Basic information

This page shows you basic information stored on every UniProtKB entry: identifier, entry name, status, dates and versions.

Entry identifier

Each UniProt entry is identified by a primary accession - the best way to access an entry. In the RDF format, the primary accession is part of the IRI that identifies the entry.

base <http://purl.uniprot.org/uniprot/>
prefix up: <http://purl.uniprot.org/core/>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix xsd: <http://www.w3.org/2001/XMLSchema#>
prefix isoform: <http://purl.uniprot.org/isoforms/>

<O22340> rdf:type up:Protein ;
         up:reviewed true ;
         up:created "2001-10-24"^^xsd:date ;
         up:modified "2015-04-01"^^xsd:date ;
         up:version 86 ;
         up:mnemonic "TPSDA_ABIGR" ;
         up:oldMnemonic "TPSD3_ABIGR", "TSD3_ABIGR" ;
         up:replaces <Q94FV9> ;
         up:sequence isoform:O22340-1 .

isoform:O22340-1 rdf:type up:Simple_Sequence ;
         up:modified "1998-01-01"^^xsd:date ;
         up:version 1 .

PREFIX up: <http://purl.uniprot.org/core/>

SELECT ?protein
WHERE {
  ?protein a up:Protein .
}

Extracting a primaryAccession from an IRI

Adapted from sparql-examples UniProt/102.

This is easy enough with some string manipulation. While UniProt primary accessions are unique within UniProtKB, they may be reused by accident or intentionally by other data sources. If you provide them as plain strings (not IRIs) in a query, you might accidentally retrieve completely wrong records - so prefer matching on the full IRI, and only extract the accession as a string for display.

PREFIX up: <http://purl.uniprot.org/core/>
PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/>

SELECT ?primaryAccession ?protein
WHERE {
  ?protein a up:Protein .
  BIND(substr(str(?protein), strlen(str(uniprotkb:)) + 1) AS ?primaryAccession)
}

UniProt entry name (mnemonic)

Adapted from sparql-examples UniProt/79.

The UniProtKB/Swiss-Prot entry name consists of up to 11 uppercase alphanumeric characters, following the convention X_Y, where:

• X is a mnemonic protein identification code of at most 5 alphanumeric characters
• _ separates the two parts
• Y is a mnemonic species identification code of at most 5 alphanumeric characters

The mnemonic code X is an abbreviation of the protein/gene name, and doesn’t necessarily match the recommended protein name or the gene name. See more details in the Entry Name documentation.

The RDF format stores the entry name in the mnemonic property, and, for convenience, lists obsolete entry names as oldMnemonic properties.

PREFIX up: <http://purl.uniprot.org/core/>

SELECT ?protein ?mnemonic
WHERE {
  ?protein a up:Protein ;
      up:mnemonic ?mnemonic .
}

Old mnemonics

Adapted from sparql-examples UniProt/80.

PREFIX up: <http://purl.uniprot.org/core/>

SELECT ?protein (GROUP_CONCAT(?oldMnemonic; separator=" and ") AS ?oldMnemonics)
WHERE {
  ?protein a up:Protein ;
      up:oldMnemonic ?oldMnemonic .
}
GROUP BY ?protein

Entry status

UniProtKB has two sections:

• UniProtKB/Swiss-Prot: entries that have been manually annotated and reviewed by UniProtKB biocurators
• UniProtKB/TrEMBL: entries that have been annotated using automated annotation pipelines

The RDF format stores the entry status in the reviewed property.

base <http://purl.uniprot.org/uniprot/>
prefix up: <http://purl.uniprot.org/core/>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix xsd: <http://www.w3.org/2001/XMLSchema#>

<O22340> rdf:type up:Protein ;
         up:reviewed true ;
         up:created "2001-10-24"^^xsd:date ;
         up:modified "2015-04-01"^^xsd:date ;
         up:version 86 ;
         up:mnemonic "TPSDA_ABIGR" .

PREFIX up: <http://purl.uniprot.org/core/>

SELECT ?protein ?entryName ?reviewed
WHERE {
  ?protein a up:Protein ;
      up:mnemonic ?entryName ;
      up:reviewed ?reviewed .
}

base <http://purl.uniprot.org/uniprot/>
prefix up: <http://purl.uniprot.org/core/>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix xsd: <http://www.w3.org/2001/XMLSchema#>

<A0A024R563> rdf:type up:Protein ;
         up:reviewed false ;
         up:created "2014-07-09"^^xsd:date ;
         up:modified "2020-10-07"^^xsd:date ;
         up:version 30 ;
         up:mnemonic "A0A024R563_HUMAN" .

PREFIX up: <http://purl.uniprot.org/core/>

SELECT ?protein ?entryName ?reviewed
WHERE {
  ?protein a up:Protein ;
      up:mnemonic ?entryName ;
      up:reviewed ?reviewed .
}

Dates and versions

Adapted from sparql-examples UniProt/93.

The date an entry was integrated into UniProtKB is stored in the created property; the last modification date and current version of the entry are stored in the modified and version properties. The last modification date and current version of the sequence are stored the same way, but on the sequence resource. Dates use the international standard ISO 8601 notation.

PREFIX up: <http://purl.uniprot.org/core/>

SELECT ?protein ?created ?modified ?version
WHERE {
  ?protein a up:Protein ;
           up:created ?created ;
           up:modified ?modified ;
           up:version ?version .
}