40: Retrieve human enzymes that metabolize sphingolipids and are annotated in ChEMBL

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 taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT DISTINCT ?protein ?chemblEntry WHERE { SERVICE <https://sparql.rhea-db.org/sparql> { ?rhea rdfs:subClassOf rh:Reaction ; rh:side/rh:contains/rh:compound/rh:chebi/rdfs:subClassOf+ CHEBI:26739 . } ?ca up:catalyzedReaction ?rhea . ?protein up:annotation/up:catalyticActivity ?ca ; up:organism taxon:9606 ; rdfs:seeAlso ?chemblEntry . ?chemblEntry up:database <http://purl.uniprot.org/database/ChEMBL> . }Use

40: Retrieve human enzymes that metabolize sphingolipids and are annotated in ChEMBL

41: Retrieve entries with sequences that are composed of fragments

PREFIX up: <http://purl.uniprot.org/core/> SELECT DISTINCT ?protein WHERE { ?protein a up:Protein ; up:sequence ?sequence . MINUS { ?sequence up:fragment [] } }Use

42: Connect patents cited in UniProtKB with those in the patent database at EPO via publication number.

43: Connect patents cited in UniProtKB with those in the patent database at EPO via publication number, whose grant date is more than twenty years in the past.

PREFIX patent: <http://data.epo.org/linked-data/def/patent/> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?grantDate ?patent ?application ?applicationNo WHERE { ?citation a up:Patent_Citation ; skos:exactMatch ?patent . BIND(SUBSTR(STR(?patent), 35) AS ?applicationNo) BIND(SUBSTR(STR(?patent), 33, 2) AS ?countryCode) SERVICE <https://data.epo.org/linked-data/query>{ ?publication patent:publicationNumber ?applicationNo ; patent:application ?application . ?application patent:grantDate ?grantDate . } BIND((year(now()) - 20) AS ?thisYearMinusTwenty) BIND(year(?grantDate) AS ?grantYear) FILTER(?grantYear < ?thisYearMinusTwenty) } ORDER BY ?grantYearUse

44: Find the Rhea and Interpro combinations in UniProtKB entries.

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?interpro ?rhea FROM <http://sparql.uniprot.org/uniprot> WHERE { ?protein up:reviewed true . ?protein up:annotation ?annotation . ?annotation up:catalyticActivity ?rhea . ?protein rdfs:seeAlso ?interpro . ?interpro up:database <http://purl.uniprot.org/database/InterPro> . } ORDER BY ?rheaUse

45: Retrieve drugs that target human enzymes involved in sterol metabolism (federated query with WikiData and Rhea).

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 taxon: <http://purl.uniprot.org/taxonomy/> PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/> PREFIX up: <http://purl.uniprot.org/core/> PREFIX wdt: <http://www.wikidata.org/prop/direct/> SELECT DISTINCT ?protein ?proteinFullName ?wikiChemical ?wikiChemicalLabel ?medicalConditionTreatedLabel WHERE { # ChEBI: retrieve members of the ChEBI class ChEBI:15889 (sterol) # Rhea: retrieve the reactions involving these ChEBI as participants SERVICE <https://sparql.rhea-db.org/sparql> { ?reaction rdfs:subClassOf rh:Reaction ; rh:status rh:Approved ; rh:side ?reactionSide . ?reactionSide rh:contains ?participant . ?participant rh:compound ?compound { ?compound rh:chebi ?chebi . ?chebi (rdfs:subClassOf)+ CHEBI:15889 } UNION { ?compound rh:chebi ?chebi . ?chebi2 rdfs:subClassOf ?chebiRestriction . ?chebiRestriction a owl:Restriction ; owl:onProperty chebihash:has_major_microspecies_at_pH_7_3 ; owl:someValuesFrom ?chebi . ?chebi2 (rdfs:subClassOf)+ CHEBI:15889 } } # UniProt: retrieve the human (taxid:9606) enzymes catalyzing these Rhea reactions ?ca up:catalyzedReaction ?reaction . ?a up:catalyticActivity ?ca . ?proteinIRI up:annotation ?a ; up:organism taxon:9606 ; up:recommendedName ?proteinRecName . ?proteinRecName up:fullName ?proteinFullName . # Find drugs in wikidata that interact with the UniProt Proteins BIND (SUBSTR(STR(?proteinIRI), STRLEN(STR(uniprotkb:))+1) AS ?protein) SERVICE <https://query.wikidata.org/sparql> { ?wp wdt:P352 ?protein . ?wikiChemical wdt:P129 ?wp . # Physically interacts with ?wikiChemical rdfs:label ?wikiChemicalLabel . ?wikiChemical wdt:P2175 ?wmc . # Medical conndition treated ?wmc rdfs:label ?medicalConditionTreatedLabel . FILTER(lang(?medicalConditionTreatedLabel) = 'en') FILTER(lang(?wikiChemicalLabel) = 'en') } }Use

46: Retrieve images of 'Anas' (Ducks) from the European Environmental Agency databases (federated query).

PREFIX eunisSpecies: <http://eunis.eea.europa.eu/rdf/species-schema.rdf#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?taxon ?ncbiTaxid ?eunisTaxon ?eunisName ?image WHERE { GRAPH <http://sparql.uniprot.org/taxonomy> { ?taxon a up:Taxon . # Taxon subclasses are materialized, do not use rdfs:subClassOf+ ?taxon rdfs:subClassOf taxon:8835 . BIND(strafter(str(?taxon), 'onomy/') AS ?ncbiTaxid) } SERVICE <https://semantic.eea.europa.eu/sparql> { ?eunisTaxon a eunisSpecies:SpeciesSynonym ; eunisSpecies:binomialName ?eunisName ; eunisSpecies:sameSpeciesNCBI ?ncbiTaxid ; <http://xmlns.com/foaf/0.1/depiction> ?image . } }Use

47: Find UniProt entries with a transmembrane region, with an Alanine in the 15 Aminoacid region preceding the transmembrane

PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?from ?interestingRegion WHERE { ?protein up:annotation ?annotation . ?annotation a up:Transmembrane_Annotation . # Get the coordinates of the Transmembrane ?annotation up:range ?range . ?range faldo:begin ?beginI . ?beginI faldo:position ?begin . ?beginI faldo:reference ?sequence . # The aas will have the specific IUPAC aminoacids ?sequence rdf:value ?aas . # We calculate the start by substracting 10 BIND(?begin - 10 AS ?tenBeforeBegin) # Can't start before the sequence starts or we might miss some results BIND(IF(?tenBeforeBegin < 1, 0, ?tenBeforeBegin) AS ?from) # Substring the IUPAC aminoacids BIND(SUBSTR(?aas, ?from, 15) AS ?interestingRegion) # The interestingRegion needds to contain an Alanine FILTER(CONTAINS(?interestingRegion, 'A')) }Use

48: Retrieve glycosylation sites and glycans on human enzymes (federated with glyconnect)

PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX foaf: <http://xmlns.com/foaf/0.1/> PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT DISTINCT ?protein ?glycosite ?glycostructure ?glycoimage WHERE{ ?protein up:annotation ?annotation . ?protein up:organism taxon:9606 . ?annotation a up:Catalytic_Activity_Annotation . ?protein up:sequence ?isoform . SERVICE <https://glyconnect.expasy.org/sparql> { ?glycosite faldo:reference ?isoform . ?glycosite faldo:position ?position . ?specificglycosite faldo:location ?glycosite . ?glycoprotein glycan:glycosylated_at ?specificglycosite . ?glycostructure glycan:glycosylates_at ?specificglycosite . ?glycostructure foaf:depiction ?glycoimage . } }Use

49: Retrieve the UniProt proteins, their catalyzed Rhea reactions, their encoding genes (Ensembl) and the anatomic entities where the genes are expressed (UBERON anatomic entites from Bgee expression data resource).

PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_> PREFIX genex: <http://purl.org/genex#> PREFIX lscr: <http://purl.org/lscr#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT DISTINCT ?protein ?ensemblGene ?reaction ?anatomicEntityLabel ?anatomicEntity WHERE { # federated query to Rhea enadpoint { SELECT DISTINCT ?reaction WHERE { SERVICE <https://sparql.rhea-db.org/sparql> { ?reaction rdfs:subClassOf rh:Reaction ; rh:equation ?reactionEquation ; rh:side ?reactionSide . ?reactionSide rh:contains ?participant . ?participant rh:compound ?compound . # compound constraint (CHEBI:16113 == cholesterol) ?compound rh:chebi CHEBI:16113 . } } } # taxonomy constraint (taxon:9606 == Homo sapiens) ?protein up:organism taxon:9606 ; up:annotation ?a ; rdfs:seeAlso / up:transcribedFrom ?ensemblGene . ?a a up:Catalytic_Activity_Annotation ; up:catalyticActivity ?ca . ?ca up:catalyzedReaction ?reaction . # federated query to Bgee (expression data) BIND(IRI(REPLACE(STR(?ensemblGene), "\\.[0-9]+$", "")) AS ?ensemblGeneNoVersion) SERVICE <https://www.bgee.org/sparql/> { ?gene lscr:xrefEnsemblGene ?ensemblGeneNoVersion ; genex:isExpressedIn ?anatomicEntity . ?anatomicEntity rdfs:label ?anatomicEntityLabel . } }Use

50: Where are the human genes encoding enzymes metabolizing N-acyl sphingosines expressed in the human body (federated query, with Rhea and Bgee)

PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_> PREFIX genex: <http://purl.org/genex#> PREFIX lscr: <http://purl.org/lscr#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT DISTINCT ?chebi ?reaction ?protein ?ensemblGene ?anatomicEntityLabel ?anatomicEntity WHERE { SERVICE <https://sparql.rhea-db.org/sparql> { ?reaction rdfs:subClassOf rh:Reaction . ?reaction rh:equation ?reactionEquation . ?reaction rh:side ?reactionSide . ?reactionSide rh:contains ?participant . ?participant rh:compound ?compound . ?compound rh:chebi ?chebi . ?chebi rdfs:subClassOf* CHEBI:52639 } ?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 . } }Use

50: Where are the human genes encoding enzymes metabolizing N-acyl sphingosines expressed in the human body (federated query, with Rhea and Bgee)

PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_> PREFIX genex: <http://purl.org/genex#> PREFIX lscr: <http://purl.org/lscr#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT DISTINCT ?chebi ?reaction ?protein ?ensemblGene ?anatomicEntityLabel ?anatomicEntity WHERE { SERVICE <https://sparql.rhea-db.org/sparql> { ?reaction rdfs:subClassOf rh:Reaction . ?reaction rh:equation ?reactionEquation . ?reaction rh:side ?reactionSide . ?reactionSide rh:contains ?participant . ?participant rh:compound ?compound . ?compound rh:chebi ?chebi . ?chebi rdfs:subClassOf* CHEBI:52639 } ?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 . } }Use

51: Find all proteins linked to arachidonate (CHEBI:32395)

PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX up: <http://purl.uniprot.org/core/> SELECT DISTINCT ?uniprot ?uniprotID ?recname ?gene ?chebi ?uniprotName WHERE { SERVICE <https://sparql.rhea-db.org/sparql> { VALUES (?chebi) { (CHEBI:32395) } ?rhea rh:side/rh:contains/rh:compound ?compound . ?compound rh:chebi ?chebi . ?chebi up:name ?uniprotName . } ?uniprot up:annotation/up:catalyticActivity/up:catalyzedReaction ?rhea . ?uniprot up:mnemonic ?uniprotID . ?uniprot up:recommendedName/up:fullName ?recname . OPTIONAL {?uniprot up:encodedBy/skos:prefLabel ?gene .} }Use

52: Retrieve drugs that target human enzymes involved in sterol metabolism (federated query with Rhea and ChEMBL via IDSM/Elixir czech republic).

PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_> PREFIX cco: <http://rdf.ebi.ac.uk/terms/chembl#> 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 skos: <http://www.w3.org/2004/02/skos/core#> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT DISTINCT ?protein ?proteinFullName ?activityType ?standardActivityValue ?standardActivityUnit ?chemblMolecule ?chemlbMoleculePrefLabel WHERE { # ChEBI: retrieve members of the ChEBI class ChEBI:15889 (sterol) # Rhea: retrieve the reactions involving these ChEBI as participants SERVICE <https://sparql.rhea-db.org/sparql> { ?reaction rdfs:subClassOf rh:Reaction ; rh:status rh:Approved ; rh:side ?reactionSide . ?reactionSide rh:contains ?participant . ?participant rh:compound ?compound { ?compound rh:chebi ?chebi . ?chebi (rdfs:subClassOf)+ CHEBI:15889 } UNION { ?compound rh:chebi ?chebi . ?chebi2 rdfs:subClassOf ?chebiRestriction . ?chebiRestriction a owl:Restriction ; owl:onProperty chebihash:has_major_microspecies_at_pH_7_3 ; owl:someValuesFrom ?chebi . ?chebi2 (rdfs:subClassOf)+ CHEBI:15889 } } # UniProt: retrieve the human (taxid:9606) enzymes catalyzing these Rhea reactions ?ca up:catalyzedReaction ?reaction . ?a up:catalyticActivity ?ca . ?protein up:annotation ?a ; up:organism taxon:9606 ; up:recommendedName ?proteinRecName . ?proteinRecName up:fullName ?proteinFullName . # Find drugs in wikidata that interact with the UniProt Proteins # ChEMBL: retrieve the corresponding targets and with drugs in clinical phase 4 # Via https://idsm.elixir-czech.cz/sparql/ SERVICE <https://idsm.elixir-czech.cz/sparql/endpoint/idsm> { ?activity a cco:Activity ; cco:hasMolecule ?chemblMolecule ; cco:hasAssay ?assay ; cco:standardType ?activityType ; cco:standardValue ?standardActivityValue ; cco:standardUnits ?standardActivityUnit . ?chemblMolecule cco:highestDevelopmentPhase ?highestDevelopmentPhase ; rdfs:label ?chemblMoleculeLabel ; skos:prefLabel ?chemlbMoleculePrefLabel . FILTER (?highestDevelopmentPhase > 3) ?assay cco:hasTarget ?target . ?target cco:hasTargetComponent/cco:targetCmptXref ?protein . ?protein a cco:UniprotRef . } }Use

52: Retrieve drugs that target human enzymes involved in sterol metabolism (federated query with Rhea and ChEMBL via IDSM/Elixir czech republic).

53: Find mouse homologs in OMABrowser of human enzymes that catalyze reactions involving Sterols (CHEBI:15889). Federating with Rhea-DB and OMABrowser.

PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_> PREFIX lscr: <http://purl.org/lscr#> PREFIX orth: <http://purl.org/net/orth#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT DISTINCT ?chebi ?reaction ?humanProtein ?mouseProtein ?cluster WHERE { SERVICE <https://sparql.rhea-db.org/sparql> { ?reaction rdfs:subClassOf rh:Reaction . ?reaction rh:side/rh:contains/rh:compound ?compound . ?compound rh:chebi ?chebi . ?chebi rdfs:subClassOf* CHEBI:15889 } ?humanProtein up:organism taxon:9606 . ?humanProtein up:annotation ?a . ?a a up:Catalytic_Activity_Annotation . ?a up:catalyticActivity ?ca . ?ca up:catalyzedReaction ?reaction . SERVICE <https://sparql.omabrowser.org/sparql/> { ?cluster a orth:ParalogsCluster . ?cluster orth:hasHomologousMember ?node1 , ?node2 . ?node1 orth:hasHomologousMember* ?orthoProtein1 . ?node2 orth:hasHomologousMember* ?orthoProtein2 . ?orthoProtein1 lscr:xrefUniprot ?mouseProtein . ?orthoProtein2 lscr:xrefUniprot ?humanProtein . # inTaxon mouse ?orthoProtein1 orth:organism/<http://purl.obolibrary.org/obo/RO_0002162> taxon:10090 . } }Use

54: Proteins with annotated binding sites for ligands similar to heme

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX sachem: <http://bioinfo.uochb.cas.cz/rdf/v1.0/sachem#> PREFIX up: <http://purl.uniprot.org/core/> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> SELECT ?protein ?mnemonic ?proteinName ?ligandSimilarityScore ?ligand WHERE { SERVICE <https://idsm.elixir-czech.cz/sparql/endpoint/chebi> { ?ssc sachem:compound ?ligand; sachem:score ?ligandSimilarityScore ; sachem:similaritySearch ?sss . # Smiles of Heme ?sss sachem:query "CC1=C(CCC([O-])=O)C2=[N+]3C1=Cc1c(C)c(C=C)c4C=C5C(C)=C(C=C)C6=[N+]5[Fe-]3(n14)n1c(=C6)c(C)c(CCC([O-])=O)c1=C2"; sachem:cutoff "8e-1"^^xsd:double ; sachem:aromaticityMode sachem:aromaticityDetect ; sachem:similarityRadius 1 ; sachem:tautomerMode sachem:ignoreTautomers . } ?protein up:mnemonic ?mnemonic ; up:recommendedName/up:fullName ?proteinName ; up:annotation ?annotation . ?annotation a up:Binding_Site_Annotation ; up:ligand/rdfs:subClassOf ?ligand . } ORDER BY DESC(?ligandSimilarityScore)Use

55: Number of proteins with annotated binding sites for metals or metal sulfur clusters (and experimental evidence for the binding)

PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_> PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?ligand ?ligandName (COUNT(DISTINCT ?protein) as ?entries) WHERE { ?protein up:annotation ?annotation . VALUES ?evs { obo:ECO_0000269 obo:ECO_0007744 } . VALUES ?chebids { CHEBI:25213 CHEBI:25214 } . ?st rdf:subject ?protein ; rdf:predicate up:annotation ; rdf:object ?annotation ; up:attribution/up:evidence ?evs . ?annotation up:ligand/rdfs:subClassOf ?ligand . ?ligand rdfs:subClassOf+ ?chebids ; rdfs:label ?ligandName . } GROUP BY ?ligand ?ligandName ORDER BY DESC(?entries)Use

56: Select Enzymes that have Ligands that have a known allosteric effect

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?ligandName ?ligandNote ?chebi WHERE { ?protein up:annotation ?annotation . ?annotation a up:Binding_Site_Annotation . ?annotation up:ligand ?ligand . ?ligand rdfs:comment ?ligandNote ; rdfs:subClassOf ?chebi ; rdfs:label ?ligandName . FILTER(REGEX(?ligandNote, "allosteric", "i")) }Use

57: Map PDB identifiers plus chains to UniProt

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?pdbId ?chain ?pdbChain ?uniprot WHERE { # A space separated list of pairs of PDB identifiers and the chain code. VALUES(?pdbId ?pdbChain) { ('6VXC' 'A') ('1BG3' 'B') } # Make an IRI out of the pdbId BIND(iri(concat('http://rdf.wwpdb.org/pdb/', ?pdbId)) AS ?pdb) # Map to UniProt entries ?uniprot rdfs:seeAlso ?pdb . ?pdb up:database <http://purl.uniprot.org/database/PDB> ; up:chainSequenceMapping ?chainSm . ?chainSm up:chain ?chainsPlusRange . # Extract the list of chains from the text representation. BIND(STRBEFORE(?chainsPlusRange, '=') AS ?chain) # Filter those that match. FILTER(CONTAINS(?chain, ?pdbChain)) }Use

58: Map UniProt to HGNC identifiers and Symbols

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?uniprot ?hgnc ?hgncSymbol WHERE { # A space separated list of UniProt primary accessions. VALUES (?acc) {('P05067') ('P00750')} BIND(iri(concat(str(uniprotkb:), ?acc)) AS ?uniprot) ?uniprot rdfs:seeAlso ?hgnc . ?hgnc up:database <http://purl.uniprot.org/database/HGNC> ; rdfs:comment ?hgncSymbol . }Use

59: Count all isoforms for a given proteome

PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> PREFIX proteome:<http://purl.uniprot.org/proteomes/> SELECT (COUNT(DISTINCT ?sequence) AS ?allIsoforms) WHERE { ?protein up:reviewed true . ?protein up:organism taxon:9606 . ?protein up:sequence ?sequence . ?protein up:proteome/^skos:narrower proteome:UP000005640 . }Use

60: Find Human proteins that catalyze reactions where substrates or product have a Cholestane skeleton

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#> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT DISTINCT ?protein ?disease ?rhea ?chebi ?omim WHERE { # Find complete ChEBIs with a Cholestane skeleton, via the Czech Elixir node IDSM Sachem chemical substructure search. 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]" ]. } # Use the fact that UniProt catalytic activities are annotated using Rhea # Mapping the found ChEBIs to Rhea reactions SERVICE <https://sparql.rhea-db.org/sparql>{ ?rhea rh:side/rh:contains/rh:compound/rdfs:subClassOf ?chebi . } # Match the found Rhea reactions with human UniProtKB proteins ?protein up:annotation/up:catalyticActivity/up:catalyzedReaction ?rhea . ?protein up:organism taxon:9606 . # Find only those human entries that have an annotated related disease, and optionaly map these to OMIM ?protein up:annotation/up:disease ?disease . OPTIONAL { ?disease rdfs:seeAlso ?omim . ?omim up:database <http://purl.uniprot.org/database/MIM> } }Use

61: Select the Gene Protein Reaction sets for Human (Ensembl Gene, Human UniProtKB, Catalyzed Rhea reactions)

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?ensemblGene ?protein ?rhea WHERE { ?protein up:reviewed true ; up:organism taxon:9606 . ?protein up:annotation ?caa ; rdfs:seeAlso ?ensemblTranscript . ?ensemblTranscript up:database <http://purl.uniprot.org/database/Ensembl> . ?caa up:catalyticActivity ?ca . ?ca up:catalyzedReaction ?rhea . ?ensemblTranscript up:transcribedFrom ?ensemblGene }Use

diseases_involving_enzymes: Find Diseases that are thought to be related to Enzymes

PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?disease ?diseaseLabel WHERE { ?protein up:enzyme|up:annotation/up:catalyticActivity/up:enzymeClass ?enzyme ; up:annotation ?diseaseAnnotation . ?diseaseAnnotation a up:Disease_Annotation ; up:disease ?disease . ?disease skos:prefLabel ?diseaseLabel . }Use

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SPARQL example query