...
How
...
IGB
...
loads
...
data
...
from
...
a
...
DAS
...
server.
...
This
...
is
...
the
...
current
...
procedure
...
for
...
loading
...
data
...
from
...
DAS
...
servers.
...
Currently,
...
this
...
only
...
works
...
on
...
two
...
DAS
...
servers
...
(it
...
no
...
longer
...
works
...
for
...
Ensembl):
...
UCSC
...
=
...
http://genome.cse.ucsc.edu/cgi-bin/das/dsn
...
...
=
...
http://www.ensembl.org/das/dsn
...
http://genome.cse.ucsc.edu/cgi-bin/das/dsn
...
http://www.ensembl.org/das/dsn
...
- initialize server:
...
for
...
- each
...
- DSN
...
- element
...
- {{
for each "SOURCE"
...
- element
...
- {{
sourceid = get "id"
...
- attribute
...
- from
...
- SOURCE
...
- element
}}
master = first "MAPMASTER"
...
- element
...
- of
...
- DSN
...
- element
...
masterURL
...
- =
...
- get
...
- text
...
- from
...
- master
...
- element
...
version
...
- key
...
- =
...
- end
...
- (after
...
- last
...
- /)
...
- of
...
- masterURL
...
one
...
- source
...
- object
...
- (=version)
...
- per
...
- version
...
- key
...
add
...
- sourceid
...
- to
...
- source
...
- object.
...
}}
...
this
...
- creates
...
- a
...
- collection
...
- of
...
- source
...
- objects
...
- (versions)
...
- select
...
- species/version
...
issue
...
- a
...
- types
...
- query
...
- =
...
- server
...
- name
...
- -/dsn
...
- suffix
...
- +
...
- <versionid>
...
- +
...
- "/types"
...
- :
...
- http://genome.cse.ucsc.edu/cgi-bin/das/<id>/types
...
for
...
- each
...
- TYPE
...
- element
...
- {
...
typeid
...
- =
...
- get
...
- "id"
...
- attribute
...
- from
...
- TYPE
...
- element
...
featureURL
...
- =
...
- server
...
- name
...
- -/dsn
...
- suffix
...
- +
...
- <versionid>
...
- +
...
- "/features?type="
...
- +
...
- <typeid>
...
add
...
- features
...
- map
...
- entry,
...
- key
...
- =
...
- typeid,
...
- value
...
- =
...
- featureURL
...
}
Proposal for using the DAS registry to find data.
It is possible to use the DAS registry to find data on DAS servers,
the problem is that all DAS servers can be set up differently, they
all follow different rules or different DAS versions, some don't follow
all the protocol rules, and some are not maintained.
DAS is a protocol, and it has different versions. The spec for the
latest version (1.6) is at: http://www.biodas.org/documents/spec-1.6.html
...
...
registry
...
itself
...
is
...
at:
...
...
...
for
...
example,
...
if
...
we
...
want
...
to
...
find
...
servers
...
for
...
H_sapiens_Feb_2009,
...
we
...
can
...
use
...
the
...
query:
...
http://www.dasregistry.org/das/sources?organism=9606&capability=features&version=37
...
...
parse
...
the
...
results.