[Biopython] EBI module expansion/development

[Francesco Gastaldello (Staff)]

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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