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

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

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> . }Use

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

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) }Use

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.

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 ?taxonUse

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 . }Use

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/rh:chebi)) ?chebi . } ?chebi chebislash:smiles ?smiles ; chebislash:inchikey ?inchiKey . }Use

drosophila_enzymes_derived_from_at_least_two_mRNAs: Find Drosophila proteins, that depend on more than one transcript (Requires cross-references to Ensembl family of resources).

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 ?protein WHERE { ?protein up:organism taxon:7227 ; a up:Protein ; up:reviewed true ; rdfs:seeAlso ?transcript . ?transcript a up:Transcript_Resource . } GROUP BY ?protein HAVING(COUNT(?transcript) >= 2)Use

drosophila_proteins_derived_from_at_least_two_mRNAs: Find Drosophila enzymes, that depend on more than one transcript (Requires cross-references to Ensembl family of resources).

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 ?protein WHERE { ?protein up:organism taxon:7227 ; a up:Protein ; up:reviewed true ; rdfs:seeAlso ?transcript . { ?protein up:annotation/a up:Catalytic_Activity_Annotation ; } UNION { ?protein up:enzyme ?enzyme . } ?transcript a up:Transcript_Resource . } GROUP BY ?protein HAVING(COUNT(?transcript) >= 2)Use

drosophila_proteins_derived_from_at_least_two_mRNAs: Find Drosophila enzymes, that depend on more than one transcript (Requires cross-references to Ensembl family of resources).

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 ?protein WHERE { ?protein up:organism taxon:7227 ; a up:Protein ; up:reviewed true ; rdfs:seeAlso ?transcript . { ?protein up:annotation/a up:Catalytic_Activity_Annotation ; } UNION { ?protein up:enzyme ?enzyme . } ?transcript a up:Transcript_Resource . } GROUP BY ?protein HAVING(COUNT(?transcript) >= 2)Use

enzyme_with_threonine_as_active_site: Find enzymes with a Tyrosine (Y) as an active site

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 WHERE { ?protein up:annotation ?activeSiteAnnotation . ?activeSiteAnnotation a up:Active_Site_Annotation ; up:range ?range . ?range faldo:begin ?begin . ?begin faldo:position ?beginPosition ; faldo:reference ?sequence . ?sequence rdf:value ?sequenceVal . FILTER(SUBSTR(?sequenceVal, ?beginPosition, 1) = 'Y') }Use

enzyme_with_threonine_as_active_site: Find enzymes with a Tyrosine (Y) as an active site

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 . }Use

enzymes_interacting_with_molecules_similar_to_dopamine: Look for enzymes catalyzing reactions with molecules similar to dopamine.

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/rh:chebi)) ?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 . }Use

enzymes_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 . } }Use

enzymes_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)Use

enzymes_with_at_least_two_transmembrane_domains: Find Hydrolases (enzymes that catalyse the hydrolysis of various bonds) that have at least two transmembrane domains

enzymes_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)Use

enzymes_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

enzymes_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) }Use

enzymes_with_mutagenesis_affecting_active_site: Find enzymes, where the active site is a region affected by mutagenesis and show the comment regarding mutagenesis effect.

genetic_disease_related_proteins: List all UniProt proteins annotated to be related to a genetic disease.

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?uniprot ?disease ?diseaseComment ?mim WHERE { GRAPH <http://sparql.uniprot.org/uniprot> { ?uniprot a up:Protein ; up:annotation ?diseaseAnnotation . ?diseaseAnnotation up:disease ?disease . } GRAPH <http://sparql.uniprot.org/diseases> { ?disease a up:Disease ; rdfs:comment ?diseaseComment . OPTIONAL { ?disease rdfs:seeAlso ?mim . ?mim up:database <http://purl.uniprot.org/database/MIM> . } } }Use

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SPARQL example query