[Biopython] Uniprot UNIfire new engine

[Peter Cock]

Hi Téletchéa,

I was not aware of this tool, but it is outside my area. Looking at the
slides title,

Exchanging protein function prediction rules with the community;
The URML format and UniFIRE engine.
Alexandre Renaux,Bioinformatics Software Engineer, EBI.

Given URML is to hold "The Fact Model", it doesn't fit under Bio.SeqIO
(which covers sequence file formats including the legacy plain text flat
files dating back to SwissProt, and their replacement UniProt XML).

I suspect this is more targeted to data integration systems like RDF
(something else UniProt are strong in) and rule reasoning systems,
which are much broader than just bioinformatics.

I've not watched the video, and only skimmed the slides. How would
you see this fitting into Biopython?

Regards,

Peter

On Fri, Jul 12, 2019 at 10:43 AM Téletchéa Stéphane
<stephane.teletchea at univ-nantes.fr> wrote:
>
> Dear all,
>
> I had the opportunity to attend to a congress last week called JOBIM in
> Nantes (France). There was a very interesting talk by Rabie Saidi from
> the EBI about the new annotation engine called UNIfire.
>
> See for more information:
> - https://www.youtube.com/watch?v=_7wuufRp-GM
> -
> https://gitlab.ebi.ac.uk/uniprot-public/unifire/blob/master/misc/media/UniFIRE-URML.pptx
> - https://gitlab.ebi.ac.uk/uniprot-public/unifire
>
> The new format of the processed data is URML, and UNIfire could be used
> locally to produce a specific analysis from a given sequence, unrelated
> to upstream UNIPROT.
>
> Has anyone started to work on this? Looking at the reference SeqIO
> parser, I do not see it :-)
> (https://github.com/biopython/biopython/blob/master/Bio/SeqIO/UniprotIO.py)
>
> And yes, I agree to participate in it, but no I cannot handle it myself
> only, not being expert enough in biopython coding :-)
>
> Best
>
> Stéphane
>
> --
> Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein
> Design In Silico
> UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322
> Nantes cedex 03, France
> Tél : +33 251 125 636 / Fax : +33 251 125 632
> http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
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