SPARQL example query

◀ ▶

18: Select the number of UniProtKB entries for each of the EC (Enzyme Commission) top level categories

 
1
PREFIX ec: <http://purl.uniprot.org/enzyme/>
2
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
3
PREFIX up: <http://purl.uniprot.org/core/>
4
SELECT ?ecClass (COUNT(?protein) as ?size)
5
WHERE
6
{
7
    VALUES (?ecClass) {(ec:1.-.-.-) (ec:2.-.-.-) (ec:3.-.-.-) (ec:4.-.-.-) (ec:5.-.-.-) (ec:6.-.-.-) (ec:7.-.-.-)} .
8
    ?protein ( up:enzyme | up:domain/up:enzyme | up:component/up:enzyme ) ?enzyme .
9
    # Enzyme subclasses are materialized, do not use rdfs:subClassOf+
10
    ?enzyme rdfs:subClassOf ?ecClass .
11
}
12
GROUP BY ?ecClass ORDER BY ?ecClass
Use

19: Find all natural variant annotations if associated via an evidence tag to an article with a PubMed identifier

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19
 
1
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
2
PREFIX up: <http://purl.uniprot.org/core/>
3
SELECT
4
    ?accession
5
    ?annotation_acc
6
    ?pubmed
7
WHERE
8
{
9
        ?protein a up:Protein ;
10
            up:annotation ?annotation .
11
        ?annotation a up:Natural_Variant_Annotation .
12
        ?linkToEvidence rdf:object ?annotation ;
13
                        up:attribution ?attribution .
14
        ?attribution up:source ?source .
15
        ?source a up:Journal_Citation .
16
  BIND(SUBSTR(STR(?protein),33) AS ?accession)
17
  BIND(IF(CONTAINS(STR(?annotation), "#SIP"), SUBSTR(STR(?annotation),33), SUBSTR(STR(?annotation),36))AS?annotation_acc)
18
  BIND(SUBSTR(STR(?source),35) AS ?pubmed)
19
}
Use

20: Find how often an article in PubMed was used in an evidence tag in a human protein (ordered by most used to least)

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16
 
1
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
2
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
3
PREFIX up: <http://purl.uniprot.org/core/>
4
SELECT
5
    ?source
6
    (COUNT(?attribution) AS ?attribitions)
7
WHERE
8
{
9
        ?protein a up:Protein ;
10
            up:organism taxon:9606 ;
11
            up:annotation ?annotation .
12
        ?linkToEvidence rdf:object ?annotation ;
13
                        up:attribution ?attribution .
14
        ?attribution up:source ?source .
15
        ?source a up:Journal_Citation .
16
} GROUP BY ?source ORDER BY DESC(COUNT(?attribution))
Use

21: Find where disease related proteins are known to be located in the cell

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14
 
1
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
2
PREFIX up: <http://purl.uniprot.org/core/>
3
SELECT
4
    ?protein
5
    ?disease
6
    ?location_inside_cell
7
    ?cellcmpt
8
WHERE
9
{
10
    ?protein up:annotation ?diseaseAnnotation , ?subcellAnnotation .
11
    ?diseaseAnnotation up:disease/skos:prefLabel ?disease .
12
    ?subcellAnnotation up:locatedIn/up:cellularComponent ?cellcmpt .
13
    ?cellcmpt skos:prefLabel ?location_inside_cell .
14
}
Use

22: For two accession numbers (ACs) find the GO term labels and group them into GO process,function and component

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32
 
1
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
2
PREFIX up: <http://purl.uniprot.org/core/>
3
PREFIX GO:<http://purl.obolibrary.org/obo/GO_>
4
SELECT
5
    (CONCAT(SUBSTR(STR(?protein), 33)) AS ?uniprot)
6
    (GROUP_CONCAT(?celtype; separator=";") AS ?celtypes)
7
    (GROUP_CONCAT(?biotype; separator=";") AS ?biotypes)
8
    (GROUP_CONCAT(?moltype; separator=";") AS ?moltypes)
9
WHERE
10
{
11
    VALUES (?ac) {("Q6GZX4") ("Q96375")}
12
    BIND (IRI(CONCAT("http://purl.uniprot.org/uniprot/",?ac)) AS ?protein)
13
    ?protein a up:Protein .
14
    ?protein up:classifiedWith ?goTerm .
15
    #Determine if the type is biological_process
16
    OPTIONAL {
17
        ?goTerm rdfs:subClassOf GO:0008150 .
18
        ?goTerm rdfs:label ?biotype .
19
    }
20
    #Determine if the type is cellular_component
21
    OPTIONAL {
22
        ?goTerm rdfs:subClassOf GO:0005575 .
23
        ?goTerm rdfs:label ?celtype .
24
    }
25
    #Determine if the type is molecular_function
26
    OPTIONAL {
27
        ?goTerm rdfs:subClassOf GO:0003674 .
28
        ?goTerm rdfs:label ?moltype .
29
    }
30
    #Filter out the uniprot keywords
31
    FILTER(bound(?biotype) || bound(?celtype) || bound(?moltype))
32
} GROUP BY ?protein
Use

23: Number of reviewed entries (UniProtKB/Swiss-Prot) that are related to kinase activity

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14
 
1
PREFIX GO: <http://purl.obolibrary.org/obo/GO_>
2
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
3
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
4
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
5
PREFIX up: <http://purl.uniprot.org/core/>
6
SELECT
7
    (COUNT(DISTINCT(?protein)) AS ?pc)
8
WHERE
9
{  
10
    ?protein rdf:type up:Protein ;
11
        up:reviewed true  ;
12
        up:organism taxon:9606 ;
13
        up:classifiedWith|(up:classifiedWith/rdfs:subClassOf) GO:0016301 .
14
}
Use

24: Find the release number of the UniProt data that is currently being queried

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6
 
1
SELECT ?version
2
FROM <https://sparql.uniprot.org/.well-known/void>
3
WHERE
4
{
5
    [] <http://purl.org/pav/version> ?version
6
}
Use

25: Find UniProtKB entry which has a protein name 'HLA class I histocompatibility antigen, B-73 alpha chain'

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10
 
1
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
2
PREFIX up: <http://purl.uniprot.org/core/>
3
SELECT ?protein ?anyKindOfName
4
WHERE
5
{
6
        ?protein a up:Protein .
7
        ?protein (up:recommendedName|up:alternativeName) ?structuredName .
8
        ?structuredName ?anyKindOfName  "HLA class I histocompatibility antigen, B alpha chain" .
9
        ?anyKindOfName rdfs:subPropertyOf up:structuredNameType .
10
}
Use

26: Find UniProtKB proteins which are cleaved and contain a domain or component named 'HLA class I histocompatibility antigen, B-73 alpha chain'

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10
 
1
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
2
PREFIX up: <http://purl.uniprot.org/core/>
3
SELECT ?protein ?anyKindOfName
4
WHERE
5
{
6
        ?protein a up:Protein .
7
        ?protein (up:recommendedName|up:alternativeName)|((up:domain|up:component)/(up:recommendedName|up:alternativeName)) ?structuredName .
8
        ?structuredName ?anyKindOfName  "HLA class I histocompatibility antigen, B-73 alpha chain" .
9
        ?anyKindOfName rdfs:subPropertyOf up:structuredNameType .
10
}
Use

26: Find UniProtKB entry, or an UniProtKB entries domain or component which has a name 'HLA class I histocompatibility antigen, B-73 alpha chain'

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10
 
1
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
2
PREFIX up: <http://purl.uniprot.org/core/>
3
SELECT ?protein ?anyKindOfName
4
WHERE
5
{
6
        ?protein a up:Protein .
7
        ?protein (up:recommendedName|up:alternativeName)|((up:domain|up:component)/(up:recommendedName|up:alternativeName)) ?structuredName .
8
        ?structuredName ?anyKindOfName  "HLA class I histocompatibility antigen, B-73 alpha chain" .
9
        ?anyKindOfName rdfs:subPropertyOf up:structuredNameType .
10
}
Use

27: Retrieve all protein names, including peptide names, associated with UniProtKB entry P05067.

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23
 
1
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
2
PREFIX up: <http://purl.uniprot.org/core/>
3
SELECT
4
  ?protein
5
  ?anyKindOfName
6
  ?names
7
  ?partType
8
WHERE
9
{
10
  BIND(<http://purl.uniprot.org/uniprot/P05067> AS ?protein)
11
  ?protein a up:Protein .
12
  {
13
    ?protein (up:recommendedName|up:alternativeName) ?structuredName .
14
  }
15
    UNION
16
  {
17
    VALUES(?partType){(up:domain) (up:component)}
18
    ?protein ?partType ?part .
19
    ?part (up:recommendedName|up:alternativeName) ?structuredName .
20
  }
21
  ?structuredName ?anyKindOfName  ?names .
22
  ?anyKindOfName rdfs:subPropertyOf up:structuredNameType .
23
}
Use

27: Find all names associated with UniProtKB entry P05067, and if the name is associated with the entry it's domains or its components

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23
 
1
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
2
PREFIX up: <http://purl.uniprot.org/core/>
3
SELECT
4
  ?protein
5
  ?anyKindOfName
6
  ?names
7
  ?partType
8
WHERE
9
{
10
  BIND(<http://purl.uniprot.org/uniprot/P05067> AS ?protein)
11
  ?protein a up:Protein .
12
  {
13
    ?protein (up:recommendedName|up:alternativeName) ?structuredName .
14
  }
15
    UNION
16
  {
17
    VALUES(?partType){(up:domain) (up:component)}
18
    ?protein ?partType ?part .
19
    ?part (up:recommendedName|up:alternativeName) ?structuredName .
20
  }
21
  ?structuredName ?anyKindOfName  ?names .
22
  ?anyKindOfName rdfs:subPropertyOf up:structuredNameType .
23
}
Use

28: Get the list of UniProtKB entries for the chromosome of proteome UP000000625

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11
 
1
PREFIX up: <http://purl.uniprot.org/core/>
2
SELECT
3
  ?protein
4
  ?proteome
5
WHERE
6
{
7
  ?protein a up:Protein ;
8
           up:reviewed true ;
9
           up:proteome ?proteome .
10
  VALUES (?proteome) {(<http://purl.uniprot.org/proteomes/UP000000625#Chromosome>)}
11
}
Use

29: Use ALLIE a service for Abbreviation / Long Form in Japanese and English to search in UniProt using Japanese.

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23
 
1
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
2
PREFIX up: <http://purl.uniprot.org/core/>
3
SELECT ?protein ?englishLabelStr
4
WHERE {
5
    SERVICE <https://data.allie.dbcls.jp/sparql>{
6
        ?x rdfs:label "アミロイド前駆体タンパク質"@ja ;
7
            rdfs:label ?englishLabel .
8
        FILTER(lang(?englishLabel) = "en")
9
    }
10
    BIND (STR(?englishLabel) AS ?englishLabelStr)
11
    ?protein a up:Protein .
12
    {
13
        ?protein (up:recommendedName|up:alternativeName) ?structuredName .
14
    }
15
    UNION
16
    {
17
        VALUES(?partType){(up:domain) (up:component)}
18
            ?protein ?partType ?part .
19
        ?part (up:recommendedName|up:alternativeName) ?structuredName .
20
    }
21
    ?structuredName ?anyKindOfName  ?englishLabelStr .
22
    ?anyKindOfName rdfs:subPropertyOf up:structuredNameType .
23
}
Use

30: Find UniProtKB entries with merged loci in Bordetella avium

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14
 
1
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
2
PREFIX up: <http://purl.uniprot.org/core/>
3
SELECT
4
  ?protein
5
  (GROUP_CONCAT(?locusName; separator=',') AS ?locusNames)
6
WHERE
7
{
8
  ?protein a up:Protein ;
9
    up:organism taxon:360910 ;
10
    up:encodedBy ?gene .
11
  ?gene up:locusName ?locusName .
12
}
13
GROUP BY ?protein
14
HAVING (COUNT(?locusName) > 1)
Use

31: Find UniParc records whose sequence point to the most database entries

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14
 
1
PREFIX up: <http://purl.uniprot.org/core/>
2
SELECT ?sequence ?entries
3
WHERE
4
{
5
    SELECT
6
        ?sequence
7
        (COUNT(?entry) AS ?entries)
8
    WHERE
9
    {
10
        GRAPH <http://sparql.uniprot.org/uniparc> {
11
            ?sequence up:sequenceFor ?entry .
12
        }
13
    } GROUP BY ?sequence
14
} ORDER BY DESC(?entries)
Use

32: Find UniProtKB entries with more than 1 Topological domain annotation

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15
 
1
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
2
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
3
PREFIX up: <http://purl.uniprot.org/core/>
4
SELECT
5
    ?protein
6
    (GROUP_CONCAT(?comment; separator=", ") AS ?comments)
7
WHERE
8
{
9
    ?protein a up:Protein ;
10
            up:annotation ?annotation .
11
    ?annotation rdf:type up:Topological_Domain_Annotation ;
12
            rdfs:comment ?comment .
13
}
14
GROUP BY ?protein
15
HAVING (COUNT(?annotation) > 1)
Use

33: Find longest comment text associated with a UniProtKB natural variant annotation

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9
 
1
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
2
PREFIX up: <http://purl.uniprot.org/core/>
3
SELECT
4
    ?annotation ?comment
5
WHERE {
6
    ?annotation a up:Natural_Variant_Annotation ;
7
        rdfs:comment ?comment .
8
}
9
ORDER BY DESC(STRLEN(?comment))
Use

34: Find the co-occurence count of topological domain comment text in UniProtKB entries

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26
 
1
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
2
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
3
PREFIX up: <http://purl.uniprot.org/core/>
4
SELECT
5
    ?comment1
6
    ?comment2
7
    (COUNT(?comment1) AS ?count1)
8
WHERE
9
{
10
    ?protein a up:Protein ;
11
               up:annotation ?annotation1 ,
12
                             ?annotation2 .
13
    ?annotation1 rdf:type up:Topological_Domain_Annotation ;
14
        rdfs:comment ?rawComment1 .
15
    ?annotation2 rdf:type up:Topological_Domain_Annotation ;
16
        rdfs:comment ?rawComment2 .
17
    BIND(IF(contains(?rawComment1, ';'),
18
            STRBEFORE(?rawComment1,';'),
19
            ?rawComment1) AS ?comment1)
20
    BIND(IF(contains(?rawComment2, ';'),
21
            STRBEFORE(?rawComment2,';'),
22
            ?rawComment2) AS ?comment2)
23
    FILTER(?annotation1 != ?annotation2)
24
}
25
GROUP BY ?comment1 ?comment2
26
ORDER BY DESC(COUNT(?comment1))
Use

35: Find the similar proteins for UniProtKB entry P05067 sorted by UniRef cluster identity

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16
 
1
PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/>
2
PREFIX up: <http://purl.uniprot.org/core/>
3
SELECT
4
    ?similar ?identity
5
FROM <http://sparql.uniprot.org/uniref>
6
FROM <http://sparql.uniprot.org/uniprot>
7
WHERE
8
{
9
    BIND (uniprotkb:P05607 AS ?protein)
10
    ?cluster up:member ?member ;
11
             up:member/up:sequenceFor ?protein;
12
             up:identity ?identity .
13
    ?member up:sequenceFor ?similar .
14
    FILTER(!sameTerm(?similar, ?protein))
15
}
16
ORDER BY DESC(?identity)
Use

36: Find the orthologous proteins for UniProtKB entry P05067 using the OrthoDB database

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31
 
1
PREFIX orthodb: <http://purl.orthodb.org/>
2
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
3
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
4
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
5
PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/>
6
PREFIX up: <http://purl.uniprot.org/core/>
7
SELECT
8
  ?protein
9
  ?orthoGroup
10
  ?scientificName
11
  ?functionComment
12
  ?prefferedGeneName
13
  ((STRLEN(?value) - ?medianLength) as ?deviationFromMedianLength)
14
WHERE
15
{
16
  uniprotkb:P05067 a up:Protein ;
17
        up:organism/up:scientificName ?scientificName ;
18
        rdfs:seeAlso ?orthoGroup ;
19
        up:encodedBy/skos:prefLabel ?prefferedGeneName ;
20
          up:sequence/rdf:value ?value .
21
  OPTIONAL {
22
    ?protein up:annotation ?functionAnnotation .
23
    ?functionAnnotation a up:Function_Annotation ;
24
      rdfs:comment ?functionComment .
25
  }
26
  SERVICE <https://sparql.orthodb.org/sparql>{
27
    ?orthoGroup orthodb:ogMedianProteinLength ?medianLength .
28
    ?orthoGroup orthodb:hasMember ?xref .
29
    ?xref orthodb:xref/orthodb:xrefResource uniprotkb:P05067 .
30
  }
31
}
Use

37: Find the human protein which contains an epitope VSTQ, where T is a phosphorylated threonine

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26
 
1
PREFIX faldo: <http://biohackathon.org/resource/faldo#>
2
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
3
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
4
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
5
PREFIX up: <http://purl.uniprot.org/core/>
6
SELECT
7
  ?protein
8
  ?comment
9
  ?begin
10
  ?end
11
WHERE
12
{
13
  ?protein a up:Protein ;
14
    up:organism taxon:9606 ;
15
    up:sequence ?sequence ;
16
    up:annotation ?annotation .
17
  ?annotation a up:Modified_Residue_Annotation ;
18
    rdfs:comment ?comment ;
19
    up:range ?range .
20
  ?range
21
    faldo:begin [ faldo:position ?begin ; faldo:reference ?sequence ] ;
22
    faldo:end [ faldo:position ?end ; faldo:reference ?sequence ] .
23
  ?sequence rdf:value ?aaSequence .
24
  FILTER (SUBSTR(?aaSequence, ?begin -2 , 4) = "VSTQ")    
25
  FILTER (CONTAINS(?comment, "Phosphothreonine"))
26
}
Use

38: For the human entry P05067 (Amyloid-beta precursor protein) find the gene start ends in WikiData

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31
 
1
PREFIX p: <http://www.wikidata.org/prop/>
2
PREFIX pq: <http://www.wikidata.org/prop/qualifier/>
3
PREFIX ps: <http://www.wikidata.org/prop/statement/>
4
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
5
PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/>
6
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
7
SELECT
8
    ?protein
9
    ?begin
10
    ?end
11
    ?chromosome
12
    ?assembly
13
WHERE {
14
    {
15
        BIND(uniprotkb:P05067 AS ?proteinIRI)
16
        BIND (SUBSTR(STR(?proteinIRI), STRLEN(STR(uniprotkb:))+1) AS ?protein)
17
    }
18
    SERVICE <https://query.wikidata.org/sparql> {
19
        ?wp wdt:P352 ?protein ;
20
            wdt:P702 ?wg .
21
        ?wg p:P644   ?wgss .
22
        ?wgss ps:P644        ?begin ;
23
          pq:P1057/wdt:P1813 ?chromosome ;
24
          pq:P659/rdfs:label ?assembly .
25
        ?wg p:P645 ?wgse .
26
        ?wgse ps:P645        ?end ;
27
          pq:P1057/wdt:P1813 ?chromosome ;
28
          pq:P659/rdfs:label ?assembly .
29
        FILTER(lang(?assembly) = "en")
30
  }
31
}
Use

39: Retrieve entries and catalytic activities in the reviewed (UniProtKB/Swiss-Prot) section that have experimental evidences,

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23
 
1
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
2
PREFIX up: <http://purl.uniprot.org/core/>
3
SELECT  
4
  ?protein
5
  ?rhea
6
WHERE {
7
  # ECO 269 is experimental evidence
8
  BIND (<http://purl.obolibrary.org/obo/ECO_0000269> as ?evidence)
9
  GRAPH <http://sparql.uniprot.org/uniprot> {
10
    ?protein up:reviewed true ;
11
      up:annotation ?a ;
12
      up:attribution ?attribution  .
13
    ?a a up:Catalytic_Activity_Annotation ;
14
      up:catalyticActivity ?ca .
15
    ?ca up:catalyzedReaction ?rhea .
16
  
17
    [] rdf:subject ?a ;
18
      rdf:predicate up:catalyticActivity ;
19
      rdf:object ?ca ;
20
      up:attribution ?attribution .
21
    ?attribution up:evidence ?evidence .
22
  }
23
}
Use

40: Retrieve human enzymes that metabolize sphingolipids and are annotated in ChEMBL

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17
 
1
PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_>
2
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
3
PREFIX rh: <http://rdf.rhea-db.org/>
4
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
5
PREFIX up: <http://purl.uniprot.org/core/>
6
SELECT DISTINCT ?protein ?chemblEntry
7
WHERE {
8
  SERVICE <https://sparql.rhea-db.org/sparql> {
9
    ?rhea rdfs:subClassOf rh:Reaction ;
10
      rh:side/rh:contains/rh:compound/rh:chebi/rdfs:subClassOf+ CHEBI:26739 .
11
  }
12
  ?ca up:catalyzedReaction ?rhea .
13
  ?protein up:annotation/up:catalyticActivity ?ca ;
14
    up:organism taxon:9606 ;
15
    rdfs:seeAlso ?chemblEntry .
16
  ?chemblEntry up:database <http://purl.uniprot.org/database/ChEMBL> .
17
}
Use

41: Retrieve UniProtKB entries with sequences that are composed of fragments

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8
 
1
PREFIX up: <http://purl.uniprot.org/core/>
2
SELECT DISTINCT
3
  ?protein
4
WHERE {
5
  ?protein a up:Protein ;
6
    up:sequence ?sequence .
7
  MINUS { ?sequence up:fragment [] }
8
}
Use
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