On 12/08/08 4:50 AM, "Henrikki Almusa" <[EMAIL PROTECTED]> wrote:
> Hi,
>
> I have some questions about combining multiple schemas within one mart
> instance.
>
> I did a biomart from multiple schemas by combining data first with a
> script. However I was asked to look into a way which would not entail
> copying the data (I currently made two copies of it, the combined one
> and then the biomart itself). So this would require two things. First to
> combine multiple schemas. Problem here is that the main tables _key
> columns values are not unique over all the schemas, they are unique
> within any one schema. Second thing is that the tables should be done as
> views and not their own tables. This would then remove all need to copy
> information.
>
> I think that second is possible to do. Though it would essentially mean
> that I have to write the SQL to create it. Martbuilder doesn't really
> help in this.
>
> First I don't know how to do. The documentation seem to indicate that
> partitioned schema can combine multiple ones, but I don't see how the
> _key column would be handled.
>
> Regards,
> --
> Henrikki Almusa
Hi Henrikki,
It is certainly possible to combine multiple source schemas into a single
biomart schema. You can either do it manually using your scripts or
automatically using Mbuilder. The logic will be the same.(for an example
look at ensembl Mbuilder config files) I am not sure what the problem with
unique keys is as they tend to identify different things and should not
clash. Perhaps if you could send us a bit more detail on how these schemas
are structured and how the resulting biomart schema looks like we would be
able to help you more.
As far as views are concerned - this is possible assuming that the
conversion logic is not too complex. However I would advise you to use
materialized schemas as otherwise you would loosing the benefits of query
optimizations
Sorry we can't help you more but we would need a bit more detail to
understand exactly what you are trying to achieve there
A.
