[DAS2] DAS2 source description
ap3 at sanger.ac.uk
Thu Dec 8 09:48:58 UTC 2005
The way Andrew suggests the source description looks already quite good
Could we add a couple things?
* we have some people doing annotations on clones and scaffolds, which
is essentially the same as annotating in chromosomal coordinates, but
for the description
a few other types of coordinate systems are needed.
* there are a couple of sources that can speak multiple "coordinate
systems", so the
<source> description should be able to deal with that.
* It would be good to have something like an "authority" field in the
coordinate systems. i.e. the institution who
defines a set of reference objects.
with this in mind one could do something like:
description="serves annotations for human in chromosome and clone
coordinates " >
<VERSION id="35" />
This would be the part that is needed for describing the actual data
and then it would be good to have some
other meta info for the sources as well:
* which DAS commands does a source understand
* a testcode (per namespace) that can be used to validate responses
* some historical data like "has been available since" "was
successfully validated the last time at"
* a link back to the homepage of the group that provides the source for
more detailed docu about the data
* an email address to contact if there is a problem/question with the
* a "nickname" for a source that should be used in a DAS client to
label tracks coming from that source.
* some optional properties that can be added like "funded by ..." "GO
evidence code: "
> That is, the SOURCES request returns information about genomic,
> protein sequence and structure databases.
good. - plus a couple of others. this should be a restricted list.
> If this occurs then there will need to be a few changes to the spec.
> For example, 'taxon' is probably only properly part of the genomic
some people annotate protein sequences from a particular organism.
e.g there is a DAS1 source that only annotates Fugu protein sequences
Andreas Prlic Wellcome Trust Sanger Institute
Hinxton, Cambridge CB10 1SA, UK
+44 (0) 1223 49 6891
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