[Biojava-dev] 23andMe Personal Genome API

[Michael Heuer]

Andreas Prlic <andreas at sdsc.edu> wrote:
> I think it would be great to have that.... Assuming you would take
> over the leadership of this module.

That's the thing, on its own, there isn't really enough there for a
complete module.  It might make sense to have code that deals with VCF
and GFF3/GVF files, but that has been done elsewhere.


> On a sidenote,  BioJava is LGPL v 2 and not 3. If this is your code,
> that should not be a prob...

Yes, I can relicense if necessary.

   michael


> On Tue, Oct 23, 2012 at 8:35 PM, Michael Heuer <heuermh at gmail.com> wrote:
>> Hello,
>>
>> There isn't much in biojava3 dealing with variation data; that has
>> been more the domain of other projects such as
>>
>> Picard  (Apache v2, MIT licenses)
>> http://picard.sourceforge.net/
>>
>> GATK (troublesome license)
>> http://www.broadinstitute.org/gatk/
>>
>> etc.
>>
>>
>> I wrote a client library for the 23andMe Personal Genome API (not
>> affiliated, just curious)
>>
>> https://api.23andme.com/docs/reference/
>>
>> hosted here temporarily
>>
>> https://github.com/heuermh/personal-genome-client  (LGPL version 3 or later)
>>
>> and was wondering if it would make sense to contribute this to
>> biojava3.  There isn't a very rich data model of variation in the
>> client classes and we don't have any in biojava3 either.  I am also
>> working on this project
>>
>> https://code.google.com/p/genotype-list/
>>
>> which has a slightly better model, but is really only applicable for
>> traditional allele nomenclature-based genotypes (e.g. HLA, KIR).
>>
>> Please let me know what you think.
>>
>>    michael