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

[Joseph Guhlin]

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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