[DAS2] [Bug 1807] New: Where do seqids come from?

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri May 27 06:20:07 UTC 2005


           Summary: Where do seqids come from?
           Product: BioDAS
           Version: 2
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Spec - GET Requests
        AssignedTo: das2 at portal.open-bio.org
        ReportedBy: dalke at dalkescientific.com

Did a stork drop them off in the cabbage patch?

I'm trying to understand regions and their relationship to sequence.

The spec says

> seqid is the sequence ID, and can correspond to an assembled chromosome, a
> contig, a clone, or any other accessionable chunk of sequence

Is the seqid exactly equivalent to a region id?

I think so given the documentation in das2_protocol.html.

The das2_protocol.html document also says

> http://server/das/genome/sourceid/version/region/regionid/subregion
> A genomic region region identified by the ID of a landmark, modified by
> a subregion relative to the landmark. As a whole, the URL is a globally
> unique identifier for a region of the genome.
> The syntax of addressing regions and subregions is described in detail later.

The das2_get.html document says

> Adding a subregion restricts the document further to regions that overlap the indicated subregion.
>    GET http://server/das/genome/sourceid/version/region/ctg2
> or
>    GET http://server/das/genome/sourceid/version/region/ctg2/34/128

What are the '24' and '128'?  Are they coordinate ranges?  Are they independently
accessionable chunks of the genome, so that


is valid?  Or do I get the sequence via


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