Difference between revisions of "Protein identifier mapping"

From irefindex
Line 17: Line 17:
 
| 2||acc||The external identifier (e.g. Q4U9M9)
 
| 2||acc||The external identifier (e.g. Q4U9M9)
 
|-
 
|-
| 3||entrezGeneid||Entrez gene id. This is provided only for RefSeq identifiers
+
| 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).  
 
| 4||irogid||Integer version redundant group identifier(e.g. 3156116, current maximum value=14005379, this is a MySQL int(11) field).  

Revision as of 09:37, 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 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