[Bioperl-l] identifier interface

[Lincoln Stein]

Matt, could you clarify what you are asking?

It is important to separate the concept of an identifier (and its correlates, 
the identifier namespace and the collection of identifiers), from the 
mechanism for resolving an identifier and regenerating its referent.  The 
analogous situation is domains names, in which there is insufficient 
information to resolve a domain name into a IP address, and a separate 
protocol, the DNS, is called for.  The nice thing about the LSID format is 
that the details of what goes into the object identifier field is left up to 
the naming authority, and so it can carry whatever information is necessary 
for the naming authority to resolve it.

There is a separate protocol for resolving LSIDs into resources, which the I3C 
is working on.  The draft that I looked at was pretty vague.

Lincoln

On Tuesday 16 July 2002 06:42 am, Matthew Pocock wrote:
> Hi.
>
> The actual interface for represeinting the info for regenerating a
> resource may need thinking about. While things like LSID are one way,
> raw accession/namespace tuples are another. Perhaps ensembl db name,
> entity class (feature, chromosome, clone...) and numeric id. There are
> too many scheims out there that may be usefull. For example, perhaps a
> company will want to store database locations in LDAP. In this case, you
> would want to easily implement a Bio::IdentifierI implementation that
> can store and expose an LDAP path. Perhaps you want to point directly to
> files, or to URLs, or using an sql_database_urn/Table_name/primary_key.
> Before tightly coupling the interface of Bio::IdentifierI to one naming
> standard, perhaps we could take a step back and think about the range of
> use cases. Just as genbank should not be defining the complete sequence
> interface, LSID should not define the complete identifier interface.
>
> So, what sorts of things would you potentialy need to know to re-create
> a resource? List below.
>
> Matthew
>
>
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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