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Update id policy to allow special case exceptions for ontologizing of pre-existing databases #81

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
Use case is pro wanting to make the connection to Uniprot clear, and so to use 
identifiers of the sort

http://purl.obolibrary.org/obo/PR_P04637 for TP53 human

Original issue reported on code.google.com by alanruttenberg@gmail.com on 16 May 2013 at 5:57

GoogleCodeExporter commented 9 years ago 
Considering we are trying to get towards meaningless IDs, what is the interest 
of using 
http://purl.obolibrary.org/obo/PR_P04637 
vs
http://purl.obolibrary.org/obo/PR_xxxxxxx and an annotation property?

Original comment by mcour...@gmail.com on 16 May 2013 at 6:02

GoogleCodeExporter commented 9 years ago 
Long story. A short answer would be to call Cathy Wu and talk to her about it. 
A longer answer would be better provided as discussion. I might be able to send 
you the complete thread.

Original comment by alanruttenberg@gmail.com on 16 May 2013 at 6:04

GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
These are UniProt accessions

Original comment by cmung...@gmail.com on 16 May 2013 at 6:07

GoogleCodeExporter commented 9 years ago 
If by PR_xxxxxxxx you mean IDs of the form currently used by PRO (nine-digit 
numeric), then the interest is in not having to mint new IDs for every existing 
identifier in the external database.

Original comment by d...@georgetown.edu on 16 May 2013 at 6:08

GoogleCodeExporter commented 9 years ago 
Alan is sending out proposed update to obo-discuss policy with 2 weeks review, 
CHris is checking on what may need to be updated on the apache conf side

Original comment by mcour...@gmail.com on 7 Jun 2013 at 5:09

GoogleCodeExporter commented 9 years ago 
See 
http://code.google.com/p/obo-foundry-operations-committee/issues/detail?id=88

Original comment by mcour...@gmail.com on 7 Jun 2013 at 5:09

GoogleCodeExporter commented 9 years ago 
Assigning to Alan.

Original comment by mcour...@gmail.com on 21 Jun 2013 at 11:00

GoogleCodeExporter commented 9 years ago 
update June 28: during call, Alan mentioned he'll take care of sending out the 
proposal

Original comment by mcour...@gmail.com on 28 Jun 2013 at 4:44

GoogleCodeExporter commented 9 years ago 
PRO wants to use isoform ids as well, which add a "-"\d+ at the end. We need to 
see whether this is compatible with OBO ids before approving this. Chris?

Original comment by alanruttenberg@gmail.com on 22 Jul 2013 at 3:22

GoogleCodeExporter commented 9 years ago 
In response to comment #10, Chris has responded that this causes no troubles on 
his side.

Original comment by alanruttenberg@gmail.com on 10 Sep 2013 at 4:13

GoogleCodeExporter commented 9 years ago 
I have made a proposed change to the google drive version of the document at 
http://goo.gl/elqRql

Text below, but better to look at the document in google drive. Formatting may 
have been lost.

Exceptions modifying the productions above

In addition to these OBO format ids, a decison was made to allow for cases 
where a non-ontology resource, such as a database, has an ontology created to 
adapt the resource into ontology form. Requests for exceptions to the standard 
format should be made to the OBO Operations Technical Group by submitting a 
ticket at http://code.google.com/p/obo-foundry-operations-committee. On 
approval this document will be augmented to add the allowable formats.

Issue 81 proposed that a variant of UniProt Accessions be used for the Protein 
Ontology in their adaptation of certain UniProtKB entries that correspond to 
their “organism-gene”  and isoform category. These accessions can be 
specified as followed:

LOCALID_PR_UNIPROT ::= [A-Z][0-9]+("-"[0-9]+)?
PR_OBO_IDENTIFIER ::=  "PR:" LOCALID_PR_UNIPROT

We amend the OBO_IDENTIFIER production to be

OBO_IDENTIFIER ::= (IDSPACE ":" LOCALID) | PR_OBO_IDENTIFIER
Format of Foundry-compliant URIs
FOUNDRY_OBO_URI ::= "http://purl.obolibrary.org/obo/" 
((IDSPACE "_" LOCALID) | 
  PR_OBO_IDENTIFIER
 )

Original comment by alanruttenberg@gmail.com on 7 Oct 2013 at 4:13

GoogleCodeExporter commented 9 years ago 
eh.

should be 

...
FOUNDRY_OBO_URI ::= "http://purl.obolibrary.org/obo/" 
((IDSPACE "_" LOCALID) | 
  ("PR_" LOCALID_PR_UNIPROT)
 )

Original comment by alanruttenberg@gmail.com on 7 Oct 2013 at 4:21

GoogleCodeExporter commented 9 years ago 
Per discussions with Darren, updated the regex to 

LOCALID_PR_UNIPROT ::= [A-Z][A-Z0-9]{5,6}+("-"[0-9]+)?

Original comment by alanruttenberg@gmail.com on 27 Oct 2013 at 5:33