[Bioperl-l] New Perl ORM for graph db Neo4j

[Joseph Guhlin]

Forgot the link, sorry: http://www.bio4j.com/

"Schema" is here:
http://blog.bio4j.com/2012/05/new-bio4j-general-domain-model-schema-available/

--Joseph

On Mon, Sep 17, 2012 at 1:21 PM, Joseph Guhlin <guhli007 at umn.edu> wrote:

> Another project using Neo4j is Bio4j. The database is generated using java
> but can be queried through the REST interface with CYPHER.
>
> I haven't had a chance to build it yet or look at it, but may do so in the
> near future.
>
> I am using Neo4j for my own project and the only thing generic enough I
> could contribute with (that also overlaps with another module) is The Gene
> Ontology. I import it (~60k node, ~600k relationships, but I ignore a few
> that others may consider key) and could clean up and contribute that code.
> I do use a bulk import script written in java that uses the native
> libraries to process everything so would have to make it work for this
> module directly (or keep the java import, as it is open source).
>
> --Joseph
>
> On Mon, Sep 17, 2012 at 12:44 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:
>
>> Yes, indeed. And lo and behold, the Open Tree of Life (
>> http://opentreeoflife.org) folks are at present building their tree
>> store on top of Neo4J. They're mostly Python, though. (Which I'm sure our
>> Biopython colleagues will love to hear.)
>>
>>         -hilmar
>>
>> On Sep 17, 2012, at 11:28 AM, Fields, Christopher J wrote:
>>
>> > Following up on this, any specific modules where this would be a boon?
>>  I could see this being very useful for Bio::Tree (and Jason's recent work
>> on creating a persistent backend for storing tree info). Bio::Ontology also…
>> >
>> > chris
>> >
>> > On Sep 17, 2012, at 12:08 PM, "Fields, Christopher J" <
>> cjfields at illinois.edu> wrote:
>> >
>> >> Agree, very nice!
>> >>
>> >> chris
>> >>
>> >> On Sep 17, 2012, at 10:00 AM, Hilmar Lapp <hlapp at drycafe.net> wrote:
>> >>
>> >>> Very nice, Mark! -hilmar
>> >>>
>> >>> On Sep 17, 2012, at 8:13 AM, Mark A. Jensen wrote:
>> >>>
>> >>>> Hello all,
>> >>>> If anyone is experimenting with Neo4j (www.neo4j.org) and needs a
>> full-featured Perl OO interface, please give REST::Neo4p (
>> https://metacpan.org/module/REST::Neo4p) a try. Send me the bugs via RT!
>> >>>> cheers,
>> >>>> MAJ
>> >>>>
>> >>>>
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>> >>> --
>> >>> ===========================================================
>> >>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>> >>> ===========================================================
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
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>> --
>> ===========================================================
>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>> ===========================================================
>>
>>
>>
>>
>>
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