Difference between revisions of "Protein identifier mapping"

From irefindex
Line 19: Line 19:
 
| 3||entrezGeneid||Entrez gene id. This is provided only for RefSeq identifiers
 
| 3||entrezGeneid||Entrez gene id. This is provided only for RefSeq identifiers
 
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| 4||irogid||Integer version redundant group identifier(e.g. 3156116, current maximum value=, this is a MySQL ).  
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| 4||irogid||Integer version redundant group identifier(e.g. 3156116, current maximum value=14005379, this is a MySQL int(11) field).  
 
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| 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)
 
| 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)

Revision as of 09:10, 21 October 2010

Last edited: 2010-10-21


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.

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
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