108_Select_all_reactions_with_no_links_to_EC_numbers: Select all reactions with no links to EC numbers

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 . FILTER (NOT EXISTS {?reaction rh:ec ?ecNumber .}) } ORDER BY ?reactionUse

109_Distribution_of_reactions_according_to_the_first_level_of_enzyme_classification: Distribution of reactions according to the first level of enzyme classification

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

110_Select_reaction_ec_protein_for_a_given_reaction: Select for a given reaction

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh:<http://rdf.rhea-db.org/> PREFIX ec:<http://purl.uniprot.org/enzyme/> PREFIX up:<http://purl.uniprot.org/core/> SELECT ?reaction ?enzyme ?protein WHERE { BIND(rh:11672 AS ?reaction) ?reaction rdfs:subClassOf rh:Reaction . ?reaction rh:ec ?enzyme SERVICE <http://sparql.uniprot.org/sparql> { ?protein up:reviewed true . OPTIONAL {?protein up:enzyme ?enzyme. } . OPTIONAL {?protein up:domain/up:enzyme ?enzyme . } . OPTIONAL {?protein up:component/up:enzyme ?enzyme .} . } }Use

111_Select_reaction_ec_protein_for_a_given_EC_number: Select for a given EC number

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh:<http://rdf.rhea-db.org/> PREFIX ec:<http://purl.uniprot.org/enzyme/> PREFIX up:<http://purl.uniprot.org/core/> SELECT ?reaction ?enzyme ?protein WHERE { BIND(ec:2.6.1.62 AS ?enzyme) ?reaction rdfs:subClassOf rh:Reaction . ?reaction rh:status rh:Approved . ?reaction rh:ec ?enzyme . SERVICE <http://sparql.uniprot.org/sparql> { ?protein up:reviewed true . OPTIONAL {?protein up:enzyme ?enzyme. } . OPTIONAL {?protein up:domain/up:enzyme ?enzyme . } . OPTIONAL {?protein up:component/up:enzyme ?enzyme .} . } }Use

112_Total_number_of_reaction_ec_protein_links: Total number of links

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh:<http://rdf.rhea-db.org/> PREFIX ec:<http://purl.uniprot.org/enzyme/> PREFIX up:<http://purl.uniprot.org/core/> SELECT (count(?reaction) as ?reactionEcProteinLinkCount) WHERE { ?reaction rdfs:subClassOf rh:Reaction . ?reaction rh:ec ?enzyme SERVICE <http://sparql.uniprot.org/sparql> { ?protein up:reviewed true . ?protein up:enzyme ?enzyme. } }Use

113_Number_of_distinct_rhea_EC_number_UniProtKB_Swiss-Prot_entries_involved_in_reaction_ec_protein_links: Number of distinct rhea, EC number, UniProtKB/Swiss-Prot entries involved in ( ) links

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh:<http://rdf.rhea-db.org/> PREFIX ec:<http://purl.uniprot.org/enzyme/> PREFIX up:<http://purl.uniprot.org/core/> SELECT (count(distinct ?reaction) as ?reactionCount) (count(distinct ?enzyme) as ?enzymeCount) (count(distinct ?protein) as ?proteinCount) WHERE { ?reaction rdfs:subClassOf rh:Reaction . ?reaction rh:ec ?enzyme SERVICE <http://sparql.uniprot.org/sparql> { ?protein up:reviewed true . ?protein up:enzyme ?enzyme. } }Use

114_Retrieve_the_set_of_reactions_catalyzed_by_enzymes_of_the_ECOLI_reference_proteome_reaction-EC-protein: Retrieve the set of reactions catalyzed by enzymes of the ECOLI reference proteome ( - - )

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh:<http://rdf.rhea-db.org/> PREFIX ec:<http://purl.uniprot.org/enzyme/> PREFIX up:<http://purl.uniprot.org/core/> PREFIX taxon:<http://purl.uniprot.org/taxonomy/> PREFIX keywords:<http://purl.uniprot.org/keywords/> SELECT ?protein ?ecNumber ?reaction where { SERVICE <https://sparql.uniprot.org/sparql> { ?protein a up:Protein . ?protein up:reviewed true . ?protein up:organism taxon:83333 . ?protein up:classifiedWith keywords:1185 . {?protein up:enzyme ?ecNumber} UNION {?protein up:domain/up:enzyme ?ecNumber} UNION {?protein up:component/up:enzyme ?ecNumber} . } ?reaction rdfs:subClassOf rh:Reaction . ?reaction rh:status rh:Approved . ?reaction rh:ec ?ecNumber . }Use

115_Retrieve_the_set_of_metabolites_involved_in_reactions_catalyzed_by_human_genes_HUMAN_reference_proteome: Retrieve the set of metabolites involved in reactions catalyzed by human genes (HUMAN reference proteome)

PREFIX rh:<http://rdf.rhea-db.org/> PREFIX taxon:<http://purl.uniprot.org/taxonomy/> PREFIX ec:<http://purl.uniprot.org/enzyme/> PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> PREFIX up:<http://purl.uniprot.org/core/> PREFIX keywords:<http://purl.uniprot.org/keywords/> SELECT ?chebi ?reaction ?ecNumber ?protein ?ensemblTranscript ?ensemblGene WHERE { SERVICE <https://sparql.uniprot.org/sparql> { ?protein a up:Protein . ?protein up:reviewed true . ?protein up:organism taxon:9606 . ?protein up:classifiedWith keywords:1185 . ?protein rdfs:seeAlso ?ensemblTranscript . ?ensemblTranscript a up:Transcript_Resource . ?ensemblTranscript up:database <http://purl.uniprot.org/database/Ensembl> . ?ensemblTranscript up:transcribedFrom ?ensemblGene . {?protein up:enzyme ?ecNumber .} UNION {?protein up:domain/up:enzyme ?ecNumber .} UNION {?protein up:component/up:enzyme ?ecNumber .} } ?reaction rdfs:subClassOf rh:Reaction . ?reaction rh:status rh:Approved . ?reaction rh:ec ?ecNumber . ?reaction rh:side ?reactionSide . ?reactionSide rh:contains ?participant . ?participant rh:compound ?compound . ?compound rh:chebi ?chebi . # only considering small molecules participants }Use

116_Retrieve_the_set_of_reactions_catalyzed_by_human_enzymes_reactions_EC_proteins_from_HUMAN_reference_proteome: Retrieve the set of reactions catalyzed by human enzymes (reactions - EC - proteins from HUMAN reference proteome)

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh:<http://rdf.rhea-db.org/> PREFIX CHEBI:<http://purl.obolibrary.org/obo/CHEBI_> PREFIX ec:<http://purl.uniprot.org/enzyme/> PREFIX up:<http://purl.uniprot.org/core/> PREFIX taxon:<http://purl.uniprot.org/taxonomy/> PREFIX keywords:<http://purl.uniprot.org/keywords/> SELECT ?protein ?ecNumber ?reaction WHERE { ?reaction rdfs:subClassOf rh:Reaction . ?reaction rh:status rh:Approved . ?reaction rh:ec ?ecNumber . ?reaction rh:side ?reactionSide . ?reactionSide rh:contains ?participant . ?participant rh:compound ?compound . # ?compound rh:chebi CHEBI:57970 . ?compound rh:chebi ?chebi . ?chebi rdfs:subClassOf+ CHEBI:18059 . SERVICE <https://sparql.uniprot.org/sparql> { ?protein a up:Protein ; up:reviewed true ; up:organism taxon:83333 ; up:classifiedWith keywords:1185 . {?protein up:enzyme ?ecNumber} UNION {?protein up:domain/up:enzyme ?ecNumber} UNION {?protein up:component/up:enzyme ?ecNumber} . } }Use

117_Retrieve_parent_reactions_and_their_catalyzing_enzymes_for_a_metabolite_that_is_not_directly_involved_in_a_reaction: Retrieve parent reactions (and their catalyzing enzymes) for a metabolite that is not directly involved in a reaction (ex: CHEBI:83137).

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 ec:<http://purl.uniprot.org/enzyme/> PREFIX up:<http://purl.uniprot.org/core/> PREFIX taxon:<http://purl.uniprot.org/taxonomy/> PREFIX keywords:<http://purl.uniprot.org/keywords/> SELECT ?chebi ?ecNumber (count(?protein) as ?proteinCount) ?reaction ?equation WHERE { ?reaction rdfs:subClassOf rh:Reaction . ?reaction rh:status rh:Approved . ?reaction rh:equation ?equation . ?reaction rh:ec ?ecNumber . ?reaction rh:side ?reactionSide . ?reactionSide rh:contains ?participant . ?participant rh:compound ?compound . ?compound rh:chebi ?chebi . CHEBI:83137 rdfs:subClassOf+ ?chebi. SERVICE <https://sparql.uniprot.org/sparql> { ?protein a up:Protein . ?protein up:reviewed true . {?protein up:enzyme ?ecNumber} UNION {?protein up:domain/up:enzyme ?ecNumber} UNION {?protein up:component/up:enzyme ?ecNumber} . } } GROUP BY ?chebi ?ecNumber ?reaction ?equationUse

118_Number_of_approved_reactions_missing_citations: Number of approved reactions missing citations

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> SELECT (count(?reaction) as ?eactionMissingCitationCount) WHERE { ?reaction rdfs:subClassOf rh:Reaction . ?reaction rh:status rh:Approved . OPTIONAL {?reaction rh:citation ?citation .} FILTER (NOT EXISTS {?reaction rh:citation ?citation .}) }Use

119_Give_me_the_set_of_approved_reactions_missing_citations: Give me the set of approved reactions missing citations

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 ?reactionUse

126_list_protein_components_ec: list = protein - components -ec

PREFIX up:<http://purl.uniprot.org/core/> PREFIX ec:<http://purl.uniprot.org/enzyme/> PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> SELECT distinct ?enzyme WHERE { ?protein up:reviewed true . ?protein up:mnemonic ?mnemonic . ?protein up:domain ?domain . ?domain up:enzyme ?enzyme . }Use

128_list_EC_numbers_not_linked_to_UniProt_entries: list = EC numbers not linked to UniProt entries

PREFIX up:<http://purl.uniprot.org/core/> PREFIX ec:<http://purl.uniprot.org/enzyme/> PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> SELECT (count(distinct ?ecNumber) as ?ecCount) WHERE { ?ecNumber rdfs:subClassOf up:Enzyme . FILTER (NOT EXISTS {?ecNumber up:obsolete true .} ) FILTER (!regex(?ecNumber,'-')) . FILTER (NOT EXISTS { ?protein up:enzyme ?ecNumber . ?protein up:reviewed true . }) FILTER (NOT EXISTS { ?protein up:domain/up:enzyme ?ecNumber . ?protein up:reviewed true . }) FILTER (NOT EXISTS { ?protein up:reviewed true . ?protein up:component/up:enzyme ?ecNumber . }) }Use

130_Where_are_the_human_genes_encoding_enzymes_metabolizing_cholesterol_expressed: Where are the human genes encoding enzymes metabolizing cholesterol expressed?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> PREFIX : <http://purl.orthodb.org/> PREFIX rh:<http://rdf.rhea-db.org/> PREFIX odbgroup:<http://purl.orthodb.org/odbgroup/> SELECT * WHERE { SERVICE <https://sparql.orthodb.org/sparql/> { ?gene a :Gene; :memberOf odbgroup:2906at28890. ?gene :xref [a :Xref; :xrefResource ?xref]. ?xref a :Uniprot. } SERVICE <https://sparql.uniprot.org/sparql> { ?xref a up:Protein; up:recommendedName [up:fullName ?name] ; up:annotation/up:catalyticActivity/up:catalyzedReaction ?reaction . } ?reaction rdfs:subClassOf rh:Reaction . ?reaction rh:directionalReaction ?directionalReaction . OPTIONAL { ?directionalReaction rdfs:seeAlso ?xref2 . } ?reaction rh:bidirectionalReaction ?bidirectionalReaction . OPTIONAL { ?bidirectionalReaction rdfs:seeAlso ?xref2 . } }Use

131_Where_are_the_human_genes_encoding_enzymes_metabolizing_cholesterol_expressed: Where are the human genes encoding enzymes metabolizing cholesterol expressed?

PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> PREFIX rh:<http://rdf.rhea-db.org/> PREFIX CHEBI:<http://purl.obolibrary.org/obo/CHEBI_> 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 { ?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 (CHEBI:16113 == cholesterol) ?compound rh:chebi CHEBI:16113 . SERVICE <https://sparql.uniprot.org/sparql> { # taxonomy constraint (taxon:9606 == Homo sapiens) ?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 . } # federated query to Bgee (expression data) SERVICE <https://www.bgee.org/sparql/> { ?gene genex:isExpressedIn ?anatomicEntity . ?gene lscr:xrefEnsemblGene ?ensemblGene . ?anatomicEntity rdfs:label ?anatomicEntityLabel . } }Use

19_draft_human_metabolome: Generate a draft human metabolome

PREFIX chebislash: <http://purl.obolibrary.org/obo/chebi/> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?uniprot ?mnemonic ?rhea ?chebi ?smiles ?inchiKey WHERE { ?rhea rh:side/rh:contains/rh:compound ?compound . ?compound (rh:chebi|(rh:reactivePart/rh:chebi)|(rh:underlyingChebi/rh:chebi)) ?chebi . ?chebi chebislash:smiles ?smiles ; chebislash:inchikey ?inchiKey . SERVICE <https://sparql.uniprot.org/sparql> { ?uniprot up:annotation/up:catalyticActivity/up:catalyzedReaction ?rhea ; up:organism taxon:9606 ; up:mnemonic ?mnemonic . } }Use

20_search_chemical_names_in_japanese: Search for Chemical names starting in Japanese, translated to english using allie

PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT * WHERE { SERVICE <https://data.allie.dbcls.jp/sparql>{ ?x rdfs:label "1,2,4-トリクロロベンゼン"@ja ; rdfs:label ?englishLabel . FILTER(lang(?englishLabel) = "en") } BIND(STR(?englishLabel) AS ?englishLabelStr) ?chebi rdfs:label|oboInOwl:hasSynonym ?englishLabelStr . }Use

21_count_rhea_examples: SELECT the number of reactions in Rhea

PREFIX rh:<http://rdf.rhea-db.org/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT (count(?reaction) as ?reactionCount) WHERE { ?reaction rdfs:subClassOf rh:Reaction . }Use

22__Select_all_reactions_and_their_equation_ordered_by_reaction_identifier: Select all reactions and their equation, ordered by reaction identifier

PREFIX rh:<http://rdf.rhea-db.org/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?reaction ?reactionId ?equation WHERE { ?reaction rdfs:subClassOf rh:Reaction . ?reaction rh:equation ?equation . ?reaction rh:id ?reactionId . } ORDER BY ?reactionUse

23_Select_all_reaction_IDs_status_and_equations_ordered_by_reaction_identifier: Select all reaction IDs, status and equations ordered by reaction identifier

PREFIX rh:<http://rdf.rhea-db.org/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?reactionId ?status ?equation WHERE { ?reaction rdfs:subClassOf rh:Reaction . ?reaction rh:equation ?equation . ?reaction rh:status ?status . ?reaction rh:id ?reactionId . } ORDER BY ?reactionUse

24_Display_only_a_subset_of_reactions: Select the 10 reactions, with the lowest identifier by alphabetic sort

PREFIX rh:<http://rdf.rhea-db.org/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?reaction ?reactionId WHERE { ?reaction rdfs:subClassOf rh:Reaction . ?reaction rh:id ?reactionId . } ORDER BY ?reaction LIMIT 10Use

25_Select_the_first_10_reactions_starting_from_the_fifth_reaction: Select the fifth to fiftheenth (inclusive) reactions, with the lowest identifier by alphabetic sort

26_Select_the_number_of_reactions_with_status_Approved: Select the number of reactions with status Approved

PREFIX rh:<http://rdf.rhea-db.org/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT (count(?reaction) as ?reactionCount) WHERE { ?reaction rdfs:subClassOf rh:Reaction . ?reaction rh:status rh:Approved . }Use

27_Select_the_number_of_reactions_that_have_Xrefs: Select the number of reactions that have cross-references

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)) }Use

28_Select_all_reactions_with_Xrefs: Select all reactions with cross-references

PREFIX rh:<http://rdf.rhea-db.org/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT DISTINCT ?reaction 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)) } ORDER BY ?reactionUse

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SPARQL example query