[DAS] DAS setup questions

Tue, 09 Apr 2002 13:09:36 -0700

Thanks for your suggestions Jim.

I've had no problem uploading data directly to ensembl so far, but I'm
still not able to serve up the same data via the sample Dazzle web app. 
For example, if I upload the first line from the sample upload file
http://dev.ensembl.org/das/example.das, I can easily view it by browsing
the region between 1 and 10000 on chromosome 1.  I just can't figure out
how to fit the same data into the sample database and webapp structure
to serve the information from there.

>From the Ensembl DAS setup document, the schema provided to work with
the EnsemblGenericSeqFeatureSource bridge/adapter looks like this:

CREATE TABLE my_feature (
  contig_id varchar(40) NOT NULL default '',
  start int(10) NOT NULL default '0',
  end int(10) NOT NULL default '0',
  strand int(2) NOT NULL default '0',
  id varchar(40) NOT NULL default '',
  score double(16,4) NOT NULL default '0.0000',
  gff_feature varchar(40) default NULL,
  gff_source varchar(40) default NULL,
  name varchar(40) default NULL,
  hstart int(11) NOT NULL default '0',
  hend int(11) NOT NULL default '0',
  hid varchar(40) NOT NULL default '',
  evalue varchar(40) default NULL,
  perc_id int(10) default NULL,
  phase int(11) NOT NULL default '0',
  end_phase int(11) NOT NULL default '0',
  KEY id_contig (contig_id),
  KEY id_pos (id,start,end)
) TYPE=MyISAM;

The sample data looks like this:

| contig_id            | start     | end       | strand | id         |
+----------------------+-----------+-----------+--------+------------+
| AC000041.2.1.45436   |         1 |        57 |     -1 | Alu        |
| AC000041.2.1.45436   |       325 |       628 |     -1 | AluSg      |
| AC000041.2.1.45436   |      1299 |      1350 |      1 | Alu        |
| AC000041.2.1.45436   |      1354 |      1661 |      1 | AluJb      |
| AC000041.2.1.45436   |      2164 |      2451 |     -1 | AluSg      |

After inserting the sample data into the database I am unable to view it
online after my das source has been added.  I'm assuming that these
annotations should appear if I browse to the AC000041 contig.  Am I
wrong about this?

Maybe the problem is in my configuration file.  I'll post it here minus
internal info (as I've seen other people do) and if someone could point
out any mistakes I've made, I'd really appreciate it.

<?xml version="1.0" ?>

<dazzle xmlns="http://www.biojava.org/2000/dazzle">
  <resource id="ensembl428_bridge" jclass="ensembl.EnsemblHolder">
    <string name="dbURL"
value="jdbc:mysql://kaka.sanger.ac.uk/homo_sapiens_core_4_28" />
    <string name="dbUser" value="anonymous" />
    <string name="dbPass" value="" />
    <int name="schemaVersion" value="4" />
  </resource>

  <datasource id="ensembl428" jclass="ensembl.EnsemblReferenceSource">
    <string name="ensemblHolderID" value="ensembl428_bridge" />
    <string name="name" value="Ensembl 4_28" />
    <string name="description" value="Human Ensembl" />
    <string name="version" value="4.28" />
    <set name="elideTypes">
      <string value="repeat" />
      <string value="similarity" />
    </set>
    <string name="stylesheet" value="ensemblbase-style.xml" />
  </datasource>

  <alias id="ensembl140" target="ensembl428" />

  <datasource id="MyDataSource"
jclass="ensembl.EnsemblGenericSeqFeatureSource">
    <string name="ensemblHolderID" value="ensembl428_bridge" />
    <string name="name" value="Ensembl Test Source" />
    <string name="description" value="Test DAS feature source" />
    <string name="version" value="1.00" />
    <string name="mapMaster"
value="http://servlet.sanger.ac.uk:8080/das/ensembl428/" />
    <string name="dbURL" value="jdbc:mysql://<my server
name>/ensembl_generic" />
    <string name="dbUser" value="<userid>" />
    <string name="dbPass" value="<password>" />
    <string name="tableName" value="my_feature" />
    <string name="stylesheet" value="generic-style.xml" />
  </datasource>

</dazzle>

Thanks,

Graeme

James Freeman wrote:
> 
> Dear Graeme,
> 
> If you are trying to view your annotations on the public ensembl website
> (http:://www.ensembl.org/), there is an some easy ways to do it,
> depending on your time constraints.
> 
> Get your annotations matched to the sequences in:
> 
> ftp://ftp.ensembl.org/pub/human-4.28/data/fasta/dna/Homo_sapiens.latestgp.fa.gz
> 
> Once you know where your annotations are relative to the above, you
> there are two options that I recommend:
> 
> The fastest by far is to upload your data directly into ensembl:
> 
> http://www.ensembl.org/Homo_sapiens/helpview?se=1&kw=upload
> 
> or if you want to set up your own client neutral (i.e. not just Ensembl,
> but also Omnigene, Geodesic, et al.) das annotation service, try the
> following:
> 
> http://www.biodas.org/servers/
> http://www.ensembl.org/Dev/Lists/das/msg01042.html
> http://www.ensembl.org/Dev/Lists/das/msg01056.html
> 
> If you are trying to create an internal version of the distributed
> Ensembl website, follow the instructions on the website and I suggest a
> Dazzle reference server and an LDAS annotation server, each of which are
> excellent at their particular jobs.
> 
> Good luck,
> 
> Jim Freeman
> Senior Scientist
> Variagenics, Inc.
> 
> Graeme Campbell wrote:
> >
> > Hi there,
> >
> > I have been attempting to set up a sample DAS installation using the
> > document "Setting up a Ensembl DAS Server"
> > (http://www.ensembl.org/Docs/das_server_v1.2.pdf), but have been
> > stumbling a bit and I was hoping someone could offer some advice.
> >
> > I'm confused about the dazzle-webapp-skeleton
> > (http://www.biojava.org/download/dazzle/dazzle-webapp-skeleton-0.95.tar.gz).
> > I get a welcome page when I point my browser at localhost:8080/das/.
> > I'm also able to get back XML (in compressed format) by pointing my
> > browser at localhost:8080/das/dsn.  However, it comes with "test" and
> > "tss" data sources.  What exactly should I be able to do with these
> > sources once they are installed?  Should I be able to connect to my
> > local das webapp from the Ensembl website and view test annotations
> > online?
> >
> > I've also set up the test database, loaded the sample data, and
> > configured another sample web-app
> > (http://www.biojava.org/download/ensembl-das/ensembl-das-webapp-20020214.tar.gz)
> > as specified in the setup document.  From this, I'm able to get back XML
> > from a DSN request that lists my new datasource, and I'm able to add the
> > das source to the web-viewer on the ensembl.org site.  However, when I
> > browse the AC000041 contig region, there are no annotations, just a
> > message saying "No * Ensembl Te.. features in this region."  I believe
> > the test data from the setup document is all in this region though - but
> > I may be misunderstanding things.
> >
> > Any guidance you could give me would be appreciated.
> >
> > Thanks,
> >
> > Graeme
> >
> > --
> > Graeme Campbell                         phone:  (604) 875-3868
> > Bioinformatics Core Facility            e-mail: graemeca@cmmt.ubc.ca
> > Centre for Molecular Medicine and Therapeutics
> > Vancouver, BC. Canada.
> > _______________________________________________
> > DAS mailing list
> > DAS@biodas.org
> > http://biodas.org/mailman/listinfo/das

-- 
Graeme Campbell				phone:	(604) 875-3868
Bioinformatics Core Facility 		e-mail:	graemeca@cmmt.ubc.ca 
Centre for Molecular Medicine and Therapeutics
Vancouver, BC. Canada.