[BioMart Users] adding data to a mart

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[BioMart Users] adding data to a mart

andrea_bio
Hello

I have a couple of minor questions

is the biomart perl api still available? although i have only ever used
biomart through the ensembl website i was aware there was a perl api. In
the rc5 user manual there is only mention on a java api.

Also am i correct in saying that there are only methods for retrieving
data in the java api? I didn't see any methods for creating or updating
database records. What does the 'power' bioinformatics user do if they
want to add records to the underlying database? I believe if there is a
virtual mart sitting on top of 'normal' databases then the user can just
issue standard CRUD database statements and the virtual mart will
seemlessly detect the inserted/updated data. Is that correct? But what
if you wanted to add new records to a materialised mart? Is there
anything in the api to cater for that?

Also i am unsure as to the purpose of the config file when i create a
mart. From experience i seem to need a config file for each dataset in
order to access the dataset from the website but i couldn't find an
explanation of the purpose of this file in the user manual.

thanks a lot
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Re: [BioMart Users] adding data to a mart

Junjun Zhang



On 11-03-24 11:41 AM, "Andrea Edwards" <[hidden email]> wrote:

> Hello
>
> I have a couple of minor questions
>
> is the biomart perl api still available? although i have only ever used
> biomart through the ensembl website i was aware there was a perl api. In
> the rc5 user manual there is only mention on a java api.

BioMart 0.8 is written in pure Java, no Perl API is available.

>
> Also am i correct in saying that there are only methods for retrieving
> data in the java api? I didn't see any methods for creating or updating
> database records. What does the 'power' bioinformatics user do if they
> want to add records to the underlying database? I believe if there is a
> virtual mart sitting on top of 'normal' databases then the user can just
> issue standard CRUD database statements and the virtual mart will
> seemlessly detect the inserted/updated data. Is that correct? But what
> if you wanted to add new records to a materialised mart? Is there
> anything in the api to cater for that?

Yes, virtual mart will automatically pick up changes made to the 'normal'
underlying database.

Materialized mart runs in read-only mode once it's been built. In the case,
original 'normal' database has been updated, in order for the materialized
mart to bring its content in-sync, a complete rebuild is needed.

>
> Also i am unsure as to the purpose of the config file when i create a
> mart. From experience i seem to need a config file for each dataset in
> order to access the dataset from the website but i couldn't find an
> explanation of the purpose of this file in the user manual.

The configs you see in the right side Portal panel are not actually files,
they are where you configure how to present the sources to the end users to
search and retrieve data from sources.

Hope this helps,

Junjun


>
> thanks a lot
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
>

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