SPARQL example query
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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 .} }Use52: 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 . } }Use53: Find mouse homologs in OMABrowser of human enzymes that catalyze reactions involving sterols (CHEBI:15889). Federating with Rhea 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 . } }Use54: Proteins with 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)Use55: Number of proteins with 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)Use56: Select enzymes that have ligands known to have an 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")) }Use57: Map a selection of PDB identifiers plus chains to UniProtKB
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)) }Use58: Map a selection of UniProtKB accession numbers (ACs) 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 . }Use59: 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 . }Use60: 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> } }Use61: 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 }Use100_uniprot_organelles_or_plasmids: List the proteins encoded by a gene that is located in an organelle other than the nucleus, or on a plasmid rather than a chromosome. In these cases the gene location is stored with encodedIn properties. Note that if a plasmid has several names, they are listed as multiple rdfs:label properties.
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?plasmidOrOrganelle ?label WHERE { ?protein a up:Protein ; up:encodedIn ?plasmidOrOrganelle . OPTIONAL { ?plasmidOrOrganelle rdfs:label ?label . } }Use101_uniprot_potential_isoforms: List all human UniProtKB entries and their computationaly mapped potential isoforms.
PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?entry ?sequence ?isCanonical WHERE { # We don't want to look into the UniParc graph which will # confuse matters GRAPH <http://sparql.uniprot.org/uniprot> { # we need the UniProt entries that are human ?entry a up:Protein ; up:organism taxon:9606 ; # and we select the computationally mapped sequences up:potentialSequence ?sequence . } }Use102_uniprot_primary_accession: Extracting an UniProtKB primary accession from our IRIs. Is done with a bit of string manipulation. While UniProt primary accession are unique within UniProtKB they may be reused by accident or itentionally by other data sources. If we provided them as strings (not IRI) and if you used them in a query that way, you might accidentaly retrieve completely wrong records.
PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?primaryAccession ?protein WHERE { ?protein a up:Protein . BIND(substr(str(?protein), strlen(str(uniprotkb:))+1) AS ?primaryAccession) }Use103_uniprot_proteome_location_of_gene: List UniProtKB proteins with genetic replicon that they are encoded on using the Proteome data.
PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT DISTINCT ?proteomeData ?replicon ?proteome WHERE { # reviewed entries (UniProtKB/Swiss-Prot) ?protein up:reviewed true . # restricted to Human taxid ?uniprot up:organism taxon:9606 . ?uniprot up:proteome ?proteomeData . BIND( strbefore( str(?proteomeData), "#" ) as ?proteome ) BIND( strafter( str(?proteomeData), "#" ) as ?replicon ) }Use104_uniprot_recomended_protein_full_name: The recommended protein full names for UniProtKB entries
PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?fullName WHERE { ?protein a up:Protein ; up:recommendedName ?recommendedName . ?recommendedName up:fullName ?fullName . }Use105_uniprot_recomended_protein_short_name: The recommended protein short names for UniProtKB entries
PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?fullName WHERE { ?protein a up:Protein ; up:recommendedName ?recommendedName . ?recommendedName up:shortName ?fullName . }Use106_uniprot_reviewed_or_not: List all UniProtKB proteins and if they are reviewed (Swiss-Prot) or unreviewed (TrEMBL)
PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?reviewed WHERE { ?protein a up:Protein . ?protein up:reviewed ?reviewed . }Use107_uniprot_sequences_and_mark_which_is_cannonical_for_human: List all human UniProtKB entries and their sequences, marking if the sequence listed is the cannonical sequence of the matching entry.
PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?entry ?sequence ?isCanonical WHERE { # We don't want to look into the UniParc graph which will # confuse matters GRAPH <http://sparql.uniprot.org/uniprot> { # we need the UniProt entries that are human ?entry a up:Protein ; up:organism taxon:9606 ; up:sequence ?sequence . # If the sequence is a "Simple_Sequence" it is likely to be the # cannonical sequence OPTIONAL { ?sequence a up:Simple_Sequence . BIND(true AS ?likelyIsCanonical) } # unless we are dealing with an external isoform # see https://www.uniprot.org/help/canonical_and_isoforms OPTIONAL { FILTER(?likelyIsCanonical) ?sequence a up:External_Sequence . BIND(true AS ?isComplicated) } # If it is an external isoform it's id would not match the # entry primary accession BIND(IF(?isComplicated, STRENDS(STR(?entry), STRBEFORE(SUBSTR(STR(?sequence), 34),'-')),?likelyIsCanonical) AS ?isCanonical) } }Use108_uniprot_signature_match_start_end: List all InterPro member database signature match start and end for a specific UniProtKB protein.
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 ?interproMemberDatabaseXref ?matchStart ?matchEnd WHERE{ GRAPH <http://sparql.uniprot.org/uniprot> { VALUES ?protein {<http://purl.uniprot.org/uniprot/P05067>} . ?protein rdfs:seeAlso ?sa . } GRAPH <http://sparql.uniprot.org/uniparc> { ?uniparc up:sequenceFor ?protein ; rdfs:seeAlso ?interproMemberDatabaseXref . ?interproDatabaseXref up:signatureSequenceMatch ?sam . ?sam faldo:begin ?sab ; faldo:end ?sae . ?sab faldo:position ?matchStart ; faldo:reference ?uniparc . ?sae faldo:position ?matchEnd ; faldo:reference ?uniparc . } }Use109_uniprot_transporter_in_liver: Find human transporter proteins in reviewed UniProtKB/Swiss-Prot, that are expressed in the liver (Uses Bgee and UBERON).
PREFIX genex: <http://purl.org/genex#> PREFIX lscr: <http://purl.org/lscr#> PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX orth: <http://purl.org/net/orth#> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX uberon: <http://purl.obolibrary.org/obo/uo#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?rhea ?protein ?anat WHERE { GRAPH <https://sparql.rhea-db.org/rhea> { ?rhea rh:isTransport true . } ?protein up:annotation ?ann . ?protein up:organism taxon:9606 . ?ann up:catalyticActivity ?ca . ?ca up:catalyzedReaction ?rhea . BIND(uberon:0002107 AS ?anat) SERVICE <https://www.bgee.org/sparql> { ?seq genex:isExpressedIn ?anat . ?seq lscr:xrefUniprot ?protein . ?seq orth:organism ?organism . ?organism obo:RO_0002162 taxon:9606 . } }Use110_uniprot_unamed_plasmids: Sometimes it is known that a gene encoding a protein UniProtKB is located on a plasmid or an organelle, but the name of the plasmid is unknown.
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?plasmidOrOrganelle ?label WHERE { ?protein a up:Protein ; up:encodedIn ?plasmidOrOrganelle . OPTIONAL { ?plasmidOrOrganelle rdfs:label ?label . } }Use111_uniprot_make_chain_sequence_fasta: Given an UniProt chain identifier, generate the matching sequence as a FASTA
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX up: <http://purl.uniprot.org/core/> PREFIX faldo: <http://biohackathon.org/resource/faldo#> SELECT (CONCAT('>', ?chainSeqId, '\n', (SUBSTR(?iupacAA, ?begin, (?end-?begin+1)))) AS ?chainFasta) WHERE { BIND("PRO_0000268053" AS ?chainSeqId) BIND(IRI(CONCAT("http://purl.uniprot.org/annotation/", ?chainSeqId)) AS ?annId) ?annId up:range ?range . ?range faldo:begin [ faldo:reference ?reference ; faldo:position ?begin ] ; faldo:end [ faldo:position ?end ] . ?reference rdf:value ?iupacAA . }Use62_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) }Use