Identifiers: Difference between revisions

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All identifiers in GO should be composed from a binary key as follows:


  GlobalID = Database ':' LocalID
[[Category:Annotation]]


The LocalID scheme is under the control of the Database. It should include no whitespace or non-ascii characters.
All identifiers in GO (e.g. referenced in GAF, ontology or associated documents) should be conform to the following format:
 
  GlobalID = Prefix ':' LocalID
 
* Prefixes (aka Database): Each prefix must be registered in the GO xrefs registry metadata yaml file (see below). 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.
 
We use the term 'identifier' as synonymous with GlobalID, although confusingly some use 'identifier' to refer to what we call LocalID. Our concept of GlobalID corresponds with the W3C standard for CURIEs, see below
 
 
== Examples ==


Examples of well behaved IDs:
Examples of well behaved IDs:
Line 13: Line 22:
* ZFIN:ZDB-GENE-980526-166
* ZFIN:ZDB-GENE-980526-166
** Database=ZFIN    LocalID=ZDB-GENE-980526-166
** Database=ZFIN    LocalID=ZDB-GENE-980526-166
* FlyBase:FBgn0011293
** Database=FlyBase LocalID=FBgn0011293
== Identifiers in GAFs ==
''IMPORTANT NOTE ON THE GAF FORMAT''


In the gene association files, Database goes in column 1, LocalID goes in column 2
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
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:
Note that in GPAD and GPI formats, a single column with GlobalID is used


* http://www.geneontology.org/doc/GO.xrf_abbs
== Prefix Registry ==
* http://www.geneontology.org/cgi-bin/xrefs.cgi


Spec:
The Database '''should''' be registered in db-xrefs.yaml, available here:


* http://www.geneontology.org/doc/GO.xrf_abbs_spec
* https://github.com/geneontology/go-site/blob/master/metadata/db-xrefs.yaml
* http://amigo.geneontology.org/xrefs


Also available in .obo format here:
Our prefix registry is coordinated with identifiers.org and the prefixcommons project: https://github.com/prefixcommons/biocontext


* http://www.berkeleybop.org/ontologies/obo-all/go_xrf_metadata/go_xrf_metadata.obo
== Identifiers, CURIES and URIs ==


It is strongly recommended that the ''primary'' abbreviation is always used in constructing the ID. However, in some contexts it is allowable to use a database abbreviation synonym.
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.


For example, the following is allowed:
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).


* UniProt:Q09212
* https://en.wikipedia.org/wiki/CURIE
* http://www.w3.org/TR/curie/


However, the following is strongly preferred:
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:


* UniProtKB:Q09212
  @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 ==
== Problems with existing usage ==


=== FLYBASE vs FB ===
The term "identifier" is used in different ways which causes confusion. Our concept of GlobalID corresponds with W3C CURIEs and should be unambiguous.
 
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 and prefix doubling ===


MGI IDs are a major problem
MGI IDs are a major problem


GAF (cols 1-3):
GAF (cols 1-3):
Line 59: Line 71:
   MGI    MGI:98297      Shh
   MGI    MGI:98297      Shh


Using the concatenation rule, this composed to the global ID
Using the concatenation rule, this composes to the global ID


* MGI:MGI:98297
* 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 - inconsistency is ''bad''!
Here we have a doubling up of the MGI prefix.


* MGI:98297
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"
 
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:
Compare with the (well-behaved) ZFIN GAFs and IDs:


   ZFIN    ZDB-GENE-980526-166    shha
   ZFIN    ZDB-GENE-980526-166    shha
(example col1,2,3 in GAF)


col1:col2 =
col1:col2 =
Line 81: Line 89:
* ZFIN:ZDB-GENE-980526-166
* ZFIN:ZDB-GENE-980526-166


This is identical to what NCBI uses in their xref (this is ''good''!)
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)
 
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
 


=== RGD ===
=== RGD ===
Line 87: Line 105:
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)
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 ====
=== FlyBase vs FB ===
 
previously there was confusion as to whether to use FB or FlyBase (or FLYBASE)
 
in GO in our registry, FB is the canonical prefix, but we include FlyBase as a synonym
 
Historically, "flybase" was used in identifiers.org but this is now resolved to be "fb" consistent with GO and other resources
 
NCBI seem to use FLYBASE


MGI and RGD should either
== See Also ==


* change their col2 in their GAFs such that only the number is used
* [http://oboformat.googlecode.com/svn/trunk/doc/obo-syntax.html#2.5 OBO Format ID syntax]
* coordinate with other databases, including NCBI to make it clear that the global ID is MGI:MGI:nnnnn
* [http://www.obofoundry.org/id-policy.shtml OBO Foundry ID policy]
 
McMurry et al 2017, Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data
 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5490878/pdf/pbio.2001414.pdf

Revision as of 20:50, 1 March 2021


All identifiers in GO (e.g. referenced in GAF, ontology or associated documents) should be conform to the following format:

 GlobalID = Prefix ':' LocalID
  • Prefixes (aka Database): Each prefix must be registered in the GO xrefs registry metadata yaml file (see below). 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.

We use the term 'identifier' as synonymous with GlobalID, although confusingly some use 'identifier' to refer to what we call LocalID. Our concept of GlobalID corresponds with the W3C standard for CURIEs, see below


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
  • FlyBase:FBgn0011293
    • Database=FlyBase LocalID=FBgn0011293

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

Note that in GPAD and GPI formats, a single column with GlobalID is used

Prefix Registry

The Database should be registered in db-xrefs.yaml, available here:

Our prefix registry is coordinated with identifiers.org and the prefixcommons project: https://github.com/prefixcommons/biocontext

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

The term "identifier" is used in different ways which causes confusion. Our concept of GlobalID corresponds with W3C CURIEs and should be unambiguous.

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

  • MGI:MGI:98297

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)

col1:col2 =

  • ZFIN:ZDB-GENE-980526-166

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)

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


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)

FlyBase vs FB

previously there was confusion as to whether to use FB or FlyBase (or FLYBASE)

in GO in our registry, FB is the canonical prefix, but we include FlyBase as a synonym

Historically, "flybase" was used in identifiers.org but this is now resolved to be "fb" consistent with GO and other resources

NCBI seem to use FLYBASE

See Also

McMurry et al 2017, Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5490878/pdf/pbio.2001414.pdf