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
Ensembl = 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
the registry itself is at: http://www.dasregistry.org
So, for example, if we want to find servers for H_sapiens_Feb_2009,
the NCBI taxonomy id for Homo Sapiens is 9606 and the NCBI version is 37
we can use the query: http://www.dasregistry.org/das/sources?organism=9606&version=37&capability=features
and parse the result. The result is an xml document with SOURCES as root element,
and several SOURCE elements. Each SOURCE element has one VERSION element, which contains
some CAPABILITY elements. There must be at least one CAPABILITY element with type attribute
of "das1:features" (the restriction in the query). There may also be a "das1:entry_points"
CAPABILITY element (these will be the available chromosomes), a "das1:types" CAPABILITY
element (each type is a feature), a "das1:stylesheet" CAPABILITY element (this explains
how to display the element, colors, etc.), a "das1:sources" CAPABILITY element (usually
this has the same SOURCE elements as the das registry query). If there is no das1:types
capability, the SOURCE element can be handled as one single feature and the title attribute
of the SOURCE element can be used for the feature name.

Each of the query_uri attribute of the das1:feature CAPABILITY can be processed as one
feature (or several if there is a das1:types CAPABILITY) of a server, the server is the
uri before the first /.
NOTE - at this point there must be some steps to restrict the features to ones that will
actually return data. Most of the features will fail for some reason, or return no data,
when queried.
For example, M_musculus_Jul_2007 will give four servers

http://feb2012.archive.ensembl.org http://genome.cse.ucsc.edu (not a duplicate of the regular IGB UCSC DAS) http://may2010.archive.ensembl.org http://pubmed2ensembl56.smith.man.ac.uk http://www.imgt.org

but the imgt

If a feature is selected, then loaded, the