular_Location_Annotation ;
  up:locatedIn <Q07973#SLin> .
<Q07973#SLin> up:cellularComponent location:Endoplasmic_reticulum_membrane .
location:Endoplasmic_reticulum_membrane skos:prefLabel "Endoplasmic reticulum membrane" ;
  skos:exactMatch <http://purl.obolibrary.org/obo/GO_0005789> .

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX ch: <http://purl.obolibrary.org/obo/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>

SELECT DISTINCT ?protein ?reaction ?upLocation ?upLocationLabel ?goId
WHERE {
  ?reaction rdfs:subClassOf rh:Reaction .
  ?reaction rh:status rh:Approved .
  ?reaction rh:equation ?reactionEquation .
  ?reaction rh:side ?reactionSide .
  ?reactionSide rh:contains ?participant .
  ?participant rh:compound ?compound .
  # compound constraint
  ?compound rh:chebi ch:CHEBI_16113 .

  # taxonomy constraint
  ?protein up:organism taxon:9606 .
  # Rhea catalyzed reactions
  ?protein up:annotation ?a1 .
  ?a1 a up:Catalytic_Activity_Annotation .
  ?a1 up:catalyticActivity ?ca .
  ?ca up:catalyzedReaction ?reaction .
  # UniProt cellular components
  ?protein up:annotation ?a2 .
  ?a2 a up:Subcellular_Location_Annotation .
  ?a2 up:locatedIn ?lIn .
  ?lIn up:cellularComponent ?upLocation .
  ?upLocation skos:prefLabel ?upLocationLabel .
  ?upLocation skos:exactMatch ?goId .
}

Reference only — not runnable on this page: Real federated version to run at https://sparql.uniprot.org/sparql

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX ch: <http://purl.obolibrary.org/obo/>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>

SELECT distinct ?protein ?reaction ?upLocation ?upLocationLabel ?goId
WHERE {
  SERVICE <https://sparql.rhea-db.org/sparql> {
    ?reaction rdfs:subClassOf rh:Reaction .
    ?reaction rh:status rh:Approved .
    ?reaction rh:equation ?reactionEquation .
    ?reaction rh:side ?reactionSide .
    ?reactionSide rh:contains ?participant .
    ?participant rh:compound ?compound .
    ?compound rh:chebi ch:CHEBI_16113 .
  }
  ?protein up:organism taxon:9606 .
  ?protein up:annotation ?a1 .
  ?a1 a up:Catalytic_Activity_Annotation .
  ?a1 up:catalyticActivity ?ca .
  ?ca up:catalyzedReaction ?reaction .
  ?protein up:annotation ?a2 .
  ?a2 a up:Subcellular_Location_Annotation .
  ?a2 up:locatedIn ?lIn .
  ?lIn up:cellularComponent ?upLocation .
  ?upLocation skos:prefLabel ?upLocationLabel .
  ?upLocation skos:exactMatch ?goId .
}

Q9: Where are the human genes encoding enzymes metabolizing cholesterol expressed?

Adapted from sparql-examples UniProt/49.

This retrieves UniProt proteins, their catalyzed reactions, their encoding genes (Ensembl), and the anatomic entities where those genes are expressed - UBERON anatomic entities coming directly from the Bgee expression-data resource’s own SPARQL endpoint. This crosses three different resources (Rhea, UniProt, Bgee) in one query, and the original tutorial warns it can take a few minutes even on the real endpoints, so it isn’t something a small in-page fixture can honestly stand in for. Run it yourself at sparql.uniprot.org:

Reference only — not runnable on this page: Federates Rhea, UniProt and Bgee - run at https://sparql.uniprot.org/sparql

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX ch: <http://purl.obolibrary.org/obo/>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX genex: <http://purl.org/genex#>
PREFIX lscr: <http://purl.org/lscr#>

SELECT distinct ?protein
                ?ensemblGene
                ?reaction
                ?anatomicEntityLabel
                ?anatomicEntity
WHERE {
  {
    SELECT * WHERE {
      SERVICE <https://sparql.rhea-db.org/sparql> {
        ?reaction rdfs:subClassOf rh:Reaction .
        ?reaction rh:status rh:Approved .
        ?reaction rh:equation ?reactionEquation .
        ?reaction rh:side ?reactionSide .
        ?reactionSide rh:contains ?participant .
        ?participant rh:compound ?compound .
        ?compound rh:chebi ch:CHEBI_16113 .
      }
    }
  }
  ?protein up:organism taxon:9606 .
  ?protein up:annotation ?a .
  ?a a up:Catalytic_Activity_Annotation .
  ?a up:catalyticActivity ?ca .
  ?ca up:catalyzedReaction ?reaction .
  ?protein rdfs:seeAlso / up:transcribedFrom ?ensemblGene .

  SERVICE <https://www.bgee.org/sparql/> {
    ?gene genex:isExpressedIn ?anatomicEntity .
    ?gene lscr:xrefEnsemblGene ?ensemblGene .
    ?anatomicEntity rdfs:label ?anatomicEntityLabel .
  }
}

Q10: Build the UniProt H. pylori proteome-scale metabolic network

Example data (Turtle) — edit it, then re-run any query below

base <http://purl.uniprot.org/uniprot/>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix rh: <http://rdf.rhea-db.org/>
prefix up: <http://purl.uniprot.org/core/>
prefix taxon: <http://purl.uniprot.org/taxonomy/>
prefix ch: <http://purl.obolibrary.org/obo/>

<O25948> up:reviewed true ;
  up:organism taxon:85962 ;
  up:mnemonic "TRPA_HELPY" ;
  up:annotation <O25948#CA> .
<O25948#CA> up:catalyticActivity <O25948#CAca> .
<O25948#CAca> up:catalyzedReaction rh:24945 .

rh:24945 rh:equation "1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate = indole-3-glycerol phosphate + CO2 + H2O" ;
  rh:side rh:24945_L .
rh:24945_L rh:contains rh:24945_L_1, rh:24945_L_2 .
rh:24945_L_1 rh:compound rh:Compound_58613 .
rh:Compound_58613 rh:chebi ch:CHEBI_58613 .
rh:24945_L_2 rh:compound rh:Compound_unspecified .

The last participant (rh:Compound_unspecified) deliberately has no rh:chebi triple, to show why the chebi binding is wrapped in OPTIONAL - not every compound in Rhea is cross-referenced to ChEBI.

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>

SELECT ?protein ?proteinId ?reaction ?reactionSide ?compound ?chebi ?reactionEquation
WHERE {
  ?protein up:reviewed ?status .
  ?protein up:organism taxon:85962 .
  ?protein up:mnemonic ?proteinId .
  ?protein up:annotation ?a .
  ?a up:catalyticActivity ?ca .
  ?ca up:catalyzedReaction ?reaction .

  ?reaction rh:equation ?reactionEquation .
  ?reaction rh:side ?reactionSide .
  ?reactionSide rh:contains ?participant .
  ?participant rh:compound ?compound .
  OPTIONAL { ?compound rh:chebi ?chebi }
}

Reference only — not runnable on this page: Real federated version to run at https://sparql.rhea-db.org/sparql

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
SELECT  ?protein
        ?proteinId
        ?reaction
        ?reactionSide
        ?compound
        ?chebi
        ?reactionEquation
WHERE {
  SERVICE <http://sparql.uniprot.org/sparql> {
    ?protein up:reviewed ?status .
    ?protein up:organism taxon:85962 .
    ?protein up:mnemonic ?proteinId .
    ?protein up:annotation ?a .
    ?a up:catalyticActivity ?ca .
    ?ca up:catalyzedReaction ?reaction .
  }
  ?reaction rh:equation ?reactionEquation .
  ?reaction rh:side ?reactionSide .
  ?reactionSide rh:contains ?participant .
  ?participant rh:compound ?compound .
  OPTIONAL {?compound rh:chebi ?chebi } .
}

Q11: Explore the H. pylori tryptophan biosynthesis pathway (GO:0000162)

This one runs entirely against UniProt data already, so nothing needs to be flattened.

Example data (Turtle) — edit it, then re-run any query below

base <http://purl.uniprot.org/uniprot/>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix up: <http://purl.uniprot.org/core/>
prefix rh: <http://rdf.rhea-db.org/>
prefix taxon: <http://purl.uniprot.org/taxonomy/>
prefix GO: <http://purl.obolibrary.org/obo/GO_>
prefix path: <http://purl.uniprot.org/pathway/>

<O25948> up:reviewed true ;
  up:mnemonic "TRPA_HELPY" ;
  up:organism taxon:85962 ;
  up:classifiedWith GO:0000162 ;
  up:annotation <O25948#CA>, <O25948#PA> .

<O25948#CA> up:catalyticActivity <O25948#CAca> .
<O25948#CAca> up:catalyzedReaction rh:24945 .

<O25948#PA> a up:Pathway_Annotation ;
  rdfs:seeAlso path:trp-biosynthesis .

path:trp-biosynthesis rdfs:label "L-tryptophan biosynthesis" .

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX GO: <http://purl.obolibrary.org/obo/GO_>

SELECT distinct ?upProteinId ?goId ?rhReaction ?upPathway
WHERE {
  ?upProtein up:reviewed true .
  ?upProtein up:mnemonic ?upProteinId .
  # taxonomy constraint
  ?upProtein up:organism taxon:85962 .
  ?upProtein up:annotation/up:catalyticActivity/up:catalyzedReaction ?rhReaction .
  ?upProtein up:classifiedWith ?goId .
  # pathway constraint (GO Biological Process)
  VALUES ?goId { GO:0000162 }
  OPTIONAL {
    ?upProtein up:annotation ?pa .
    ?pa a up:Pathway_Annotation .
    ?pa rdfs:seeAlso/rdfs:label ?upPathway .
  }
}
ORDER BY ?upPathway

Q12: H. pylori enzyme complexes for the tryptophan biosynthesis pathway (MetaNetX)

The mnx:gpr/mnx:cata/mnx:cplx traversal is adapted from sparql-examples MetaNetX/11.

This extends Q11 with a SERVICE call to MetaNetX to resolve the enzyme complexes behind a reaction. MetaNetX is a third, specialized resource with its own reconciled-network data model, not something a toy fixture can usefully stand in for - run this one directly against the live endpoint.

Reference only — not runnable on this page: Federates UniProt with MetaNetX - run at https://sparql.uniprot.org/sparql

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX mnx: <https://rdf.metanetx.org/schema/>
PREFIX mnet: <https://rdf.metanetx.org/mnet/>
PREFIX GO: <http://purl.obolibrary.org/obo/GO_>

SELECT distinct
    ?upPathway
    ?upProteinId
    ?rhReaction
    ?mnxr
    ?cplx_label
    ?mnet
WHERE{
    ?upProtein up:reviewed true .
    ?upProtein up:mnemonic ?upProteinId .
    ?upProtein up:organism taxon:85962 .
    ?upProtein up:classifiedWith GO:0000162 .
    ?upProtein up:annotation/up:catalyticActivity/up:catalyzedReaction ?rhReaction .
    OPTIONAL {?upProtein up:annotation ?pa .
              ?pa a up:Pathway_Annotation ;
                  rdfs:seeAlso/rdfs:label ?upPathway . }
    SERVICE <https://rdf.metanetx.org/sparql> {
        ?mnxr mnx:reacXref ?rhReaction .
        ?reac mnx:mnxr     ?mnxr       .
        ?gpr  mnx:reac     ?reac       ;
              mnx:cata     ?cata       .
        ?cata mnx:cplx     ?cplx       .
        ?cplx rdfs:label   ?cplx_label .
        ?mnet mnx:gpr      ?gpr        .
        VALUES ?mnet {mnet:seed_Opt85962_1}
    }
}
ORDER BY ?upPathway

Visualization: taxonomic distribution of Rhea reactions in UniProtKB/Swiss-Prot

Taxonomic domain	NCBI taxid
Archaea	2157
Bacteria	2
Eukaryota	2759
Viruses	10239

Q20: Retrieve UniProtKB/Swiss-Prot proteins, their taxonomic domain and their catalyzed Rhea reactions

The original tutorial feeds this query’s results into a Venn diagram (via matplotlib) showing how many Rhea reactions are annotated in each taxonomic domain, and how much they overlap - a visualization over the entire UniProtKB/Swiss-Prot dataset. That’s neither a single runnable query result nor something a toy fixture can meaningfully visualize, so this one is reference-only; the original also warns it can take a few minutes even on the live endpoint.

Reference only — not runnable on this page: Feeds a Venn diagram over the full dataset - run at https://sparql.uniprot.org/sparql

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX keywords: <http://purl.uniprot.org/keywords/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>

SELECT distinct ?upProtein
                ?taxid
                ?domain
                ?domainName
                ?rhReaction
WHERE {
  # UniProtKB/Swiss-Prot entries (reviewed)
  ?upProtein up:reviewed true .
  ?upProtein up:organism ?taxid .
  ?taxid rdfs:subClassOf ?domain .
  VALUES (?domain) { (taxon:2157) (taxon:2) (taxon:2759) (taxon:10239)}
  ?domain up:scientificName ?domainName .
  ?upProtein up:annotation/up:catalyticActivity/up:catalyzedReaction ?rhReaction .
}

IDSM/Sachem service

Q30: Retrieve the Rhea reactions that involve cholesterol or cholesterol derivatives

This performs a chemical substructure search: given a molecule as a SMILES string, the IDSM/Sachem service finds every ChEBI compound that contains it as a substructure. That’s a specialized cheminformatics engine reached over SERVICE, not something an in-browser example dataset can reproduce - run this one directly against the live endpoint.

Reference only — not runnable on this page: Chemical substructure search via IDSM/Sachem - run at https://sparql.rhea-db.org/sparql

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX sachem: <http://bioinfo.uochb.cas.cz/rdf/v1.0/sachem#>
PREFIX idsm: <https://idsm.elixir-czech.cz/sparql/endpoint/>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX rh: <http://rdf.rhea-db.org/>

SELECT DISTINCT ?chebi
                ?chebiUniprotName
                ?rhReaction
                ?rhReactionEquation
WHERE {
  SERVICE idsm:chebi {
    ?chebi sachem:substructureSearch
    [ sachem:query "C1[C@@]2([C@]3(CC[C@]4([C@]([C@@]3(CC=C2C[C@H](C1)O)[H])(CC[C@@]4([C@H](C)CCCC(C)C)[H])[H])C)[H])C" ] .
  }
  ?rhReaction rdfs:subClassOf rh:Reaction .
  ?rhReaction rh:equation ?rhReactionEquation .
  ?rhReaction rh:status ?status .
  VALUES (?status) {(rh:Approved) (rh:Preliminary)}
  ?rhReaction rh:side ?reactionSide .
  ?reactionSide rh:contains ?participant .
  ?participant rh:compound ?compound .
  ?compound rh:chebi ?chebi .
  ?chebi up:name ?chebiUniprotName .
}