[Biopython-dev] Phylo: support for JSON trees

[David Winter]

Hi All,

There is at least one JSON specification for phylogenies. The Open Tree of
Life project (http://opentreeoflife.org/) uses a json "translation" of
nexml they call nexson: https://opentree.wikispaces.com/NexSON.

There is python code that handles at least some reading/writing ofthe
format: https://github.com/OpenTreeOfLife/peyotl

It's specific to open tree project, but it's at least something that's out
there.

On Wed, Dec 9, 2015 at 3:21 PM, Fields, Christopher J <cjfields at illinois.edu
> wrote:

> Agreed.  This is veering towards the deadly sin of reinvention.  Instead
> of that, maybe a good look should be taken at the current XML tree formats
> to see if they can reasonably be represented in or translated to JSON.  And
> only if a JSON-based format doesn't already exist.
>
> Chris
>
> > On Dec 9, 2015, at 4:12 PM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> >
> > Hi Fabio,
> >
> > You're right JSON has a lot of advantages (people said this about XML
> > too), but inventing your own file format is not something to be taken
> > lightly.
> >
> > Are there really no pre-existing tree formats using JSON?
> >
> > Peter
> >
> >> On Wed, Dec 9, 2015 at 9:12 PM, Fabio Zanini <fabio.zanini at fastmail.fm>
> wrote:
> >> Hi all,
> >>
> >> I've been working with phylogenetic trees for a few years and found it
> >> very convenient to convert Bio.Phylo trees to/from JSON, e.g.
> >>
> >> {'name': 'root', 'children': [
> >>  {'name': 'leaf1', 'branch_length': 0.01, children: []},
> >>  {'name': 'leaf2', 'branch_length': 0.02, children: []}]
> >> }
> >>
> >> I would like to implement such import/export functions into Bio.Phylo if
> >> there is interest. Because Python has a JSON parser already, it's like
> >> 50 lines of code altogether.
> >>
> >> The main arguments in favour of this are:
> >> - *JSON is standard for the web*, and the web is where all is moving
> >> (Jupyter, bokeh, but also specific tree-oriented web apps such as
> >> http://nextflu.org)
> >> - embedding metadata is trivial (just add more keys to those dicts!)
> >>
> >> How's that sound, shall I make a github PR?
> >>
> >> Cheers,
> >> Fabio
> >>
> >>
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-- 
David Winter
Postdoctoral Research Associate
Center for Evolutionary Medicine and Informatics
The Biodesign Institute
Arizona State University

ph: +1 480 519 5113
w: www.david-winter.info
lab: http://cartwrig.ht/lab/
blog: sciblogs.co.nz/the-atavism
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