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Difference between revisions of "Protein identifier mapping"

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We have made a file which provides mappings between iRefIndex identifiers and popular external identifiers. The file is a tab delimited text file and the first row starting with the "#" provides the column headers.
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We have made a file which provides mappings between iRefIndex identifiers and popular external identifiers.  
 
The current files contains all UniProt, allRefSeq identifier (please refer http://irefindex.uio.no/wiki/Sources_iRefIndex_7.0 for version information) and an other identifiers in selected cases. Other identifiers are provided as accession/identifiers for iRefindex identifiers provided only when they do not have a UniProt or RefSeq identifier.
 
The current files contains all UniProt, allRefSeq identifier (please refer http://irefindex.uio.no/wiki/Sources_iRefIndex_7.0 for version information) and an other identifiers in selected cases. Other identifiers are provided as accession/identifiers for iRefindex identifiers provided only when they do not have a UniProt or RefSeq identifier.
  

Revision as of 03:07, 21 October 2010

Last edited: 2010-10-21


We have made a file which provides mappings between iRefIndex identifiers and popular external identifiers. The current files contains all UniProt, allRefSeq identifier (please refer http://irefindex.uio.no/wiki/Sources_iRefIndex_7.0 for version information) and an other identifiers in selected cases. Other identifiers are provided as accession/identifiers for iRefindex identifiers provided only when they do not have a UniProt or RefSeq identifier.

File download location: ftp://ftp.no.embnet.org/irefindex/data/current/Mappingfiles/

The column descriptions:

Column number Column name Description
1 db Source of the external identifier (e.g. UniProt, RefSeq)
2 acc The external identifier (e.g. Q4U9M9)
3 entrezGeneid Entrez gene id. This is provided only for RefSeq identifiers for other identifiers the value is -1 from this field.
4 irogid Integer version redundant group identifier(e.g. 3156116, current maximum value=14005379, this is a MySQL int(11) field).
5 rogid String version of the redundant object group (64 bit version of the hash digest of primary amino acid sequence with the NSBI taxonomy identifier appended at the end)
6 icrogid Integer version of the canonical(1) redundant object group (A selected irogid to represent the canonical group)
7 crogid String version of the canonical(1) redundant object group (A selected rogid to represent the canonical group)

(1) Please refer the following page for details on canonicalization process. http://irefindex.uio.no/wiki/Canonicalization