[DAS] Configuring a valid MAPMASTER?

[Andy Jenkinson]

The SourceAdaptor POD documents the build_types method. Just return an array containing a hash per type. For example:
return ( { 'type' => 'expression_tag', 'category' => 'experimental' } );

A more complete implementation would also include an ontology term and the 'count' for each type (i.e. the number of features of each type). Note that the build_types command takes segment parameters like the build_features method, except the segment is optional for build_types:
/das/yoursource/types
/das/yoursource/types?segment=X:1,100

Just make sure the content matches the types and categories used by the features command.

See the spec for more details:
http://www.biodas.org/documents/spec-1.6.html#types

On 7 Feb 2011, at 14:48, Chris Cole wrote:

> Hi Andy,
> 
> Thanks for the help. Looks like I was close...
> 
> I now get an error regarding the 'types' command. I haven't implemented it so that's not a surprise. However, I'm struggling to find documentation on the build_types() function and what data it should return. My source data only has one type: 'expression_tag' so how should I return that?
> Cheers,
> 
> Chris
> 
> On 07/02/11 11:40, Andy Jenkinson wrote:
>> Hi Chris,
>> 
>> The 'reference' Ensembl sources are suitable for use as mapmasters, as they provide sequence information:
>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/entry_points
>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/sequence?segment=1:1,100
>> 
>> So, barring any particular nuance of IGB, the correct mapmaster URL would be:
>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference
>> 
>> (assuming thaliana)
>> 
>> The reason for all this is I guess that IGB does not support the DAS 1.53E/1.6 sources command, which provides species and coordinate information directly.
>> 
>> Cheers,
>> Andy
>> 
>> On 7 Feb 2011, at 10:34, Chris Cole wrote:
>> 
>>> Hi,
>>> 
>>> I have a functioning ProServer install that works fine with Ensembl, but I'd like to get it working with IGB as well. However, it fails to load as it has a 'Missing MAPMASTER element'. I see I need to specify a URI to a known MAPMASTER source, but I've no idea how.
>>> 
>>> The server is for Arabidopsis data and I've found the Ensembl DAS sources for plants, but which can I use as a mapmaster?
>>> http://plants.ensembl.org/das/dsn
>>> Or am I barking up the wrong tree?
>>> 
>>> Any pointers much appreciated.
>>> Cheers,
>>> 
>>> Chris
>>> 
>>> 
>>> _______________________________________________
>>> DAS mailing list
>>> DAS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/das
>> 
> 
> 
> -- 
> Dr Chris Cole
> Senior Bioinformatics Research Officer
> College of Life Sciences
> University of Dundee
> Dow Street
> Dundee
> DD1 5EH
> Scotland, UK
> 
> url: http://network.nature.com/profile/drchriscole
> e-mail: chris at compbio.dundee.ac.uk
> Tel: +44 (0)1382 388 721
> 
> The University of Dundee is a registered Scottish charity, No: SC015096