[BioRuby] Ensembl API

[jan aerts (RI)]

I actually just started working on this API last night (in between some
deadlines I got to catch), so haven't gotten so far as to think about
caching. I'm basically working through the perl API tutorial
(http://www.ensembl.org/info/software/core/core_tutorial.html) and try
to implement all those examples. (At the moment, I'm at the bit that
says "Break chromosomal slices into smaller 100k component slices"...)

Some hurdles that I see coming are the caching and projecting features
from one coord system to another. We'll see what happens when we get
there.

As for a public place: I would _very_ much appreciate help with the API,
although

QUESTION FOR BIORUBY COMMUNITY AND DEVELOPERS:
* Do you think it would be best to create a sourceforge project for
this, or should I add it directly into bioruby (e.g. Bio::Api::Ensembl)?
I suppose the second option would be best, but the stuff I have is
probably not polished enough yet... and *far* from complete.
* Secondly: if a new release is coming: would it be best to wait untill
_after_ that release?

jan.


-----Original Message-----
From: Michael Han [mailto:mh6 at sanger.ac.uk] 
Sent: 10 May 2007 09:51
To: jan aerts (RI)
Subject: Re: [BioRuby] Ensembl API


On 10 May 2007, at 08:58, jan aerts ((RI)) wrote:
> Michael,
>
> As you mention that we maybe won't be able to cover everything with 
> the default activerecord behaviour: what problems are you thinking of?
>
> Note: I'd like to use the perl API as a guide. And indeed working out 
> the Slice object was quite simple...

Yes, I was thinking of the slices in combination with the different
assembly levels.
A change to the mapping part of that broke the last EnsEMBL release.
There were some cases where a seq_region maps one-to-many to other
seq_regions (also with gaps).
Did you put all the caching stuff from the Perl API into it? And if not,
is the performance ok?

It would be also great if you could put the code into some public place
(RubyForge as example), then it would be easier to see what is already
working/being worked at and what not.

> jan.
>
> -----Original Message-----
> From: Michael Han [mailto:mh6 at sanger.ac.uk]
> Sent: 09 May 2007 14:38
> To: jan aerts (RI)
> Subject: Re: [BioRuby] Ensembl API
>
> On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
>> Has anyone worked on an Ensembl API? There is a perl API and the 
>> database schema is well-documented. On first impression, it seems 
>> straightforward to make one using ActiveRecord, but I wouldn't want 
>> to
>
>> waste efforts on that if someone else is already working on it.
>>
>> See http://www.ensembl.org/info/software/core/index.html
>>
>> Dr Jan Aerts
>> Bioinformatics Group
>
> Hi Jan,
>
> I am not sure if you can cover everything with a the default active- 
> record behavior.
> But I would be a happy user of a ruby EnsEMBL API.
> If you need/want help with it, I would also volunteer.
>
> Michael