[DAS] entry_points query

[ian Longden]

avilella wrote:

>Hi all,
>
>I have been trying to get the grips with biodas the last couple of days,
>and playing around with the several servers that are listed by Dr. F.
>Cheung.
>
>Any there is something that I don't understand about entry_points query:
>
>If I query any of the databases for something like:
>
>PREFIX/das/DSN/entry_points
>
>Which is what you would query according to the specification (1.5),
>you don't get anything.
>
>Now if instead you query with lowecase dsn:
>
>PREFIX/das/dsn/entry_points
>
>you get:
>
>(1) the same result as dsn query for some sites, like for example:
>
>http://genome.cse.ucsc.edu/cgi-bin/das/dsn/entry_points
>http://www.wormbase.org/db/das/dsn/entry_points
>http://www.tigr.org/docs/tigr-scripts/tgi/das/dsn/entry_points
>
>(2) You don't get anything, like for example:
>
>http://servlet.sanger.ac.uk:8080/das/dsn/entry_points
>http://tomcat.molgen.mpg.de:8080/das/dsn/entry_points
>http://supfam.org/SUPERFAMILY/cgi-bin/das/dsn/entry_points
>  
>
Okay so lets take the servlet example.
Use the
http://servlet.sanger.ac.uk:8080/das/dsn
to get the valid dsn's
which will give you something like:-
-
<DASDSN>
-
<DSN>
<SOURCE id="ens1431cds" version="14">Ensembl 14.31 CDS</SOURCE>
<MAPMASTER>http://das.ensembl.org/das/ensembl1431/</MAPMASTER>
<DESCRIPTION>Ensembl CDS</DESCRIPTION>
</DSN>
-
<DSN>
<SOURCE id="ens1431snp" version="14.31">snps</SOURCE>
<MAPMASTER>http://das.ensembl.org/das/ensembl1431/</MAPMASTER>
<DESCRIPTION>Human genome SNPs from Ensembl</DESCRIPTION>
</DSN>

And then to get the entry points for that dsn replace dsn with the dsn name.
 e.g.  for the first dsn ensembl1431


http://servlet.sanger.ac.uk:8080/das/ensembl1431/entry_points

should be used to obtain the entry points.
The documentation does not know what valid dsn's are hence dsn is written.


Hope this clears it up.

>(3) You get an error 402 Bad command arguments (arguments invalid):
>------------------------------
>DAS Error 402
>
> Path is dsn/entry_points?
>------------------------------
>
>like for example in:
>
>http://genome.ornl.gov/das/das.cgi/dsn/entry_points
>
>This is the list that I have checked:
>
>http://servlet.sanger.ac.uk:8080/das
>http://genome.cse.ucsc.edu/cgi-bin/das/dsn
>http://www.wormbase.org/db/das/dsn
>http://genome.ornl.gov/das/das.cgi/dsn
>http://tomcat.molgen.mpg.de:8080/das
>http://eugenes.org/cgi-bin/srsdas/dsn
>http://supfam.org/SUPERFAMILY/cgi-bin/das/dsn
>http://www.tigr.org/docs/tigr-scripts/tgi/das/dsn
>
>*http://stash.mrc-lmb.cam.ac.uk:8080/das
>*http://das.bcgsc.ca:8080/das
>*http://gadfly.gen.cam.ac.uk:8080/das
>*http://ensembl.gsc.riken.go.jp/cgi-bin/das/dsn
>
>*Not there anymore.
>
>Any hint of what may be happening?
>
>Thanks in advance,
>
>    Albert.
>
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