[Biojava-dev] 23andMe Personal Genome API

[Andreas Prlic]

I see. Sounds like it would fit to the -genome module? Please re-use
the GFF file parser and don;t commit an alternative one...

A

On Wed, Oct 24, 2012 at 2:16 PM, Michael Heuer <heuermh at gmail.com> wrote:
> 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



-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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