Difference between revisions of "Protein identifier mapping"
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Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}} | Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}} | ||
| + | We have made a file which provides mappings between iRefIndex identifiers and popular external identifiers. | ||
| + | The current files contain all UniProt and RefSeq identifiers known to the current version of iRefIndex as documented on the [[Sources_iRefIndex|sources page]]. For specific source documentation, see the sources for each [[iRefIndex_Release_Notes|released version]]. | ||
| − | + | Other database identifiers are provided as database/accession pairs only when the iRefIndex identifier (ROGID) does not have a corresponding UniProt or RefSeq record with an identical sequence. | |
File download location: | File download location: | ||
| − | + | http://irefindex.org/download/irefindex/data/current/Mappingfiles/ | |
The column descriptions: | The column descriptions: | ||
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| 2||acc||The external identifier (e.g. Q4U9M9) | | 2||acc||The external identifier (e.g. Q4U9M9) | ||
|- | |- | ||
| − | | 3||entrezGeneid||Entrez | + | | 3||entrezGeneid||Entrez Gene ID. This is provided '''only''' for RefSeq identifiers; for other identifiers the value is -1 for this field. See note 1. |
|- | |- | ||
| − | | 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 of the redundant group identifier(rogid)(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 | + | | 5||rogid||String version of the redundant object group identifier (64 bit version of the hash digest of primary amino acid sequence with the NCBI taxonomy identifier appended at the end). See note 2. |
|- | |- | ||
| − | | 6||icrogid||Integer version of the canonical | + | | 6||icrogid||Integer version of the canonical redundant object group (crogid) (A selected irogid to represent the canonical group). See note 3. |
|- | |- | ||
| − | | 7||crogid||String version of the canonical(1) redundant object group (A selected rogid to represent the canonical group) | + | | 7||crogid||String version of the canonical(1) redundant object group (A selected rogid to represent the canonical group). See note 3. |
|- | |- | ||
| | | | ||
|} | |} | ||
| − | (1) Please refer the following page for details on canonicalization process. | + | '''Notes:''' |
| − | + | ||
| + | (1) Some protein sequence records can be mapped to an EntrezGene record but will not have an entry in this column because they are not RefSeq records. In these cases, use the irogid (or icrogid) to retrieve all other entries in this table with identical sequences (or belonging to the same canonical group)- one of these may have an entry in this Entrez Gene Id in this column. | ||
| + | |||
| + | |||
| + | (2) Please see http://www.ncbi.nlm.nih.gov/pubmed/18823568 for algorithm describing how you can generate this key from a protein sequence. | ||
| + | |||
| + | |||
| + | (3) Please refer the following page for details on canonicalization process. | ||
| + | [[Canonicalization]] | ||
| + | |||
| + | |||
| + | |||
| + | [[Category:iRefIndex]] | ||
Latest revision as of 17:07, 14 March 2013
Last edited: 2013-03-14
We have made a file which provides mappings between iRefIndex identifiers and popular external identifiers. The current files contain all UniProt and RefSeq identifiers known to the current version of iRefIndex as documented on the sources page. For specific source documentation, see the sources for each released version.
Other database identifiers are provided as database/accession pairs only when the iRefIndex identifier (ROGID) does not have a corresponding UniProt or RefSeq record with an identical sequence.
File download location: http://irefindex.org/download/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 for this field. See note 1. |
| 4 | irogid | Integer version of the redundant group identifier(rogid)(e.g. 3156116, current maximum value=14005379, this is a MySQL int(11) field). |
| 5 | rogid | String version of the redundant object group identifier (64 bit version of the hash digest of primary amino acid sequence with the NCBI taxonomy identifier appended at the end). See note 2. |
| 6 | icrogid | Integer version of the canonical redundant object group (crogid) (A selected irogid to represent the canonical group). See note 3. |
| 7 | crogid | String version of the canonical(1) redundant object group (A selected rogid to represent the canonical group). See note 3. |
Notes:
(1) Some protein sequence records can be mapped to an EntrezGene record but will not have an entry in this column because they are not RefSeq records. In these cases, use the irogid (or icrogid) to retrieve all other entries in this table with identical sequences (or belonging to the same canonical group)- one of these may have an entry in this Entrez Gene Id in this column.
(2) Please see http://www.ncbi.nlm.nih.gov/pubmed/18823568 for algorithm describing how you can generate this key from a protein sequence.
(3) Please refer the following page for details on canonicalization process.
Canonicalization
