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

[Mark A. Jensen]

W00t! Glad to see there is scope for this; now I can say I did one useful thing for BP in two years!

There is batch support (as well as traversals) in the REST api; looks like the next two features I should add.

cheers all MAJ

Batch is an interesting problem,
>-----Original Message-----
>From: Joseph Guhlin [mailto:guhli007 at umn.edu]
>Sent: Monday, September 17, 2012 02:21 PM
>To: 'Hilmar Lapp'
>Cc: 'Fields, Christopher J', <bioperl-l at lists.open-bio.org>, 'Mark A. Jensen'
>Subject: Re: [Bioperl-l] New Perl ORM for graph db Neo4j
>
>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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