SPARQL example query
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115_Number_of_complete_EC_numbers_described_at_protein_level_at_domain_levels_at_component_level: Number of _complete_ EC numbers described at protein level, at domain levels, at component level
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 ?ecProt) as ?ecNumberInProteinCount) (count(distinct ?ecDomain) as ?ecNumberInDomainCount) (count(distinct ?ecComponent) as ?ecNumberInComponentCount) WHERE { ?protein up:reviewed true . OPTIONAL {?protein up:enzyme ?ecProt . } . OPTIONAL {?protein up:domain/up:enzyme ?ecDomain . } . OPTIONAL {?protein up:component/up:enzyme ?ecComponent . } . }Use116_biosodafrontend_rabit_mouse_orthologs: Rabbit's proteins encoded by genes that are orthologous to Mouse's HBB-Y gene and their cross reference links to Uniprot
PREFIX lscr: <http://purl.org/lscr#> PREFIX orth: <http://purl.org/net/orth#> PREFIX up: <http://purl.uniprot.org/core/> PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT DISTINCT ?PROTEIN_1 ?PROTEIN_2 ?UNIPROT_XREF_1 ?UNIPROT_XREF_2 WHERE { ?taxon_1 up:commonName 'Mouse' . ?taxon_2 up:commonName 'Rabbit' . SERVICE <https://sparql.omabrowser.org/sparql/> { ?cluster a orth:OrthologsCluster . ?cluster orth:hasHomologousMember ?node1 . ?cluster orth:hasHomologousMember ?node2 . ?node2 orth:hasHomologousMember* ?PROTEIN_2 . ?node1 orth:hasHomologousMember* ?PROTEIN_1 . ?PROTEIN_1 a orth:Protein . ?PROTEIN_1 orth:organism/obo:RO_0002162 ?taxon_1 ; rdfs:label 'HBB-Y' ; lscr:xrefUniprot ?UNIPROT_XREF_1 . ?PROTEIN_2 a orth:Protein . ?PROTEIN_2 orth:organism/obo:RO_0002162 ?taxon_2 . ?PROTEIN_2 lscr:xrefUniprot ?UNIPROT_XREF_2 . FILTER ( ?node1 != ?node2 ) } }Use117_biosodafrontend_glioblastoma_orthologs_rat: Which are the proteins associated with glioblastoma and the orthologs expressed in the rat brain?
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX orth: <http://purl.org/net/orth#> PREFIX sio: <http://semanticscience.org/resource/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> PREFIX lscr: <http://purl.org/lscr#> PREFIX genex: <http://purl.org/genex#> SELECT DISTINCT ?protein ?orthologous_protein ?gene ?annotation_text WHERE { { SELECT ?protein ?annotation_text WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:annotation ?annotation . ?annotation rdfs:comment ?annotation_text . ?annotation a up:Disease_Annotation . FILTER CONTAINS (?annotation_text, "glioblastoma") } } SERVICE <https://sparql.omabrowser.org/sparql/> { SELECT ?orthologous_protein ?protein ?gene WHERE { ?protein_OMA a orth:Protein . ?orthologous_protein a orth:Protein . ?cluster a orth:OrthologsCluster . ?cluster orth:hasHomologousMember ?node1 . ?cluster orth:hasHomologousMember ?node2 . ?node2 orth:hasHomologousMember* ?protein_OMA . ?node1 orth:hasHomologousMember* ?orthologous_protein . ?orthologous_protein orth:organism/obo:RO_0002162 taxon:10116 . # rattus norvegicus ?orthologous_protein sio:SIO_010079 ?gene . ?protein_OMA lscr:xrefUniprot ?protein . FILTER(?node1 != ?node2) } } SERVICE <https://www.bgee.org/sparql/> { ?gene genex:isExpressedIn ?a . ?a rdfs:label "brain" . ?gene orth:organism ?s . ?s obo:RO_0002162 taxon:10116. } }Use118_biosodafrontend_rat_brain_human_cancer: What are the Homo sapiens genes associated with cancer and their orthologs expressed in the Rattus norvegicus brain?
PREFIX up:<http://purl.uniprot.org/core/> PREFIX taxon:<http://purl.uniprot.org/taxonomy/> PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> PREFIX orth:<http://purl.org/net/orth#> PREFIX dcterms:<http://purl.org/dc/terms/> PREFIX obo:<http://purl.obolibrary.org/obo/> PREFIX lscr:<http://purl.org/lscr#> PREFIX genex:<http://purl.org/genex#> PREFIX sio: <http://semanticscience.org/resource/> SELECT ?gene ?orthologous_protein2 WHERE { { SELECT ?protein1 WHERE { ?protein1 a up:Protein; up:organism/up:scientificName 'Homo sapiens' ; up:annotation ?annotation . ?annotation rdfs:comment ?annotation_text. ?annotation a up:Disease_Annotation . FILTER CONTAINS (?annotation_text, "cancer") } } SERVICE <https://sparql.omabrowser.org/sparql/> { SELECT ?orthologous_protein2 ?protein1 ?gene WHERE { ?protein_OMA a orth:Protein . ?orthologous_protein2 a orth:Protein . ?cluster a orth:OrthologsCluster . ?cluster orth:hasHomologousMember ?node1 . ?cluster orth:hasHomologousMember ?node2 . ?node2 orth:hasHomologousMember* ?protein_OMA . ?node1 orth:hasHomologousMember* ?orthologous_protein2 .?orthologous_protein2 orth:organism/obo:RO_0002162/up:scientificName 'Rattus norvegicus' . ?orthologous_protein2 sio:SIO_010079 ?gene . ?protein_OMA lscr:xrefUniprot ?protein1 . FILTER(?node1 != ?node2) } } SERVICE <https://www.bgee.org/sparql/> { ?gene genex:isExpressedIn ?anatEntity . ?anatEntity rdfs:label 'brain' . ?gene orth:organism ?org . ?org obo:RO_0002162 taxon:10116 . } }Use119_uniref_distinct_ec_in_seed: Distinct Enzymes in UniRef50 seed entries
PREFIX up:<http://purl.uniprot.org/core/> SELECT (COUNT(DISTINCT ?enzyme) AS ?distinctEnzymesInUniRef50Seed) WHERE { GRAPH <http://sparql.uniprot.org/uniprot>{ ?protein ( up:enzyme | up:domain/up:enzyme | up:component/up:enzyme ) ?enzyme . } GRAPH <http://sparql.uniprot.org/uniref>{ ?protein up:seedFor ?cluster . ?cluster up:identity 0.5 . } }Use120_for_taxon_find_reference_proteomes: For a ncbi taxon identifier as a digit find it's reference proteome(s) if they exist
PREFIX up:<http://purl.uniprot.org/core/> PREFIX taxon:<http://purl.uniprot.org/taxonomy/> SELECT ?taxon ?reference_proteome WHERE { VALUES (?taxid) { (623) # Shigella flexneri (633) # Yersinia pseudotuberculosis } # Convert the digit to a correct IRI BIND(IRI(CONCAT(STR(taxon:), ?taxid)) AS ?taxon) ?taxon up:scientificName ?taxonName . OPTIONAL { ?reference_proteome a up:Reference_Proteome . ?reference_proteome up:organism ?taxon . } }Use121_proteins_and_diseases_linked: List all UniProtKB proteins and the diseases are annotated to be related.
PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?disease WHERE { ?protein a up:Protein ; up:annotation ?annotation . ?annotation a up:Disease_Annotation ; up:disease ?disease . ?disease a up:Disease . }Use122_enzymes_transporting_lipids_in_reviewed_human: List all UniProtKB SwissProt entries, facilitation the transport of lipids.
PREFIX up: <http://purl.uniprot.org/core/> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> SELECT ?protein ?chebi WHERE { GRAPH <https://sparql.rhea-db.org/rhea> { ?rhea rh:isTransport true . ?rhea rh:side/rh:contains/rh:compound ?compound . ?compound (rh:chebi|(rh:reactivePart/rh:chebi)|rh:underlyingChebi) ?chebi . } # CHEBI:18059 is the class for all Lipids ?chebi rdfs:subClassOf* CHEBI:18059 . # Select human reviewed entries from Swiss-Prot ?protein up:reviewed true ; up:organism taxon:9606 . # Link protein to catalytic activity, then to Rhea reaction ?protein up:annotation ?annotation . ?annotation up:catalyticActivity ?catalytic_activity_obj . ?catalytic_activity up:catalyzedReaction ?rhea . }Use123_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 . }) }Use124_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 . }Use125_CORDIS_EURIO_cited_project_results_in_uniprot: Use the CORDIS EURIO Knowledge Graph in combination with UniProt to find the count of outputs(DOIs) of their funded projects cited in UniProt.
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> PREFIX dcterms: <http://purl.org/dc/terms/> PREFIX up: <http://purl.uniprot.org/core/> PREFIX eurio: <http://data.europa.eu/s66#> PREFIX patent: <http://purl.uniprot.org/EPO/> PREFIX pubmed: <http://purl.uniprot.org/pubmed/> SELECT (IRI(CONCAT('https://cordis.europa.eu/project/id/', SAMPLE(?identifier))) AS ?id) (SAMPLE(?project_title) AS ?project_titles) (COUNT(DISTINCT ?doi_string) AS ?doisInSwissProt) (COUNT(DISTINCT ?protein) AS ?entriesInSwissProt) WHERE { SERVICE <https://cordis.europa.eu/datalab/sparql> { ?project a eurio:Project ; eurio:identifier ?identifier ; eurio:title ?project_title ; eurio:hasResult ?result . ?result eurio:doi ?doi . } #EURIO use literals of type xsd:anyURI to represent DOIs #without the leading doi: indicator BIND(CONCAT("doi:", STR(?doi)) AS ?doi_string) ?citation a up:Journal_Citation ; dcterms:identifier ?doi_string . ?protein up:citation ?citation . BIND(xsd:int(?identifier) AS ?intid) } GROUP BY ?project ORDER BY DESC(?intid)Use126_count_venom_related_proteins: Count the number of entries that are annotated to be related to venomous activity in selected taxonomic groups
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> PREFIX location: <http://purl.uniprot.org/locations/> SELECT (COUNT(DISTINCT ?protein) AS ?proteins) ?grouping ?groupingScientificName WHERE { VALUES ?grouping { taxon:6103 #sea anemones taxon:8570 #snakes taxon:6855 #scorpions taxon:6893 #Araneae taxon:50557 #Insecta taxon:37797 #Conoidea } ?grouping up:scientificName ?groupingScientificName . ?taxon rdfs:subClassOf ?grouping. ?protein up:organism ?taxon . { ?protein up:annotation ?tsa . ?tsa a up:Tissue_Specificity_Annotation ; rdfs:comment ?tsac . FILTER(REGEX(?tsac, 'venom', 'i')) } UNION { ?protein up:annotation ?scla . # location:177 is nematocyst ?scla a up:Subcellular_Location_Annotation ; up:locatedIn/up:cellularComponent location:177 . } } GROUP BY ?grouping ?groupingScientificName ORDER BY ?proteinsUse127_uniprot_human_reviewed_to_chebi: UniProt entries use ChEBI in the following annotations: Ligands, Cofactors and Enzymatic Activity. This query shows how these can all be retrieved in one go, to make a UniProt to ChEBI mapping. The example query is made smaller by retrieving only human entries in Swiss-Prot.
PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_> PREFIX up: <http://purl.uniprot.org/core/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT (SUBSTR(STR(?protein), STRLEN(STR(uniprotkb:))+1) AS ?proteinAc) (GROUP_CONCAT(DISTINCT ?chebiId; separator=',') AS ?chebis) WHERE { ?protein up:reviewed true ; up:organism taxon:9606 . { ?protein up:annotation ?ligandAnnotation . ?ligandAnnotation up:ligand/rdfs:subClassOf ?chebi } UNION { ?protein up:annotation ?cofactorAnnotation . ?cofactorAnnotation up:cofactor ?chebi . } UNION { ?protein up:annotation ?catalyticActivityAnnotation . ?catalyticActivityAnnotation a up:Catalytic_Activity_Annotation ; up:catalyticActivity ?catalyticActivity . ?catalyticActivity up:catalyzedReaction ?rhea . ?rhea rh:side/rh:contains/rh:compound ?compound . ?compound (rh:chebi|(rh:reactivePart/rh:chebi)|rh:underlyingChebi) ?chebi . } GRAPH <http://sparql.uniprot.org/chebi> { ?chebi a owl:Class . } BIND((CONCAT('chebi:',SUBSTR(STR(?chebi), STRLEN(STR(CHEBI:))+1))) AS ?chebiId) } GROUP BY ?proteinUse128_distinct_rhea_in_different_taxons_grouped_by_eco: Count of unique Rhea reactions/Evidence code pairs annotated in different taxa in Swiss-Prot
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX up: <http://purl.uniprot.org/core/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT (COUNT(DISTINCT ?rhea) as ?uniqueRheaCount) ?taxon ?taxonName ?eco WHERE { #Select taxa VALUES (?taxon) { (taxon:9606) # Homo sapiens (taxon:7742) # Vertebrata (taxon:33208) # Metazoa (taxon:33090) # Viridiplantae (taxon:4751) # Fungi (taxon:2) # Bacteria (taxon:2157) # Archaea (taxon:10239) # Viruses } ?taxon up:scientificName ?taxonName . GRAPH <http://sparql.uniprot.org/taxonomy>{ ?subc rdfs:subClassOf ?taxon . } GRAPH <http://sparql.uniprot.org/uniprot>{ { ?protein up:organism ?subc . } UNION { # Only useful in the Homo sapiens case ?protein up:organism ?taxon . } ?protein up:reviewed true . ?protein up:annotation ?annot . ?annot up:catalyticActivity ?caa . ?caa up:catalyzedReaction ?rhea . [] rdf:subject ?annot ; rdf:object ?caa ; up:attribution/up:evidence ?eco } } GROUP BY ?taxon ?taxonName ?eco ORDER BY ?taxonName ?ecoUse129_taxon_rhea_annotation_count: List Taxa Identifiers and the number of annotated Rhea reactions in each that have experimental evidence.
PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX ECO: <http://purl.obolibrary.org/obo/ECO_> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?taxon (COUNT(?rhea) AS ?experimentalRheaAnnotated) WHERE { GRAPH <http://sparql.uniprot.org/uniprot> { ?protein up:organism ?taxon ; up:annotation ?catalyticActivityAnnotation . ?catalyticActivityAnnotation up:catalyticActivity ?catalyticActivity . ?catalyticActivity up:catalyzedReaction ?rhea . [] rdf:subject ?catalyticActivityAnnotation ; rdf:object ?catalyticActivity ; up:attribution ?attr . ?attr up:evidence ECO:0000269 . } } GROUP BY ?taxonUse130_taxon_any_rhea_annotation_count: List Taxa Identifiers and the number of annotated Rhea reactions for each
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?taxon (COUNT(?rhea) AS ?rheaAnnotated) WHERE { GRAPH <http://sparql.uniprot.org/uniprot> { ?protein up:organism ?taxon ; up:annotation ?catalyticActivityAnnotation . ?catalyticActivityAnnotation up:catalyticActivity ?catalyticActivity . ?catalyticActivity up:catalyzedReaction ?rhea . } } GROUP BY ?taxonUse62_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 . }Use63_diseases_involving_enzymes_located_in_mitochondrion: Find (Human genetic) diseases that are thought to be related to Enzymes, known to be located in the Mitochondrion
PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT DISTINCT ?disease WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:annotation ?disease_annotation , ?subcellularLocation . { ?protein up:enzyme [] . } UNION { ?protein up:annotation/a up:Catalytic_Activity_Annotation . } ?disease_annotation a up:Disease_Annotation ; up:disease ?disease . ?subcellularLocation a up:Subcellular_Location_Annotation ; up:locatedIn ?location . ?location up:cellularComponent ?component . ?component up:partOf* <http://purl.uniprot.org/locations/173> . }Use64_diseases_related_to_mutation_in_active_site: Find (Human Genetic) diseases, that are related to a natural variant on the active site of an enzyme.
PREFIX faldo: <http://biohackathon.org/resource/faldo#> 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 ?disease WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:annotation ?disease_annotation, ?active_site_annotation, ?natural_variant_annotation . { ?protein up:enzyme [] . } UNION { ?protein up:annotation/a up:Catalytic_Activity_Annotation . } ?disease_annotation a up:Disease_Annotation ; up:disease ?disease . ?active_site_annotation a up:Active_Site_Annotation ; up:range ?active_site_range . ?active_site_range faldo:begin ?active_site_begin . ?active_site_begin faldo:position ?active_site_position ; faldo:reference ?sequence . ?natural_variant_annotation a up:Natural_Variant_Annotation ; up:range ?natural_variant_range ; skos:related ?disease . ?natural_variant_range faldo:begin ?natural_variant_begin ; faldo:end ?natural_variant_end . ?natural_variant_begin faldo:position ?natural_variant_begin_position . ?natural_variant_end faldo:position ?natural_variant_end_position ; faldo:reference ?sequence . FILTER(?natural_variant_begin_position >= ?active_site_position && ?active_site_position <= ?natural_variant_end_position) }Use65_distinct_extinct_organisms_in_uniprotkb: How many distinct extinct organisms are represented in UniProtKB
PREFIX keywords: <http://purl.uniprot.org/keywords/> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?taxon (SAMPLE(?name) AS ?anName) (COUNT(DISTINCT ?protein) AS ?entriesPerExtinctTaxon) WHERE { GRAPH<http://sparql.uniprot.org/taxonomy>{ ?taxon a up:Taxon ; up:scientificName ?name . } ?protein up:organism ?taxon ; up:classifiedWith keywords:952 . } GROUP BY ?taxon ORDER BY ?taxonUse66_distinct_rhea_transport_in_reviewed_uniprot: Count number of unique Rhea transport reactions annotated in reviewed UniProtKB entries.
PREFIX rh: <http://rdf.rhea-db.org/> PREFIX up: <http://purl.uniprot.org/core/> SELECT (COUNT(DISTINCT ?rhea) AS ?distinctRheaTransportInUniProt) WHERE { GRAPH <https://sparql.rhea-db.org/rhea> { ?rhea rh:isTransport true . } ?protein up:annotation ?ann . ?ann up:catalyticActivity ?ca . ?ca up:catalyzedReaction ?rhea . }Use67_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 { ?uniprot up:annotation/up:catalyticActivity/up:catalyzedReaction ?rhea ; up:organism taxon:9606 ; up:mnemonic ?mnemonic . SERVICE <https://sparql.rhea-db.org/sparql> { ?rhea rh:side/rh:contains/rh:compound ?compound . ?compound (rh:chebi|(rh:reactivePart/rh:chebi)|rh:underlyingChebi) ?chebi . } ?chebi chebislash:smiles ?smiles ; chebislash:inchikey ?inchiKey . }Use70_enzymes_interacting_with_molecules_similar_to_dopamine: Look for enzymes catalyzing reactions with molecules similar to dopamine.
PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX sachem: <http://bioinfo.uochb.cas.cz/rdf/v1.0/sachem#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?rhea ?chebi WHERE { # Use the smiles of dopamine CHEBI:18243 SERVICE <https://idsm.elixir-czech.cz/sparql/endpoint/chebi>{ ?chebi sachem:similarCompoundSearch [ sachem:query "NCCc1ccc(O)c(O)c1" ] . } GRAPH<https://sparql.rhea-db.org/rhea>{ ?rhea rh:side/rh:contains/rh:compound ?compound . ?compound (rh:chebi|(rh:reactivePart/rh:chebi)|rh:underlyingChebi) ?chebi . } ?protein up:reviewed true ; up:annotation ?caa . ?caa up:catalyticActivity/up:catalyzedReaction ?rhea . }Use71_enzymes_interacting_with_molecules_similar_to_dopamine_with_variants_related_to_disease: Look for enzymes catalyzing reactions with molecules similar to dopamine, with natural variants related to a disease.
PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX sachem: <http://bioinfo.uochb.cas.cz/rdf/v1.0/sachem#> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?rhea ?chebi ?disease WHERE { # Use the smiles of dopamine CHEBI:18243 SERVICE <https://idsm.elixir-czech.cz/sparql/endpoint/chebi>{ ?chebi sachem:similarCompoundSearch [ sachem:query "NCCc1ccc(O)c(O)c1" ] . } GRAPH<https://sparql.rhea-db.org/rhea>{ ?rhea rh:side/rh:contains/rh:compound ?compound . ?compound (rh:chebi|(rh:reactivePart/rh:chebi)|rh:underlyingChebi) ?chebi . } ?protein up:reviewed true ; up:annotation ?caa, ?natural_variant_annotation, ?disease_annotation . ?caa up:catalyticActivity/up:catalyzedReaction ?rhea . ?natural_variant_annotation a up:Natural_Variant_Annotation ; skos:related ?disease . ?disease_annotation a up:Disease_Annotation ; up:disease ?disease . }Use72_enzymes_mapping_to_PDB: Select a mapping of UniProtKB enzymes to PDB entries using the UniProtKB cross-references to the PDB database.
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 ?protein ?db WHERE { ?protein a up:Protein . ?protein rdfs:seeAlso ?db . ?db up:database <http://purl.uniprot.org/database/PDB> . { ?protein up:enzyme ?enzyme . } UNION { ?protein up:annotation/rdf:type up:Catalytic_Activity_Annotation . } }Use73_enzymes_related_to_protein: Select Enzyme Classification (EC) classes that have a protein associated to them
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> SELECT DISTINCT ?enzyme WHERE { ?protein a up:Protein . { ?protein up:enzyme ?enzyme . } UNION { ?protein up:annotation ?caa . ?caa a up:Catalytic_Activity_Annotation . ?caa up:catalyticActivity ?ca . ?ca up:enzymeClass ?enzyme } UNION { ?protein up:component/up:enzyme ?enzyme . } UNION { ?protein up:domain/up:enzyme ?enzyme . } }Use