Status of BioMart integration?

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Status of BioMart integration?

Josh Goodman
Hi all,

First, thanks again for putting on the InterMine training this week.  I
found it very useful and look forward to seeing future improvements.

Second, I want to ask you what the status of the InterMine/BioMart
integration is.  I remember something being mentioned at a GMOD meeting a
few years back but after poking around the Trac wiki a bit it seems that
this work has stalled (unless I'm misinterpreting the information).

Can you clarify for me what the short and long term plans for integration
are?  If there are plans can you give a brief summary?

The reason I'm asking is that for the FlyBase project there are some
interesting data sets in existing BioMart servers that we would like to
use without pulling them into a local InterMine service.  Ideally, what we
are looking for is a solution that utilizes the BioMart web service API to
display or query the data on demand from these other web services.

What I'm trying to determine is that if there are no immediate plans (~2
years or less) for this type of support then FlyBase will need to start
working on code to glue these systems together for our purposes.  If there
are indeed short term plans for this, then we would want to adjust our
resources and plans accordingly.

Cheers,
Josh

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Re: Status of BioMart integration?

Richard Smith
Hi Josh,
Thanks for coming to the workshop, I hope it gave you a good idea of how
to get started with InterMine.

BioMart integration is written into our latest grant but we don't have
any concrete plans to implement it yet.  The idea would be that we
would write a BioMart-compatible web service wrapper for InterMine, so
a Mine could be made available to BioMart's query federation system.

This seems technically achievable, though in fact a more common request
is to access BioMart instances via the InterMine web interface.  This
would be much harder to implement as InterMine doesn't have the same
idea of federation built into it - our inter-operation thus far is
premised on transferring typed lists of data between Mines.

So, I think we'll do some more investigation of making a BioMart web
service wrapper for InterMine within the next two years but we don't
have concrete plans right now.

I hope that helps, I think in the short term you could assume that we
won't have implemented this kind of integration.  We're very happy to
advise on any type of glue code you're implementing though.

Cheers,
Richard.



On 16/09/2010 17:17, Josh Goodman wrote:

> Hi all,
>
> First, thanks again for putting on the InterMine training this week. I
> found it very useful and look forward to seeing future improvements.
>
> Second, I want to ask you what the status of the InterMine/BioMart
> integration is. I remember something being mentioned at a GMOD meeting a
> few years back but after poking around the Trac wiki a bit it seems that
> this work has stalled (unless I'm misinterpreting the information).
>
> Can you clarify for me what the short and long term plans for
> integration are? If there are plans can you give a brief summary?
>
> The reason I'm asking is that for the FlyBase project there are some
> interesting data sets in existing BioMart servers that we would like to
> use without pulling them into a local InterMine service. Ideally, what
> we are looking for is a solution that utilizes the BioMart web service
> API to display or query the data on demand from these other web services.
>
> What I'm trying to determine is that if there are no immediate plans (~2
> years or less) for this type of support then FlyBase will need to start
> working on code to glue these systems together for our purposes. If
> there are indeed short term plans for this, then we would want to adjust
> our resources and plans accordingly.
>
> Cheers,
> Josh
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>


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