UniProt SPARQL: retrieving proteins of a complete proteome (Escherichia coli K12)

Question

[amorgat]

My question: how to retrieve all entries of Escherichia coli K12 proteome using UniProt SPARQL endpoint?

endpoint: http://sparql.uniprot.org/sparql

Context: I want to get entries of UniProt ECOLI (Escherichia coli K-12) complete proteome. I expect to find only UniProtKB/Swiss-Prot proteins (reviewed entries).

I did the following things:

Retrieve the list of proteins with KW 'complete proteome' (keywords:181) and taxon:83333 (Escherichia coli K-12)

PREFIX keywords:<http://purl.uniprot.org/keywords/> 
PREFIX taxon:<http://purl.uniprot.org/taxonomy/> 
PREFIX up:<http://purl.uniprot.org/core/> 
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>      
SELECT ?reviewed (count(distinct ?protein) as ?proteinCount)
WHERE
{
    ?protein a up:Protein ;
                   up:organism ?organism ;
                    up:organism taxon:83333 ;
                     up:classifiedWith|(up:classifiedWith/rdfs:subClassOf)?kw ;
                      up:reviewed ?reviewed .
    ?kw a up:Concept .
    VALUES (?kw) { (keywords:181) }
}
GROUP BY ?reviewed

result:

|reviewed |proteinCount|

|"true"xsd:boolean |"4313"xsd:int|

|"false"xsd:boolean |"2"xsd:int|

It is an unexpected result for me, as there are 2 TrEMBL entries (up:reviewed false).

In fact, an organism may have several proteomes. Well, with E. coli, I should have anticipated that... anyway! Definition of proteomes is well-documented in the UniProt web site (reference_proteome). And effectively there are 2 proteomes for Escherichia coli K-12:

• UP000000318 (Escherichia coli ATCC 27325)
• UP000000625 (Escherichia coli MG1655) - Reference proteome

Instead of keywords:181 (complete proteome), I should have used keywords:1185 (reference proteome) (KW-1185):

PREFIX keywords:<http://purl.uniprot.org/keywords/> 
PREFIX taxon:<http://purl.uniprot.org/taxonomy/> 
PREFIX up:<http://purl.uniprot.org/core/> 
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> 

SELECT ?reviewed (count(distinct ?protein) as ?proteinCount)
WHERE
{
    ?protein a up:Protein ;
                   up:organism ?organism ;
                    up:organism taxon:83333 ;
                     up:classifiedWith|(up:classifiedWith/rdfs:subClassOf)?kw ;
                      up:reviewed ?reviewed .
    ?kw a up:Concept .
    VALUES (?kw) { (keywords:1185) }
}
GROUP BY ?reviewed

result:

|reviewed |proteinCount|

|"true"xsd:boolean |"4313"xsd:int|

bingo!

Let's display proteome data for taxon:83333

PREFIX taxon:<http://purl.uniprot.org/taxonomy/> 
PREFIX up:<http://purl.uniprot.org/core/> 
PREFIX proteome:<http://purl.uniprot.org/proteome/> 
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> 

SELECT ?proteome ?reviewed  (count(distinct ?protein) as ?proteinCount)
WHERE
{
    ?protein a up:Protein ;
                   up:organism ?organism ;
                    up:organism taxon:83333 ;
                     up:proteome ?proteome ;
                      up:reviewed ?reviewed .
}
GROUP BY ?reviewed ?proteome

proteome reviewed proteinCount

http://purl.uniprot.org/proteomes/UP000000318#Chromosome "true"xsd:boolean "4255"xsd:int

http://purl.uniprot.org/proteomes/UP000000318#Chromosome "false"xsd:boolean "2"xsd:int

http://purl.uniprot.org/proteomes/UP000000625#Chromosome "true"xsd:boolean "4313"xsd:int

And now, get the list of proteins for UP000000625#Chromosome

SPARQL query:

PREFIX proteome:<http://purl.uniprot.org/proteome/> 
PREFIX uniprotkb:<http://purl.uniprot.org/uniprot/> 
PREFIX up:<http://purl.uniprot.org/core/> 
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> 

SELECT ?proteome ?protein
WHERE
{
    ?protein a up:Protein ;
                   up:reviewed true ;
                    up:proteome ?proteome .
    VALUES (?proteome) {(proteome:UP000000625#Chromosome)}
}

Unfortunately, I get an error message

Encountered " "}" "} "" at line 13, column 1. Was expecting one of: ")" ... "true" ... "false" ... "UNDEF" ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...

Replacing UP000000625#Chromosome by UP000000625 gives no result

Question: who know how to retrieve proteins of a given UniProt proteome (UP000000625 in my case)?

Answer 1

[me]

There are two issues with this query. The first is that in the PREFIX declaration there is an s missing at the end of proteome i.e.

PREFIX proteome:<http://purl.uniprot.org/proteome/>

should be

PREFIX proteome:<http://purl.uniprot.org/proteomes/>

The second one is more frustrating and is that the character '#' used in the fragment IRI is also seen as the start of a comment in the sparql query.

This means the query needs to be written as

PREFIX uniprotkb:<http://purl.uniprot.org/uniprot/> 
PREFIX up:<http://purl.uniprot.org/core/> 
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> 

SELECT ?proteome ?protein
WHERE
{
     ?protein a up:Protein ;
               up:reviewed true ;
                up:proteome ?proteome .
  VALUES (?proteome) {(<http://purl.uniprot.org/proteomes/UP000000625#Chromosome>)}
}

Which produces results as seen here