[ensembl-dev] Question about registry data

[Andy Yates]

Hi Marc

Yes your assumption is correct an your local instance will be used in conjunction with ensembldb.

Hope this helps

Andy

Sent from my mobile.

On 16 Aug 2012, at 06:08, "Marc P. Hoeppner" <mphoeppner at gmail.com> wrote:

> 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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>> 
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> 
> 
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