[Biopython] EBI module expansion/development

[Ivan Gregoretti]

Hello Francesco and community.

>From the standpoint of organisation and clarity, it feels reasonable
to try contacting the developer and incorporating
https://github.com/bebatut/ebisearch first.

If that effort fails, it is then dbfetch what should be incorporated
into Biopython.

Thank you.

Ivan


Ivan Gregoretti, PhD
Bioinformatics



On Mon, Aug 28, 2017 at 2:28 PM, Francesco Gastaldello (Staff)
<f.gastaldello at dundee.ac.uk> wrote:
>
>
> Hi all,
>
>
>
> Recently the module Bio.EBI.dbfetch has been reviewed and made ready for
> merging into the master branch.
>
>
>
> The module is restricted to the ‘dbfetch’ service only.
>
>
>
> Few days ago Peter found out a script that can deal with the entire EBI
> Search API: https://github.com/bebatut/ebisearch
>
>
>
> This script goes way beyond dbfetch only and provide access to the EBI
> Search API in full, which in turn provide access to the following
> repositories:
>
>
>
> European Nucleotide Archive (ENA)
>
> Ensembl Genomes
>
> RNAcentral
>
> InterPro
>
> dbfetch/WSDbfetch
>
> MetaboLights
>
> Enzyme portal
>
> Expression Atlas
>
> Gene & protein summaries
>
> PomBase
>
> Job Dispatcher
>
> HMMER
>
> LRG
>
> EMBOSS
>
> Omics Discovery Index
>
>
>
> More info here: http://www.ebi.ac.uk/ebisearch/overview.ebi
>
>
>
> I would like to know if people are interested in any of the following
> options:
>
>
>
> Ignore the scripts and merge the Bio.EBI.dbfetch module to the Biopython
> master
> Contact the developer for this script and incorporate it into Biopython
>
>
>
> The licence term for this script is pretty relaxed (
> https://github.com/bebatut/ebisearch/blob/master/LICENSE ) but extending a
> request for collaboration before hand is in order.
>
>
>
> Any thoughts?
>
>
>
> Regards,
>
> Francesco
>
>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
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