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Simple Genomics Use Case

From: Brian Gilman <gilmanb@mac.com>
Date: Tue, 4 Nov 2003 07:54:50 -0500
Message-Id: <1391D574-0EC6-11D8-AA85-000393C2C8D0@mac.com>
Cc: public-semweb-lifesci@w3.org
To: Eric Neumann <ENeumann@BeyondGenomics.com>
Hello everyone,

	Sorry this took so long. My use case is fairly simple this comes from 
a library of use cases that I have sitting here on my hard drive.

	A gene Id is required for retrieval of a gene annotation and ontology 
information. The unique gene Id is not available directly form chip 
design information, where IMAGE clone and probe set information are 
only available for each reporter (clone in spotted array chips, probe 
set in oligo array chips). This use case describes the process of 
obtaining a unique Id such as GenBank Accession Number, LocusLink Id or 
Gene Symbol for the clone or probe set. 

Basic Course
The actor selects the DNA sequence to retrieve a unique gene ID.

2.         The actor sets the threshold for the sequence similarity.

3.         The actor chooses which type of gene identifier to retrieve 
(i.e., GenBank Accession Number).

4.         The actor chooses chip identifier type (e.g., clone id or 
probe set id).

5.         The actor submits the gene identifier search request.

6.         A list of gene identifier within sequence similarity 
threshold is presented to the actor and the use case ends.


Post Conditions

1.         List of genes (gene symbol, GenBank ID, Unigene ID and Locus 
link ID) are presented to the actor.

2.         The options for retrieval of expression data or expression 
pattern are also presented.



1.        The query is submitted to an external data source, and 
network traffic results in long delay (see issue 2).  

2.        A unique gene ID is not available for the clone or probe 
set.  The actor is notified and prompted to input another identifier



1.        Currently, both Affymetrix and IMAGE consortium have a 
database for mapping probe set and clone information to some unique 
gene ID information. It would be easy if the map information could be 
implemented in DC project. But Affymetix may only give DNA sequence 
information in the future.

2.        If the query is submitted during busy time, should the 
request “time out”, and resubmit at a later time?

3.        If the request is resubmitted, should it be done 
automatically by the system, and then emailed to the actor?

4. If presented with a list of ID's how do you know who the authority 
is for the ID (LSID issue)
Brian Gilman
President Panther Informatics Inc.
9 Acadia Park #2
Somerville, MA 02143
Phone: 617-591-1722
Cell: 617-335-8276
AIM: gilmanb1

Received on Tuesday, 4 November 2003 08:00:38 UTC

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