Aspergillus niger BridgeDb

[strand]

Hi,

It seems that the supported target (or source) datasources for the
newly added BridgeDb file for Aspergillus niger does not include
Ensembl though the primary identifiers appear to be Ensembl IDs.
(http://webservice.bridgedb.org/Black%20mold/targetDataSources)

Is this by design or a defect?

More generally, is it correct to assume that all the datasources cited
within a BridgeDb file are supported as source and target datasources
for an organism?

Thank you.
Anupama.

[Martijn van Iersel]

Hi Anupama

> It seems that the supported target (or source) datasources for the
> newly added BridgeDb file for Aspergillus niger does not include
> Ensembl though the primary identifiers appear to be Ensembl IDs.
> (http://webservice.bridgedb.org/Black%20mold/targetDataSources)
>
> Is this by design or a defect?

This is actually a defect. It looks like we forgot to store the full
name for the Ensembl Aspergillus datasource, as it is in fact listed as
'null' in that list.

There is a workaround though, you can use the code EnAn, as in the
following example:

http://webservice.bridgedb.org/Black%20mold/xrefs/EnAn/CADANGAG00000001

>
> More generally, is it correct to assume that all the datasources cited
> within a BridgeDb file are supported as source and target datasources
> for an organism?

Yes, at least for all the .bridge databases (which are based on Apache
Derby), that is in fact true.

>
> Thank you.
> Anupama.
>

[strand]

Thank you for the clarifications and workaround Martijn!

Extending your last point, I have a few more questions specific to the
relational databases based BridgeDb mappers -

1. What determines the supported datasources for each organism in the
mappers?
2. How do the different versions of the derby databases for an
organism differ from each other?
3. Do the sql dumps differ from their derby equivalents? - I am trying
to understand if there is an advantage of using one over the other
only in terms of their mapping support - eg: coverage, update status,
supported datasources etc.

Thanks,
- Anupama

[Alexander Pico]

Anupama,

Our species-specific .bridge Derby databases are derived from the available datasources and links from Ensembl. We have a build pipeline based in their Perl API. The different versions diff per the changes to between Ensembl versions. There is an info field with the Ensembl version for each derby file. Our sql dumps are identical to the corresponding derby files.

- Alex

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