TO BE REVIEWED
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 (aka Database): 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/authority. The characters must all be printable ascii characters, excluding spaces.
Examples of well behaved IDs:
- Database=GO LocalID=0008152
- Database=SGD LocalID=S000006435
- Database=ZFIN LocalID=ZDB-GENE-980526-166
Identifiers in GAFs
IMPORTANT NOTE ON THE GAF FORMAT
In the gene association (GAF) files, the global ID is split across two column: 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
The Database should be registered in GO.xrf_abbs, available here:
We are in the process of moving the primary version of this file to a yaml file with primary location in a github repo:
Identifiers, CURIES and URIs
The GO uses semantic web standards such as OWL and RDF. In these standards, URIs are used to uniquely identify ontology terms, genes and associated provenance entities such as publications.
In order to reconcile URIs with the identifier scheme used in formats such as obo, GAF, and how we display identifiers in publications and portals such as AmiGO, we conceive of GlobalIDs as *Compact URIs* (CURIES).
We assume a constant set of prefixes. For all ontologies used in GO, we assume that these have an OBO library PURL URI, so we have an implicit set of prefix declarations:
@prefix GO: http://purl.obolibrary.org/obo/GO_ @prefix CL: http://purl.obolibrary.org/obo/CL_ @prefix CHEBI: http://purl.obolibrary.org/obo/CHEBI_
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 and prefix doubling
MGI IDs are a major problem
GAF (cols 1-3):
MGI MGI:98297 Shh
Using the concatenation rule, this composes to the global ID
Here we have a doubling up of the MGI prefix.
Note that NCBI previously used 'non-doubled- global identifiers of the form MGI:nnn, but they are now switching to the doubled form MGI:MGI:nnn - see http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=genenews article from Wed, 06 Aug 2014 "Important change coming for HGNC and MGI database identifiers"
Compare with the (well-behaved) ZFIN GAFs and IDs:
ZFIN ZDB-GENE-980526-166 shha
(example col1,2,3 in GAF)
This is identical to what NCBI uses in their xref
MGI previously confirmed that the global ID is MGI:MGI:nnnnn, and the local internal ID is MGI:nnnn (but this seems to have changed)
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)
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