Identifiers: Difference between revisions
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[[Category:Curator Guides]] [[Category:Annotation]] [[Category:Formats]] | [[Category:Curator Guides]] [[Category:Annotation]] [[Category:Formats]] | ||
All identifiers in GO (e.g. referenced in GAF, ontology or associated documents) should be | All identifiers in GO (e.g. referenced in GAF, ontology or associated documents) should be conform to the following format: | ||
GlobalID = | GlobalID = Prefix ':' LocalID | ||
The LocalID scheme is under the control of the Database. It should include no whitespace or non-ascii characters. | We use the term 'identifier' as synonymous with GlobalID, although confusingly some use 'identifier' to refer to what we call LocalID. | ||
* Prefixes: Each prefix must be registered in the GO xrfs registry file. It should correspond to some known authority. The characters must all be alphanumeric (a-z, A-Z, 0-9), underscores or dashes. | |||
* The LocalID scheme is under the control of the Database/authorit. It should include no whitespace or non-ascii characters. The characters must all be printable ascii characters, excluding spaces. | |||
== Examples == | |||
Examples of well behaved IDs: | Examples of well behaved IDs: | ||
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* ZFIN:ZDB-GENE-980526-166 | * ZFIN:ZDB-GENE-980526-166 | ||
** Database=ZFIN LocalID=ZDB-GENE-980526-166 | ** Database=ZFIN LocalID=ZDB-GENE-980526-166 | ||
== Identifiers in GAFs == | |||
In the gene association files, Database goes in column 1, LocalID goes in column 2 | In the gene association files, Database goes in column 1, LocalID goes in column 2 | ||
For filling in the WITH column, the ''Global'' ID should be used. This has to be the case, otherwise it would be difficult to tell where the ID came from | For filling in the WITH column, the ''Global'' ID should be used. This has to be the case, otherwise it would be difficult to tell where the ID came from | ||
== Prefix Registry == | |||
The Database '''should''' be registered in GO.xrf_abbs, available here: | The Database '''should''' be registered in GO.xrf_abbs, available here: | ||
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* http://www.geneontology.org/doc/GO.xrf_abbs_spec | * http://www.geneontology.org/doc/GO.xrf_abbs_spec | ||
== Problems with existing usage == | == Problems with existing usage == |
Revision as of 16:21, 8 December 2014
All identifiers in GO (e.g. referenced in GAF, ontology or associated documents) should be conform to the following format:
GlobalID = Prefix ':' LocalID
We use the term 'identifier' as synonymous with GlobalID, although confusingly some use 'identifier' to refer to what we call LocalID.
- Prefixes: Each prefix must be registered in the GO xrfs registry file. It should correspond to some known authority. The characters must all be alphanumeric (a-z, A-Z, 0-9), underscores or dashes.
- The LocalID scheme is under the control of the Database/authorit. It should include no whitespace or non-ascii characters. The characters must all be printable ascii characters, excluding spaces.
Examples
Examples of well behaved IDs:
- GO:0008152
- Database=GO LocalID=0008152
- SGD:S000006435
- Database=SGD LocalID=S000006435
- ZFIN:ZDB-GENE-980526-166
- Database=ZFIN LocalID=ZDB-GENE-980526-166
Identifiers in GAFs
In the gene association files, Database goes in column 1, LocalID goes in column 2
For filling in the WITH column, the Global ID should be used. This has to be the case, otherwise it would be difficult to tell where the ID came from
Prefix Registry
The Database should be registered in GO.xrf_abbs, available here:
Spec:
Problems with existing usage
FLYBASE vs FB
We have both FB and FlyBase registered here Also in the fb gene_association files, the col1 is FB but the assigned_by column is FlyBase. NCBI seem to use FLYBASE
Josh has been alerted, bringing this up with FlyBase
MGI
MGI IDs are a major problem
GAF (cols 1-3):
MGI MGI:98297 Shh
Using the concatenation rule, this composez to the global ID
- MGI:MGI:98297
Here we have a doubling up of the MGI prefix. Note that this is inconsistent with NCBI xrefs, which use MGI:98297 - this inconsistency has yet to be resolved with NCBI
Note also that typically people used the local ID in their WITH columns; eg rat has:
RGD RGD:3673 Shh GO:0001525 RGD:1580654 ISS MGI:98297 P sonic hedgehog homolog (Drosophila) gene taxon:10116 20060820 RGD
(NOTE: RGD have fixed this. Thanks RGD!)
Compare with the (well-behaved) ZFIN GAFs and IDs:
ZFIN ZDB-GENE-980526-166 shha
col1:col2 =
- ZFIN:ZDB-GENE-980526-166
This is identical to what NCBI uses in their xref
MGI has confirmed that the global ID is MGI:MGI:nnnnn, and the local internal ID is MGI:nnnn
RGD
RGD previously used the same pattern as MGI. As of 2008/06/23 they have confirmed their policy and fixed their files. RGD:nnnn is the global ID. The local ID is purely a number (for both genes and references)
recommendation
MGI should either
- change their col2 in their GAFs such that only the number is used (PREFERRED)
- coordinate with other databases, including NCBI to make it clear that the global ID is MGI:MGI:nnnnn