1: Select all taxa from the UniProt taxonomy

PREFIX up: <http://purl.uniprot.org/core/> SELECT ?taxon FROM <http://sparql.uniprot.org/taxonomy> WHERE { ?taxon a up:Taxon . }Use

2: Select all bacterial taxa and their scientific name from the UniProt taxonomy

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 ?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 . }Use

3: Select all UniProt entries, and their organism and amino acid sequences (including isoforms), for E. coli K12 and all its strains

PREFIX 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 . }Use

3: Select all UniProt entries, and their organism and amino acid sequences (including isoforms), for E. coli K12 and all its strains

4: 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' }Use

5: Select a mapping of UniProt to PDB entries using the UniProt cross-references to the PDB database

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> }Use

5: Select a mapping of UniProt to PDB entries using the UniProt cross-references to the PDB database

6: 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' }Use

7: 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') }Use

7: Select reviewed UniProt entries (Swiss-Prot), and their recommended protein name, that have a preferred gene name that contains the text 'DNA'

8: Select the preferred gene name and disease annotation of all human UniProt entries that are known to be involved in a disease

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 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 ?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 }Use

8: Select the preferred gene name and disease annotation of all human UniProt entries that are known to be involved in a disease

9: Select all human UniProt entries with a sequence variant that leads to a 'loss of function'

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 ?text WHERE { ?protein a up:Protein . ?protein up:organism taxon:9606 . ?protein up:annotation ?annotation . ?annotation a up:Natural_Variant_Annotation . ?annotation rdfs:comment ?text . FILTER (CONTAINS(?text, 'loss of function')) }Use

9: Select all human UniProt entries with a sequence variant that leads to a 'loss of function'

10: Select all human UniProt entries with a sequence variant that leads to a tyrosine to phenylalanine substitution

PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX 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 ?annotation ?begin ?text WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:annotation ?annotation . ?annotation a up:Natural_Variant_Annotation ; rdfs:comment ?text ; up:substitution ?substitution ; up:range/faldo:begin [ faldo:position ?begin ; faldo:reference ?sequence ] . ?sequence rdf:value ?value . BIND (substr(?value, ?begin, 1) as ?original) . FILTER(?original = 'Y' && ?substitution = 'F') . }Use

10: Select all human UniProt entries with a sequence variant that leads to a tyrosine to phenylalanine substitution

11: Select all UniProt entries with annotated transmembrane regions and the regions' begin and end coordinates on the canonical sequence

PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?begin ?end WHERE { ?protein a up:Protein . ?protein up:annotation ?annotation . ?annotation a up:Transmembrane_Annotation . ?annotation up:range ?range . ?range faldo:begin/faldo:position ?begin . ?range faldo:end/faldo:position ?end }Use

11: Select all UniProt entries with annotated transmembrane regions and the regions' begin and end coordinates on the canonical sequence

12: Select all UniProt entries that were integrated on the 30th of November 2010

PREFIX up: <http://purl.uniprot.org/core/> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> SELECT ?protein WHERE { ?protein a up:Protein . ?protein up:created '2010-11-30'^^xsd:date }Use

12: Select all UniProt entries that were integrated on the 30th of November 2010

PREFIX up: <http://purl.uniprot.org/core/> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> SELECT ?protein WHERE { ?protein a up:Protein . ?protein up:created '2010-11-30'^^xsd:date }Use

13: Was any UniProt entry integrated on the 9th of January 2013

PREFIX up: <http://purl.uniprot.org/core/> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> ASK WHERE { ?protein a up:Protein . ?protein up:created '2013-01-09'^^xsd:date }Use

13: Was any UniProt entry integrated on the 9th of January 2013

PREFIX up: <http://purl.uniprot.org/core/> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> ASK WHERE { ?protein a up:Protein . ?protein up:created '2013-01-09'^^xsd:date }Use

14: Construct new triples of the type 'HumanProtein' from all human UniProt entries

PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> CONSTRUCT { ?protein a up:HumanProtein . } WHERE { ?protein a up:Protein . ?protein up:organism taxon:9606 }Use

14: Construct new triples of the type 'HumanProtein' from all human UniProt entries

15: Select all triples that relate to the EMBL CDS entry AA089367.1:

DESCRIBE <http://purl.uniprot.org/embl-cds/AAO89367.1>Use

15: Select all triples that relate to the EMBL CDS entry AA089367.1:

DESCRIBE <http://purl.uniprot.org/embl-cds/AAO89367.1>Use

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SPARQL example query