[ensembl-dev] Question about registry data

[Marc P. Hoeppner]

Hi Andy,

thanks for the clarification. I guess my concern was partly that using 
multiple DB connections wouldn't give me full control over what is 
pulled from where. For performance reasons, I would like to use my local 
databases - so I was a little worried that also providing the official 
DB as source may result in data getting loaded from there. Am I correct 
to assume that the order of connection attempts is the same as the order 
in which the databases are provided in the registry connection? I.E. if 
I first specify the local db, then the ensembldb.ensembl.org, that it 
will always try to find things locally first and only fall back on 
ensembl if a db wasn't found?

/Marc
> Hi Marc,
>
> Just to point something out first you can always use the method load_registry_from_multiple_dbs to load from multiple databases e.g.
>
> Bio::EnsEMBL::Registry->load_registry_from_multiple_dbs(
> {
>    -HOST => 'ensembldb.ensembl.org', -PORT => 5306, -USER => 'anonymous',
> },
> {
>    -HOST => 'mysql.ebi.ac.uk', -PORT => 4157, -USER => 'anonymous',
> }
> );
>
> As to answer your question we store a lot of information in the core DB meta tables e.g. aliases are stored under species.alias. However things like the group, version detection & species name detection are done via the Registry & regular expressions performed on the database name (with the exception of multi-species DBs whose species names are stored along side their species id in the meta table).
>
> Best regards,
>
> Andy
>
> Andrew Yates                   Ensembl Core Software Project Leader
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensembl.org/
>
> On 15 Aug 2012, at 12:05, Marc P. Hoeppner wrote:
>
>> Hi,
>>
>> I have been using a local install of some of the EnsEMBL databases for a while now, but am always required to load multiple dbs (including ensembldb.ensembl.org) - otherwise the registry object will lack information on e.g. aliases of species names. My question therefore is where that information is physically stored and what I would have to do on my end (the local install) to get all that meta data without also connecting to the official mysql mirror? Is that information perhaps stored in a SQL table/database?
>>
>> Kind regards,
>>
>> Marc
>>
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