Re: [Gusdev-gusdev] LoadPfam

[Angel P. <an...@pc...>]

On Fri, 28 Feb 2003, Pjm wrote:

> Hi all,
>
> While updating LoadPfam I have come accross some interesting "things". A PFam
> release has links to databases such as 'INTERPRO; IPR000308;'. The old schema
> just had a link DBref ->ExternalDatabase. The new schema has a middle table to
> take into account a release of database.
>
> My first issue is populating these tables - I found some XML for GUSdev that I
> am tweaking to setup ExternalDatabase and ExternalDatabaseRelease for testing
> LoadPfam. I will assume all releases for now are version one, just for testing.
>   When I do it proper, shall I just insert the latest release only?

This really depends on the representation that your situation needs. For
instance, when we represent either GenBank or dbEST, we use a "continuous"
release and update the ExternalDatabaseRelease entry to reflect either the
last day dbEST was imported or the last release of GenBank that was
imported. DoTS build team correct me if I am wrong here.

This allows us to have an alternate key on the
(external_database_release_id, source_id) tuple and also a small number of
ext_db_rel_id's to query for a particular type of source_id.

For other databases, you may want to keep the entries distinct between
releases. A good example of this would be unigene, that does not really
have stable identifiers for a set of constiuent sequences (e.g. when sets
split or merge, they old ID is completely lost). Another would be for
handling ontologies such as the MGED Ontology, where terms and definitions
may change, but you want to keep track of the changes in order to
successfully migrate data from one release to the next and be able to
track down deprecated terms.

>
> Do I need to create a small plugin to create new DB releases as needed?
> Shouldn't be hard.

Most times if a plugin is this simple, it is better to rely on
UpdateGusFromXML to do the work for you.

>
> LoadPfam itself will assume any reference to a DB in the PFam file is to the
> latest DB. For example, picking the last release of INTERPRO will mean getting
> the youngest record by using ExternalDatabaseRelease.release_date for INTERPRO
> and link a SRes.DBref to it.
>

Yes this works, but if you do not need multiple releases of Pfam, we may
want to consider the continuous release route. DoTS build team comments?

> How does this sound?
>
> Have a good weekend,
> Paul.
>
>
>
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

-- 
Angel Pizarro
Programmer Analyst
Center for Bioinformatics
an...@pc...