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

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

1: Select all Rhea reactions

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> # Query 1 # Select all Rhea reactions (unspecified direction) # and return identifier (id), accession, boolean attributes (isChemicallyBalanced, isTransport) and chemical equation. # SELECT ?rhea ?id ?accession ?isChemicallyBalanced ?isTransport ?equation WHERE { ?rhea rdfs:subClassOf rh:Reaction . ?rhea rh:id ?id . ?rhea rh:accession ?accession . ?rhea rh:equation ?equation . ?rhea rh:isTransport ?isTransport . ?rhea rh:isChemicallyBalanced ?isChemicallyBalanced . }Use

2: Select all Rhea reactions annotated with a given Pubmed ID

PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> # 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 ?rheaUse

3: Select the specific form of RHEA:11628, a reaction that deals with general chemical classes (i.e. select the equivalent reactions involving instances of the chemical classes in RHEA:11628

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> # Query 3 # Select the specific form of RHEA:11628. # This query mimics the Related reactions sections of # https://www.rhea-db.org/rhea/11628 # SELECT ?rhea ?equation ?childrenRhea ?childrenEquation WHERE { VALUES (?rhea) {(rh:11628)} ?rhea rh:equation ?equation . ?childrenRhea rdfs:subClassOf+ ?rhea . ?childrenRhea rh:equation ?childrenEquation . }Use

4: Select all cross-references for a given reaction

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> # Query 4 # Select all cross-references mapped to RHEA:21016 # # This query mimics the Cross-references section of # https://www.rhea-db.org/rhea/21016 # SELECT distinct ?rhea ?rheaDir ?xref WHERE { ?rhea rdfs:subClassOf rh:Reaction . VALUES (?rhea) {(rh:21016)} { ?rhea rdfs:seeAlso ?xref . BIND(?rhea as ?rheaDir) } UNION { ?rhea rh:directionalReaction ?directionalReaction . ?directionalReaction rdfs:seeAlso ?xref . BIND(?directionalReaction as ?rheaDir ) } UNION { ?rhea rh:bidirectionalReaction ?bidirectionalReaction . ?bidirectionalReaction rdfs:seeAlso ?xref . BIND(?bidirectionalReaction as ?rheaDir ) } }Use

5: Select all Rhea reactions mapped to KEGG reactions

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> # Query 5 # Select all Rhea reactions mapped to KEGG reactions # KEGG reactions are mapped to Rhea bidirectional reactions # Rhea web query: https://www.rhea-db.org/rhea?query=kegg:* # SELECT ?rhea ?kegg ?rheaDir WHERE { ?rhea rdfs:subClassOf rh:Reaction . ?rhea rh:bidirectionalReaction ?rheaDir . ?rheaDir rdfs:seeAlso ?kegg . FILTER (regex(str(?kegg),'kegg')) }Use

6: Select all Rhea reactions mapped to MetaCyc reactions

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> # Query 6 # Select all Rhea reactions mapped to MetaCyc reactions # MetaCyc reactions are mapped to either undirected, left-to-right, right-to-left or bidirectional reactions # Rhea web query: https://www.rhea-db.org/rhea?query=metacyc:* # SELECT distinct ?rhea ?rheaDir ?metacyc WHERE { ?rhea rdfs:subClassOf rh:Reaction . { ?rhea rdfs:seeAlso ?metacyc . FILTER CONTAINS(str(?metacyc), "METACYC") BIND(?rhea as ?rheaDir) } UNION { ?rhea rh:directionalReaction ?directionalReaction . ?directionalReaction rdfs:seeAlso ?metacyc . FILTER CONTAINS(str(?metacyc), "METACYC") BIND(?directionalReaction as ?rheaDir ) } UNION { ?rhea rh:bidirectionalReaction ?bidirectionalReaction . ?bidirectionalReaction rdfs:seeAlso ?metacyc . FILTER CONTAINS(str(?metacyc), "METACYC") BIND(?bidirectionalReaction as ?rheaDir ) } }Use

7: Select all Rhea reactions mapped to Reactome reactions

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> # Query 7 # Select all Rhea reactions mapped to Reactome reactions # MetaCyc reactions are mapped to either undirected, left-to-right or right-to-left reactions # Rhea web query: https://www.rhea-db.org/rhea?query=reactome:* # SELECT distinct ?rhea ?rheaDir ?reactome WHERE { ?rhea rdfs:subClassOf rh:Reaction . { ?rhea rdfs:seeAlso ?reactome . FILTER CONTAINS(str(?reactome), "reactome") BIND(?rhea as ?rheaDir) } UNION { ?rhea rh:directionalReaction ?directionalReaction . ?directionalReaction rdfs:seeAlso ?reactome . FILTER CONTAINS(str(?reactome), "reactome") BIND(?directionalReaction as ?rheaDir ) } }Use

8: Select all Rhea reactions mapped to GO molecular functions

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> # Query 8 # Select all Rhea reactions mapped to GO molecular function # # This query corresponds to the Rhea website query: # https://www.rhea-db.org/rhea?query=go:* # SELECT ?go ?rhea ?equation WHERE { ?rhea rdfs:subClassOf rh:Reaction . ?rhea rdfs:seeAlso ?go . FILTER CONTAINS(str(?go), "GO_") ?rhea rh:equation ?equation . }Use

9: Select all Rhea reactions mapped to enzyme classification (EC numbers)

PREFIX ec: <http://purl.uniprot.org/enzyme/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> # Query 9 # Select all Rhea reactions mapped to EC numbers (enzyme classification) # # This query corresponds to the Rhea website query: # https://www.rhea-db.org/rhea?query=ec:* # SELECT ?ec ?ecNumber ?rhea ?accession ?equation WHERE { ?rhea rdfs:subClassOf rh:Reaction . ?rhea rh:accession ?accession . ?rhea rh:ec ?ec . BIND(strafter(str(?ec),str(ec:)) as ?ecNumber) ?rhea rh:isTransport ?isTransport . ?rhea rh:equation ?equation . }Use

10: Select all Rhea reactions linked to an enzyme classification (sub)-class

PREFIX ec: <http://purl.uniprot.org/enzyme/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> # Query 10 # Select all Rhea reactions mapped to # # This query corresponds to the Rhea website query: # https://www.rhea-db.org/rhea?query=ec:1.* # https://www.rhea-db.org/rhea?query=ec:1.1.* # https://www.rhea-db.org/rhea?query=ec:1.1.1.* # SELECT ?ec ?ecNumber ?rhea ?accession ?equation WHERE { ?rhea rdfs:subClassOf rh:Reaction . ?rhea rh:accession ?accession . ?rhea rh:ec ?ec . BIND(strafter(str(?ec),str(ec:)) as ?ecNumber) # class (e.g EC 1.-.-.-) FILTER (regex(?ecNumber,'^1\\.')) # sub-class (e.g EC 1.1.-.-) #FILTER (regex(?ecNumber,'^1\\.1\\.')) # sub-sub-class (e.g EC 1.1.1.-) #FILTER (regex(?ecNumber,'^1\\.1\\.1\\.')) ?rhea rh:equation ?equation . }Use

11: Distribution of reactions according to the first class of the enzyme classification (federated query)

PREFIX ec: <http://purl.uniprot.org/enzyme/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> # Query 11 # Retrieve the count of reactions mapped to each level (main class) of the enzyme classification # # This query mimics the Filter section of the Rhea website (Browse all reactions) # https://www.rhea-db.org/rhea?query= SELECT ?ecClass (STR(?ecName) AS ?ecClassName) (COUNT(?rhea) AS ?rheaCount) WHERE { SERVICE <https://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 . } ?rhea rdfs:subClassOf rh:Reaction . ?rhea rh:ec ?ecNumber . } GROUP BY ?ecClass ?ecNameUse

12: Select all Rhea reactions linked to protein sequences (enzymes and transporters) in UniProtKB

PREFIX rh: <http://rdf.rhea-db.org/> PREFIX up: <http://purl.uniprot.org/core/> # Query 12 # Select all Rhea reactions used to annotate enzyme sequences in UniProtKB # return the number of UniProtKB entries # Federated query using a service to UniProt SPARQL endpoint # # This query corresponds to the Rhea website query: # https://www.rhea-db.org/rhea?query=uniprot:* # SELECT ?uniprotCount ?rhea ?accession ?equation WHERE { SERVICE <https://sparql.uniprot.org/sparql> { SELECT ?rhea (count(?uniprot) as ?uniprotCount) { ?uniprot up:annotation/up:catalyticActivity/up:catalyzedReaction ?rhea . } GROUP BY ?rhea } ?rhea rh:accession ?accession . ?rhea rh:equation ?equation . }Use

13: Select all Rhea reactions used in UniProtKB/Swiss-Prot for a given organism (NCBI taxonomy ID).

PREFIX rh: <http://rdf.rhea-db.org/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> # Query 13 # Select all Rhea reactions used to annotate Escherichia coli (taxid=83333) in UniProtKB/Swiss-Prot # return the number of UniProtKB entries # # Federated query using a service to UniProt SPARQL endpoint # # This query cannot be performed using the Rhea search website SELECT ?uniprot ?mnemo ?rhea ?accession ?equation WHERE { SERVICE <https://sparql.uniprot.org/sparql> { VALUES (?taxid) { (taxon:83333) } GRAPH <http://sparql.uniprot.org/uniprot> { ?uniprot up:reviewed true . ?uniprot up:mnemonic ?mnemo . ?uniprot up:organism ?taxid . ?uniprot up:annotation/up:catalyticActivity/up:catalyzedReaction ?rhea . } } ?rhea rh:accession ?accession . ?rhea rh:equation ?equation . }Use

14: Select all Rhea reactions that have a given ChEBI ID as reaction participant

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/> # Query 14 # Select all Rhea reactions that have CHEBI:29985 (L-glutamate) as reaction participant # # This query corresponds to the Rhea website query: # https://www.rhea-db.org/rhea?query=chebi:29985 SELECT distinct ?chebi ?rhea ?equation WHERE { ?rhea rdfs:subClassOf rh:Reaction . ?rhea rh:equation ?equation . ?rhea rh:side/rh:contains/rh:compound ?compound . # # the ChEBI can be used either as a small molecule, the reactive part of a macromolecule or as a polymer. # ?compound (rh:chebi|(rh:reactivePart/rh:chebi)|(rh:underlyingChebi/rh:chebi)) ?chebi . VALUES (?chebi) { (CHEBI:29985) } }Use

15: Select all ChEBI compounds used in Rhea as reaction participant

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX up: <http://purl.uniprot.org/core/> # Query 15 # Select all ChEBI compounds used in Rhea as reaction participant # # This query can not be expressed in the Rhea website SELECT ?chebi ?name (count(?rhea) as ?countRhea) WHERE { ?rhea rdfs:subClassOf rh:Reaction . ?rhea rh:side/rh:contains/rh:compound ?compound . # # the ChEBI can be used either as a small molecule, the reactive part of a macromolecule or as a polymer. # ?compound (rh:chebi|(rh:reactivePart/rh:chebi)|(rh:underlyingChebi/rh:chebi)) ?chebi . ?chebi up:name ?name . } GROUP BY ?chebi ?name ORDER BY DESC(?countRhea)Use

16: Select all Rhea reactions that have a pair of ChEBI IDs as reaction participant and in opposite side

PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX up: <http://purl.uniprot.org/core/> # Query 16 # Select all Rhea reactions that have a pair of ChEBI IDs as reaction participant and in opposite side # Return Rhea reactions that have CHEBI:29985 (L-glutamate) as reaction participant in one side # and CHEBI:58359 (L-glutamine) in the other side # # This query cannot be expressed in the Rhea website SELECT ?chebi1 ?name1 ?chebi2 ?name2 ?rhea ?equation WHERE { VALUES (?chebi1) { (CHEBI:29985) } ?chebi1 up:name ?name1 . ?rhea rh:side ?reactionSide1 . ?reactionSide1 rh:contains / rh:compound / rh:chebi ?chebi1 . VALUES (?chebi2) { (CHEBI:58359) } ?chebi2 up:name ?name2 . ?rhea rh:side ?reactionSide2 . ?reactionSide2 rh:contains / rh:compound / rh:chebi ?chebi2 . ?reactionSide1 rh:transformableTo ?reactionSide2 . ?rhea rh:equation ?equation . }Use

17: Select all Rhea reactions that involve a lipid, i.e. children of CHEBI:18059 in the ChEBI hierarchy.

PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_> PREFIX chebihash: <http://purl.obolibrary.org/obo/chebi#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX up: <http://purl.uniprot.org/core/> # Query 17 # Select all Rhea reactions that involve a lipid, i.e. children of CHEBI:18059 in the ChEBI hierarchy. # # This query corresponds to the Rhea website query: # https://www.rhea-db.org/rhea?query=chebi:18059 # SELECT distinct ?chebi ?name ?rhea ?equation WHERE { ?rhea rdfs:subClassOf rh:Reaction . ?rhea rh:equation ?equation . ?rhea rh:side/rh:contains/rh:compound ?compound . # # the ChEBI can be used either as a small molecule, the reactive part of a macromolecule or as a polymer. # { ?chebi rdfs:subClassOf* CHEBI:18059 . # lipid ?compound (rh:chebi|(rh:reactivePart/rh:chebi)|(rh:underlyingChebi/rh:chebi)) ?chebi . } UNION { # add non-pH 7.3 species ?not7_3 rdfs:subClassOf* CHEBI:18059 . # lipid ?not7_3 rdfs:subClassOf ?chebiRestriction . ?chebiRestriction a owl:Restriction . ?chebiRestriction owl:onProperty chebihash:has_major_microspecies_at_pH_7_3 . ?chebiRestriction owl:someValuesFrom ?chebi . ?compound (rh:chebi|(rh:reactivePart/rh:chebi)|(rh:underlyingChebi/rh:chebi)) ?chebi . } ?chebi up:name ?name . }Use

18: Use IDSM Sachem to find ChEBIs with a a Cholestane skeleton (in SMILES). Then match returned ChEBIs to Rhea undirected reactions.

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX sachem: <http://bioinfo.uochb.cas.cz/rdf/v1.0/sachem#> SELECT ?rhea ?chebi WHERE { SERVICE <https://idsm.elixir-czech.cz/sparql/endpoint/chebi> { ?chebi sachem:substructureSearch [ sachem:query "[C@]12(CCC3CCCC[C@]3(C)[C@@]1([H])CC[C@]1(C)[C@@]([H])([C@@](C)([H])CCCC(C)C)CC[C@@]21[H])[H]" ]. } ?rhea rh:side/rh:contains/rh:compound/rdfs:subClassOf ?chebi . }Use

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