[BioRuby] [Biopython-dev] JSON format for sequence data

[Peter Cock]

Hi Lior,

As with XML, there are infinitely many ways to structure your data
and store it in JSON. The problem is social (agreeing a standard)
rather than particularly technical.

I can think of one precedent with sequence data, TogoWS offers
JSON versions of various database entries,

http://togows.dbcls.jp/

e.g. Here's a UniProt entry as the original flat file or as JSON:

http://togows.org/entry/ebi-uniprot/A1AG1_HUMAN
http://togows.org/entry/ebi-uniprot/A1AG1_HUMAN.json

Or, an NCBI record in GenBank format and as JSON:

http://togows.org/entry/ncbi-nucleotide/J00231
http://togows.org/entry/ncbi-nucleotide/J00231.json

I presume this JSON model reflects the BioRuby object model,
CC'ing the BioRuby mailing list.

Peter

On Thu, Dec 3, 2015 at 12:47 PM, Lior Zimmerman <lior at igc.bio> wrote:
> Dear members,
>
> I'm relatively new to the framework and was wondering why there's no JSON
> format for sequence data, and whether there are plans to decide on one.
> JSON can incorporate much more data than traditional formats (e.g. double
> strand overhangs, more elaborate descriptions, NGS quality, and much more)
>
>
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