SPARQL example query
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/rh:chebi)) ?chebi . } ?protein up:reviewed true ; up:annotation ?caa . ?caa up:catalyticActivity/up:catalyzedReaction ?rhea . }Useenzymes_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.
Useenzymes_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.
Useenzymes_mapping_to_PDB: Select a mapping of UniProt Enzymes to PDB entries using the UniProt cross-references to the PDB database
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 . } }Useenzymes_mapping_to_PDB: Select a mapping of UniProt Enzymes to PDB entries using the UniProt 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 . } }Useenzymes_with_at_least_two_transmembrane_domains: Find Hydrolases (enzymes that catalyse the hydrolysis of various bonds) that have at least two transmembrane domains
SELECT ?protein WHERE { ?protein up:enzyme|up:annotation/up:catalyticActivity/up:enzymeClass ?enzymeClass ; up:annotation ?transMembraneAnnotation . ?enzymeClass rdfs:subClassOf <http://purl.uniprot.org/enzyme/3.-.-.-> . ?transMembraneAnnotation a up:Transmembrane_Annotation . } GROUP BY ?protein HAVING (COUNT(DISTINCT ?transMembraneAnnotation) >= 2)Useenzymes_with_at_least_two_transmembrane_domains: Find Hydrolases (enzymes that catalyse the hydrolysis of various bonds) that have at least two transmembrane domains
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein WHERE { ?protein up:enzyme|up:annotation/up:catalyticActivity/up:enzymeClass ?enzymeClass ; up:annotation ?transMembraneAnnotation . ?enzymeClass rdfs:subClassOf <http://purl.uniprot.org/enzyme/3.-.-.-> . ?transMembraneAnnotation a up:Transmembrane_Annotation . } GROUP BY ?protein HAVING (COUNT(DISTINCT ?transMembraneAnnotation) >= 2)Useenzymes_with_at_least_two_transmembrane_domains_PDB_xray: Find enzymes that have at least two transmembrane domains, whose structure is elucidated through X-Ray analysis
SELECT ?protein WHERE { ?protein a up:Protein ; up:annotation ?transmembrane_annotation ; rdfs:seeAlso ?wwPDB . { ?protein up:enzyme ?enzyme . } UNION { ?protein up:annotation/a up:Catalytic_Activity_Annotation . } ?wwPDB up:database <http://purl.uniprot.org/database/PDB> ; up:method up:X-Ray_Crystallography . ?transmembrane_annotation a up:Transmembrane_Annotation . } GROUP BY ?protein HAVING(COUNT(DISTINCT ?transmembrane_annotation ) >= 2)Useenzymes_with_at_least_two_transmembrane_domains_PDB_xray: Find enzymes that have at least two transmembrane domains, whose structure is elucidated through X-Ray analysis
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein WHERE { ?protein a up:Protein ; up:annotation ?transmembrane_annotation ; rdfs:seeAlso ?wwPDB . { ?protein up:enzyme ?enzyme . } UNION { ?protein up:annotation/a up:Catalytic_Activity_Annotation . } ?wwPDB up:database <http://purl.uniprot.org/database/PDB> ; up:method up:X-Ray_Crystallography . ?transmembrane_annotation a up:Transmembrane_Annotation . } GROUP BY ?protein HAVING(COUNT(DISTINCT ?transmembrane_annotation ) >= 2)Useenzymes_with_mutagenesis_affecting_active_site: Find enzymes, where the active site is a region affected by mutagenesis and show the comment regarding mutagenesis effect.
SELECT ?protein ?mutagenesisBeginPosition ?activeSiteBeginPosition ?mutagenesisRangeEndPosition ?mutagenesisComment WHERE { ?protein up:annotation ?activeSiteAnnotation , ?mutagenesisAnnotation . ?mutagenesisAnnotation a up:Mutagenesis_Annotation ; up:range ?mutagenesisRange ; rdfs:comment ?mutagenesisComment . ?activeSiteAnnotation a up:Active_Site_Annotation ; up:range ?activeSiteRange . ?activeSiteRange faldo:begin ?activeSiteBegin . ?activeSiteBegin faldo:position ?activeSiteBeginPosition ; faldo:reference ?sequence . ?mutagenesisRange faldo:begin ?mutagenesisRangeBegin ; faldo:end ?mutagenesisRangeEnd . ?mutagenesisRangeBegin faldo:position ?mutagenesisBeginPosition ; faldo:reference ?sequence . ?mutagenesisRangeEnd faldo:position ?mutagenesisRangeEndPosition . FILTER(?mutagenesisBeginPosition <= ?activeSiteBeginPosition && ?activeSiteBeginPosition <= ?mutagenesisRangeEndPosition) }Useenzymes_with_mutagenesis_affecting_active_site: Find enzymes, where the active site is a region affected by mutagenesis and show the comment regarding mutagenesis effect.
PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?mutagenesisBeginPosition ?activeSiteBeginPosition ?mutagenesisRangeEndPosition ?mutagenesisComment WHERE { ?protein up:annotation ?activeSiteAnnotation , ?mutagenesisAnnotation . ?mutagenesisAnnotation a up:Mutagenesis_Annotation ; up:range ?mutagenesisRange ; rdfs:comment ?mutagenesisComment . ?activeSiteAnnotation a up:Active_Site_Annotation ; up:range ?activeSiteRange . ?activeSiteRange faldo:begin ?activeSiteBegin . ?activeSiteBegin faldo:position ?activeSiteBeginPosition ; faldo:reference ?sequence . ?mutagenesisRange faldo:begin ?mutagenesisRangeBegin ; faldo:end ?mutagenesisRangeEnd . ?mutagenesisRangeBegin faldo:position ?mutagenesisBeginPosition ; faldo:reference ?sequence . ?mutagenesisRangeEnd faldo:position ?mutagenesisRangeEndPosition . FILTER(?mutagenesisBeginPosition <= ?activeSiteBeginPosition && ?activeSiteBeginPosition <= ?mutagenesisRangeEndPosition) }Usegenetic_disease_related_proteins: List all UniProt proteins annotated to be related to a genetic disease.
Usegenetic_disease_related_proteins: List all UniProt proteins annotated to be related to a genetic disease.
Usemnemonic_also_known_as_id: List all UniProt protein ID (mnemonic) for current UniProt entries.
SELECT ?uniprot ?mnemonic WHERE { GRAPH <http://sparql.uniprot.org/uniprot> { ?uniprot a up:Protein ; up:mnemonic ?mnemonic . } }Usemnemonic_also_known_as_id: List all UniProt protein ID (mnemonic) for current UniProt entries.
PREFIX up: <http://purl.uniprot.org/core/> SELECT ?uniprot ?mnemonic WHERE { GRAPH <http://sparql.uniprot.org/uniprot> { ?uniprot a up:Protein ; up:mnemonic ?mnemonic . } }Useobsolete_mnemonic_also_known_as_id: List all UniProt protein ID (mnemonic) that where used in the past for current UniProt entries.
SELECT ?uniprot ?obsoleteMnemonic WHERE { GRAPH <http://sparql.uniprot.org/uniprot> { ?uniprot a up:Protein ; up:oldMnemonic ?obsoleteMnemonic . } }Useobsolete_mnemonic_also_known_as_id: List all UniProt protein ID (mnemonic) that where used in the past for current UniProt entries.
PREFIX up: <http://purl.uniprot.org/core/> SELECT ?uniprot ?obsoleteMnemonic WHERE { GRAPH <http://sparql.uniprot.org/uniprot> { ?uniprot a up:Protein ; up:oldMnemonic ?obsoleteMnemonic . } }Userhea_reactions_annotated_as_experimental_and_only_small_molecules: Find all rhea (only small molecule) that are used in UniProt where the annotation has a paper and is tagged having experimental evidence.
SELECT ?rhea ?catalyzedReaction ?source WHERE { { SELECT DISTINCT ?rhea WHERE { GRAPh<https://sparql.rhea-db.org/rhea> { ?rhea rdfs:subClassOf rh:Reaction . ?rhea rh:side/rh:contains/rh:compound ?compound2 . ?uc rdfs:subClassOf rh:Compound . } ?compound2 rdfs:subClassOf ?uc . BIND(IF(?uc = rh:SmallMolecule, 0, 1) AS ?c) } GROUP BY ?rhea HAVING (SUM(?c) = 0) } ?catalyzedReaction up:catalyzedReaction ?rhea . ?reif rdf:object ?catalyzedReaction ; up:attribution ?attr . ?attr up:evidence ECO:0000269 ; up:source ?source . ?source a up:Citation . }Userhea_reactions_annotated_as_experimental_and_only_small_molecules: Find all rhea (only small molecule) that are used in UniProt where the annotation has a paper and is tagged having experimental evidence.
PREFIX ECO: <http://purl.obolibrary.org/obo/ECO_> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?rhea ?catalyzedReaction ?source WHERE { { SELECT DISTINCT ?rhea WHERE { GRAPh<https://sparql.rhea-db.org/rhea> { ?rhea rdfs:subClassOf rh:Reaction . ?rhea rh:side/rh:contains/rh:compound ?compound2 . ?uc rdfs:subClassOf rh:Compound . } ?compound2 rdfs:subClassOf ?uc . BIND(IF(?uc = rh:SmallMolecule, 0, 1) AS ?c) } GROUP BY ?rhea HAVING (SUM(?c) = 0) } ?catalyzedReaction up:catalyzedReaction ?rhea . ?reif rdf:object ?catalyzedReaction ; up:attribution ?attr . ?attr up:evidence ECO:0000269 ; up:source ?source . ?source a up:Citation . }Userhea_reactions_associated_with_ec_in_uniprotkb: List Rhea reactions associated with an EC (enzyme classification).
SELECT ?rhea ?EC WHERE { ?CatalyticActivity up:catalyzedReaction ?rhea ; up:enzymeClass ?EC . }Userhea_reactions_associated_with_ec_in_uniprotkb: List Rhea reactions associated with an EC (enzyme classification).
PREFIX up: <http://purl.uniprot.org/core/> SELECT ?rhea ?EC WHERE { ?CatalyticActivity up:catalyzedReaction ?rhea ; up:enzymeClass ?EC . }Userhea_reactions_not_associated_with_ec_in_uniprotkb: List Rhea reactions thar are not associated with an EC (enzyme classification).
SELECT ?rhea ?EC WHERE { ?CatalyticActivity up:catalyzedReaction ?rhea . MINUS { ?CatalyticActivity up:enzymeClass ?EC . } }Userhea_reactions_not_associated_with_ec_in_uniprotkb: List Rhea reactions thar are not associated with an EC (enzyme classification).
PREFIX up: <http://purl.uniprot.org/core/> SELECT ?rhea ?EC WHERE { ?CatalyticActivity up:catalyzedReaction ?rhea . MINUS { ?CatalyticActivity up:enzymeClass ?EC . } }Usetaxonomy_hierarchy: Find all taxonomic records that describe species of the genus Homo.
SELECT ?species ?genus WHERE { BIND(taxon:9605 AS ?genus) ?species a up:Taxon ; up:rank up:Species ; rdfs:subClassOf ?genus . ?genus a up:Taxon ; up:rank up:Genus . }Usetaxonomy_hierarchy: Find all taxonomic records that describe species of the genus Homo.
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 ?species ?genus WHERE { BIND(taxon:9605 AS ?genus) ?species a up:Taxon ; up:rank up:Species ; rdfs:subClassOf ?genus . ?genus a up:Taxon ; up:rank up:Genus . }Usetaxonomy_host: Find taxon records that are known to have part of their life cycle in other organisms (e.g. parasite, symbiont, infection)
SELECT ?virus ?host WHERE { ?virus up:host ?host . }Use