[DAS2] current status of DAS

[Andreas Kahari]

Sent to list on behalf of Eugene Kulesha (non-subscriber).
    - Andreas K.

----- Forwarded message from Eugene Kulesha <ek at ebi.ac.uk> -----
Subject: Re: [DAS2] current status of DAS
Date: Mon, 25 Sep 2006 10:46:48 +0100
From: Eugene Kulesha <ek at ebi.ac.uk>
To: Rowan Kuiper <rowankuiper at hotmail.com>
CC: das2 at lists.open-bio.org
References: <BAY109-F146C16DA17D1AFD45A87C6BA270 at phx.gbl>

>- First of all, will DAS2 ever be finished. 
good question :) although it stopped worrying me a long time ago ;)

>DAS is still alive or is there something else that took its place?
it certainly is in Ensembl

>- Why don?t all servers support all commands. Some reference servers for 
>example don?t support the entry_point command. How do I request features 
>when I don?t know which segments the server contains? I imagine that these 
>great differences in how to use different servers could be very problematic 
>when implementing a viewer.
i guess it was done in part so das could be adopted quicker, but I have to 
admit that I was very much frustrated by
the fact that very few sources implement 'entry_points' command


>- It seems that the only way to retrieve information from a server is to do 
>a request for a certain region. Is there a way to ask for a specific 
>features.
yes, features?feature_id=XXXX would give you the feature ( if feature_id is 
implemented )

http://www.ensembl.org/das/Homo_sapiens.NCBI36.transcripts/features?feature_id=ENSE00001253754


>- When I have to serve data that needs some extension on the XML structure, 
>would it be a problem to just do it. How would clients handle these 
>extensions. Ignore them or somehow parse them?
I'm not quite sure what Bio::DasLite ( this is what we use to parse DAS 
responses) would do ..
but even if it parses the extension Ok, Ensembl will ignore the unknown 
properties ..


>- And last, one of the goals of DAS is to be able to integrate biological 
>data. When I for example want to compare my data to EnsEMBL features I will 
>have to set up my own server that serves features referenced to the same 
>genome as the EnsEMBL features. So I wonder if there exists reference 
>servers that contain the current genomes  of EnsEMBL, NCBI or UCSC.  I 
>found http://das.ensembl.org/das/ensembl_Homo_sapiens_core_38_36 which 
>always replies an out of memory error even with the entry_points command 
>and http://das.ensembl.org/das/ensembl1834 which seems to work properly but 
>its transcript server ens1834trans also returns out of memory errors.

http://www.ensembl.org/das/dsn have the list of all the sources that we 
serve from internal ensembl data

amongst them there are reference sources, e.g

http://www.ensembl.org/das/Homo_sapiens.NCBI36.reference
http://www.ensembl.org/das/Mus_musculus.NCBIM36.reference


Cheers

Eugene Kulesha


----- End forwarded message -----

-- 
Andreas Kähäri
Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)