Phylo Trees BioSQL BioPython API

Question

[Rick]

Hi,

Is there a python API for uploading a Phylogenetics tree in biosql/phylo Database Extensions? I have seen an extension of BioSQL for Phylogenetics but I haven't found any python API for that.

Regards

[Peter]

It would have been helpful to include links to the BioSQL phylogenetic extension PhyloDB you seem to be talking about, e.g: http://www.biosql.org/wiki/Extensions

[Rick]

Thank you Peter for the tip.

Answer 1

[Peter]

No, not currently. Would you like to extend the Biopython BioSQL support to do this?

[Rick]

Hi,

We want to store/retreive phylogenetic trees and taxonomies in the Database. I have seen some perl script here: https://github.com/biosql/biosql/tree/master/scripts. We use python in our project, We'll try to understand how it works and We try to release a python version.

Regards

[Peter]

If you mean load_ncbi_taxonomy.pl that is not part of PhyloDB, but rather core functionality in BioSQL. That Perl script comes with BioSQL and pre-loads the NCBI taxonomy into the BioSQL database. Just reimplementing that in Python serves no real use-case to my mind.

Also, Biopython can already fill the BioSQL taxonomy tables incrementally with the NCBI taxonomy downloaded via the Entrez API when loading records into the database.

In any case, join the BioSQL mailing list to discuss this.