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Rhea citations and cross-references

Every Rhea reaction can point outward in two different ways: a citation, a PubMed reference backing the reaction, and a cross-reference, a link to the equivalent reaction in another database such as KEGG, MetaCyc or MACiE. This page covers both.

Unlike the metabolism tutorial, almost none of this needs SERVICE. Citations and cross-references live directly on the reaction data in the Rhea endpoint itself, so every query below runs against a small fixture built just for this page - no federation required.

Citations

Q1: Select all citations of a given reaction

Adapted from sparql-examples Rhea/40.

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 pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>

rh:19553 rdfs:subClassOf rh:Reaction ;
  rh:status rh:Approved ;
  rh:equation "L-tryptophan + H2O = indole + pyruvate + NH4(+)" ;
  rh:citation pubmed:16790938, pubmed:236639, pubmed:9551100 .

rh:19069 rdfs:subClassOf rh:Reaction ;
  rh:status rh:Approved ;
  rh:equation "(R)-S-lactoylglutathione = methylglyoxal + glutathione" ;
  rh:citation pubmed:14841219, pubmed:4574550 .

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

SELECT ?reaction ?citation
WHERE {
  BIND(rh:19553 AS ?reaction)
  ?reaction rdfs:subClassOf rh:Reaction .
  ?reaction rh:citation ?citation .
}

Q2: Count citations per reaction, most-cited first

Adapted from sparql-examples Rhea/41.

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 pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>

rh:19553 rdfs:subClassOf rh:Reaction ;
  rh:citation pubmed:16790938, pubmed:236639, pubmed:9551100 .

rh:19069 rdfs:subClassOf rh:Reaction ;
  rh:citation pubmed:14841219, pubmed:4574550 .

rh:19545 rdfs:subClassOf rh:Reaction ;
  rh:citation pubmed:15788404 .

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

SELECT ?reaction (COUNT(DISTINCT ?citation) AS ?countPubmedPerReaction)
WHERE {
  ?reaction rdfs:subClassOf rh:Reaction .
  ?reaction rh:citation ?citation .
}
GROUP BY ?reaction
ORDER BY DESC(COUNT(DISTINCT ?citation))

Q3: Average number of citations, among reactions that have at least one

Adapted from sparql-examples Rhea/42.

A nested SELECT first counts citations per reaction, then the outer query averages those counts. Reactions with zero citations never appear in the inner query, so they don’t pull the average down - that’s a different question, asked in Q5 below.

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 pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>

rh:19553 rdfs:subClassOf rh:Reaction ;
  rh:citation pubmed:16790938, pubmed:236639, pubmed:9551100 .

rh:19069 rdfs:subClassOf rh:Reaction ;
  rh:citation pubmed:14841219, pubmed:4574550 .

rh:19545 rdfs:subClassOf rh:Reaction ;
  rh:citation pubmed:15788404 .

PREFIX rh: <http://rdf.rhea-db.org/>

SELECT (AVG(?linksToPubmedPerReaction) AS ?avgLinksToPubmedPerReaction)
WHERE {
  SELECT ?reaction (COUNT(DISTINCT ?citation) AS ?linksToPubmedPerReaction)
  WHERE {
    ?reaction rh:citation ?citation .
  }
  GROUP BY ?reaction
  ORDER BY DESC(?linksToPubmedPerReaction)
}

Q4: Find reactions cited by a given PubMed ID

Adapted from sparql-examples Rhea/30.

rh:citation points at a PubMed IRI, not a plain number, so to show the PubMed ID as readable text the query strips the IRI down to its last segment with STRAFTER.

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 pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>

rh:19553 rdfs:subClassOf rh:Reaction ;
  rh:status rh:Approved ;
  rh:equation "L-tryptophan + H2O = indole + pyruvate + NH4(+)" ;
  rh:citation pubmed:16790938 .

rh:19069 rdfs:subClassOf rh:Reaction ;
  rh:status rh:Approved ;
  rh:equation "(R)-S-lactoylglutathione = methylglyoxal + glutathione" ;
  rh:citation pubmed:14841219 .

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/>

SELECT ?reaction ?pubMedID ?reactionEquation
WHERE {
  BIND(pubmed:16790938 AS ?cit)
  ?reaction rdfs:subClassOf rh:Reaction .
  ?reaction rh:status rh:Approved .
  ?reaction rh:equation ?reactionEquation .
  ?reaction rh:citation ?cit .
  BIND(strafter(str(?cit), str(pubmed:)) AS ?pubMedID)
}

Q5: Approved reactions that are missing a citation

Adapted from sparql-examples Rhea/119.

Not every approved reaction has a citation yet. OPTIONAL plus FILTER NOT EXISTS finds the reactions where the pattern never matches at all - the same trick used for the chebi cross-reference in the metabolism tutorial’s H. pylori query. Swap the SELECT ?reaction for SELECT (COUNT(?reaction) AS ?count) and you get Rhea/118, just a count instead of the list.

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 pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>

rh:19553 rdfs:subClassOf rh:Reaction ;
  rh:status rh:Approved ;
  rh:equation "L-tryptophan + H2O = indole + pyruvate + NH4(+)" ;
  rh:citation pubmed:16790938 .

rh:10484 rdfs:subClassOf rh:Reaction ;
  rh:status rh:Approved ;
  rh:equation "N-feruloylglycine + H2O = (E)-ferulate + glycine" .

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

SELECT ?reaction
WHERE {
  ?reaction rdfs:subClassOf rh:Reaction .
  ?reaction rh:status rh:Approved .
  OPTIONAL { ?reaction rh:citation ?citation . }
  FILTER (NOT EXISTS { ?reaction rh:citation ?citation . })
}
ORDER BY ?reaction

Cross-references to other databases

A cross-reference is not stored as directly as a citation. Rhea reactions come in three forms: the reaction itself (its rh:equation and status), a bidirectional form (rh:bidirectionalReaction, the reaction written as an equilibrium), and one or more directional forms (rh:directionalReaction, the same chemistry written left-to-right or right-to-left). A cross-reference to KEGG, MetaCyc, MACiE or another database is attached with rdfs:seeAlso, but it can sit on either the directional or the bidirectional form depending on the database - which is why every query below checks both.

Q6: Retrieve all cross-references for a given reaction

Adapted from sparql-examples Rhea/35.

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:19069 rdfs:subClassOf rh:Reaction ;
  rh:status rh:Approved ;
  rh:equation "(R)-S-lactoylglutathione = methylglyoxal + glutathione" ;
  rh:directionalReaction rh:19071 ;
  rh:bidirectionalReaction rh:19072 .

rh:19071 rdfs:seeAlso <http://identifiers.org/biocyc/ECOCYC:GLYOXI-RXN>,
  <http://identifiers.org/macie/M0032> .

rh:19072 rdfs:seeAlso <http://identifiers.org/biocyc/METACYC:GLYOXI-RXN>,
  <http://identifiers.org/kegg.reaction/R02530> .

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

SELECT ?reaction ?xref
WHERE {
  BIND(rh:19069 AS ?reaction)
  ?reaction rdfs:subClassOf rh:Reaction .
  ?reaction rh:directionalReaction ?directionalReaction .
  OPTIONAL { ?directionalReaction rdfs:seeAlso ?xref . }
  ?reaction rh:bidirectionalReaction ?bidirectionalReaction .
  OPTIONAL { ?bidirectionalReaction rdfs:seeAlso ?xref . }
}

Q7: Count how many reactions have at least one cross-reference

Adapted from sparql-examples Rhea/27.

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:19069 rdfs:subClassOf rh:Reaction ;
  rh:directionalReaction rh:19071 ;
  rh:bidirectionalReaction rh:19072 .

rh:19071 rdfs:seeAlso <http://identifiers.org/biocyc/ECOCYC:GLYOXI-RXN>,
  <http://identifiers.org/macie/M0032> .

rh:19072 rdfs:seeAlso <http://identifiers.org/biocyc/METACYC:GLYOXI-RXN>,
  <http://identifiers.org/kegg.reaction/R02530> .

rh:11932 rdfs:subClassOf rh:Reaction ;
  rh:directionalReaction rh:11933 ;
  rh:bidirectionalReaction rh:10003 .

rh:11933 rdfs:seeAlso <http://identifiers.org/biocyc/METACYC:ACETONE-CYANHYDRIN-LYASE-RXN>,
  <http://identifiers.org/macie/M0217> .

rh:12520 rdfs:subClassOf rh:Reaction ;
  rh:directionalReaction rh:12522 ;
  rh:bidirectionalReaction rh:12523 .

rh:12520 deliberately carries no rdfs:seeAlso at all - it has directional and bidirectional forms like every reaction, just no cross-reference on either of them, which is why the count below is 2, not 3.

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

SELECT (COUNT(DISTINCT ?reaction) AS ?distinctReactionCount)
WHERE {
  ?reaction rdfs:subClassOf rh:Reaction .
  ?reaction rh:directionalReaction ?directionalReaction .
  ?reaction rh:bidirectionalReaction ?bidirectionalReaction .
  OPTIONAL { ?directionalReaction rdfs:seeAlso ?xref . }
  OPTIONAL { ?bidirectionalReaction rdfs:seeAlso ?xref . }
  FILTER (BOUND(?xref))
}

Q8: Count reactions cross-referenced to KEGG specifically

Adapted from sparql-examples Rhea/36.

Cross-references aren’t typed by predicate - a KEGG link and a MetaCyc link both arrive as a plain rdfs:seeAlso. To scope a query to one specific external database, match the shape of its identifier IRI instead, with a regex filter against the known namespace.

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:19069 rdfs:subClassOf rh:Reaction ;
  rh:directionalReaction rh:19071 ;
  rh:bidirectionalReaction rh:19072 .

rh:19071 rdfs:seeAlso <http://identifiers.org/biocyc/ECOCYC:GLYOXI-RXN>,
  <http://identifiers.org/macie/M0032> .

rh:19072 rdfs:seeAlso <http://identifiers.org/biocyc/METACYC:GLYOXI-RXN>,
  <http://identifiers.org/kegg.reaction/R02530> .

rh:11932 rdfs:subClassOf rh:Reaction ;
  rh:directionalReaction rh:11933 ;
  rh:bidirectionalReaction rh:10003 .

rh:11933 rdfs:seeAlso <http://identifiers.org/biocyc/METACYC:ACETONE-CYANHYDRIN-LYASE-RXN>,
  <http://identifiers.org/macie/M0217> .

rh:11932 has cross-references too, but only on its directional form, to MetaCyc and MACiE - no KEGG anywhere. That’s what makes this a real test of the regex scoping, not just a repeat of Q7’s count.

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

SELECT (COUNT(?reaction) AS ?reactionCount)
WHERE {
  ?reaction rdfs:subClassOf rh:Reaction .
  ?reaction rh:bidirectionalReaction ?bidirectionalReaction .
  ?bidirectionalReaction rdfs:seeAlso ?xref .
  FILTER (regex(str(?xref), str(kegg:)))
}

Going further: resolve a KEGG reaction back to Rhea and its enzymes

Adapted from sparql-examples Rhea/137 (“kegg reaction to rhea ec and uniprot enzymes”) - not yet published on the sparql-examples site, so no link here.

Cross-references also work in reverse: given a KEGG reaction accession, the same rh:bidirectionalReaction/rdfs:seeAlso link resolves it back to the matching Rhea reaction(s) and their EC numbers, and from there SERVICE reaches into UniProt for the enzymes that actually catalyze it in a given organism. This crosses two live endpoints, so it’s reference-only here - run it directly against Rhea:

Reference only — not runnable on this page: Federates Rhea with UniProt - 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 kegg: <http://identifiers.org/kegg.reaction/>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>

SELECT ?reaction ?equation ?ec ?protein
WHERE {
  BIND (kegg:R00162 AS ?keggReaction)
  ?reaction rdfs:subClassOf rh:Reaction ;
    rh:status rh:Approved ;
    rh:equation ?equation ;
    rh:ec ?ec ;
    rh:bidirectionalReaction ?bi .
  ?bi rdfs:seeAlso ?keggReaction .

  SERVICE <https://sparql.uniprot.org/sparql> {
    ?protein a up:Protein ;
      up:reviewed true ;
      up:organism taxon:9606 .
    {
      ?protein up:enzyme ?ec
    } UNION {
      ?protein up:domain/up:enzyme ?ec
    } UNION {
      ?protein up:component/up:enzyme ?ec
    }
  }
}