[DAS2] use cases

Andrew Dalke dalke at dalkescientific.com
Tue Mar 14 15:14:44 UTC 2006

I think these cover the basic use cases.  Let me know if there
are other reasonable ones I should add.

Use Case #1

Biologist viewing genomic region wants to add information
from server www.biodas.org/das2/ .

Example of use:
   - Go to "open DAS server" option.  Type/paste URL for
DAS server.
   + DAS viewer connects to server, verifies that it
annotates the same sequence source and has under (say)
10 types so it makes a new track for each type and does
a request for all the features in the current display.

Use Case #2

Biologist wants all lac repressors on build 12 of mouse.

Example of use:
   - Start DAS viewer.  Go to "find server" option.  Select
"mouse" from the list of "model organisms".  Select "build 12"
from a pull-down menu of build descriptions.  Select all
the listed servers.
   - Go to "find annotations" option

Now what?  Is "lac repressor" a name?  Is it a combination
of a name and ontology term?  Is it a pure ontology term?

Use Case #3

Biologist wants to find all the annotation servers for the most
recent build of H. sapiens.

Example of use:
  - Start DAS viewer.  Go to "find server" option.  Type "human"
(or "H. sapiens" or "Homo sapiens").  Search.
  + DAS viewer consults internal NCBI taxonomy table to get taxid.
DAS viewer displays all matches.
  - Sort by build date, select all matching servers by hand

   DAS has no field to search by build date

Use Case #4

Bioinformaticist wants to make annotations available for
build v32 of human.

Example of use:
   - Go to registry server to get a human-readable description
of the COORDINATES fields for build v32.
   - decide to point people to a reference server instead of
providing local sequence data
   - create the sources, types and features document
   - put them on a web server
   - go to registry and submit site for future inclusion

Use Case #5

IT wants people to use local mirrors of reference
server when possible.

Example of use:
   - set up a local registry server
   + server connects to Andreas' registry server and downloads
all the data
   + server rewrites "segments" sections to use local server
   - configure all DAS viewers to consult local registry server

					dalke at dalkescientific.com

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