Examples
- Select all taxa from the UniProt taxonomySELECT ?taxon FROM <http://sparql.uniprot.org/taxonomy> WHERE { ?taxon a up:Taxon . }
- Select all taxa from the UniProt taxonomyPREFIX up: <http://purl.uniprot.org/core/> SELECT ?taxon FROM <http://sparql.uniprot.org/taxonomy> WHERE { ?taxon a up:Taxon . }
- Select all bacterial taxa and their scientific name from the UniProt taxonomySELECT ?taxon ?name WHERE { ?taxon a up:Taxon . ?taxon up:scientificName ?name . # Taxon subclasses are materialized, do not use rdfs:subClassOf+ ?taxon rdfs:subClassOf taxon:2 . }
- Select all bacterial taxa and their scientific name from the UniProt taxonomyPREFIX 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 ?name WHERE { ?taxon a up:Taxon . ?taxon up:scientificName ?name . # Taxon subclasses are materialized, do not use rdfs:subClassOf+ ?taxon rdfs:subClassOf taxon:2 . }
- Select all UniProt entries, and their organism and amino acid sequences (including isoforms), for E. coli K12 and all its strainsSELECT ?protein ?organism ?isoform ?sequence WHERE { ?protein a up:Protein . ?protein up:organism ?organism . # Taxon subclasses are materialized, do not use rdfs:subClassOf+ ?organism rdfs:subClassOf taxon:83333 . ?protein up:sequence ?isoform . ?isoform rdf:value ?sequence . }
- Select all UniProt entries, and their organism and amino acid sequences (including isoforms), for E. coli K12 and all its strainsPREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 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 ?organism ?isoform ?sequence WHERE { ?protein a up:Protein . ?protein up:organism ?organism . # Taxon subclasses are materialized, do not use rdfs:subClassOf+ ?organism rdfs:subClassOf taxon:83333 . ?protein up:sequence ?isoform . ?isoform rdf:value ?sequence . }
- Select the UniProt entry with the mnemonic 'A4_HUMAN'SELECT ?protein WHERE { ?protein a up:Protein . ?protein up:mnemonic 'A4_HUMAN' }
- Select the UniProt entry with the mnemonic 'A4_HUMAN'PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein WHERE { ?protein a up:Protein . ?protein up:mnemonic 'A4_HUMAN' }
- Select a mapping of UniProt to PDB entries using the UniProt cross-references to the PDB databaseSELECT ?protein ?db WHERE { ?protein a up:Protein . ?protein rdfs:seeAlso ?db . ?db up:database <http://purl.uniprot.org/database/PDB> }
- Select a mapping of UniProt to PDB entries using the UniProt cross-references to the PDB databasePREFIX 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> }
- Select all cross-references to external databases of the category '3D structure databases' of UniProt entries that are classified with the keyword 'Acetoin biosynthesis (KW-0005)'SELECT DISTINCT ?link WHERE { ?protein a up:Protein . ?protein up:classifiedWith keywords:5 . ?protein rdfs:seeAlso ?link . ?link up:database ?db . ?db up:category '3D structure databases' }
- Select all cross-references to external databases of the category '3D structure databases' of UniProt entries that are classified with the keyword 'Acetoin biosynthesis (KW-0005)'PREFIX keywords: <http://purl.uniprot.org/keywords/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> SELECT DISTINCT ?link WHERE { ?protein a up:Protein . ?protein up:classifiedWith keywords:5 . ?protein rdfs:seeAlso ?link . ?link up:database ?db . ?db up:category '3D structure databases' }
- Select reviewed UniProt entries (Swiss-Prot), and their recommended protein name, that have a preferred gene name that contains the text 'DNA'SELECT ?protein ?name WHERE { ?protein a up:Protein . ?protein up:reviewed true . ?protein up:recommendedName ?recommended . ?recommended up:fullName ?name . ?protein up:encodedBy ?gene . ?gene skos:prefLabel ?text . FILTER CONTAINS(?text, 'DNA') }
- Select reviewed UniProt entries (Swiss-Prot), and their recommended protein name, that have a preferred gene name that contains the text 'DNA'PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?name WHERE { ?protein a up:Protein . ?protein up:reviewed true . ?protein up:recommendedName ?recommended . ?recommended up:fullName ?name . ?protein up:encodedBy ?gene . ?gene skos:prefLabel ?text . FILTER CONTAINS(?text, 'DNA') }
- Select the preferred gene name and disease annotation of all human UniProt entries that are known to be involved in a diseaseSELECT ?name ?text WHERE { ?protein a up:Protein . ?protein up:organism taxon:9606 . ?protein up:encodedBy ?gene . ?gene skos:prefLabel ?name . ?protein up:annotation ?annotation . ?annotation a up:Disease_Annotation . ?annotation rdfs:comment ?text }
- More examples
About
This SPARQL endpoint contains all UniProt data. It is free to access and supports the SPARQL 1.1 Standard.
There are 0 triples in this release (2024_04). The query timeout is 45 minutes. All triples are available in the default graph. There are 21 named graphs.