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<title>MOBY Use Case SNP panel genotypes</title>
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<h1>Haplotype Mapping Project Use Cases </h1>
<h2><A NAME= PanelSNP>Name: </a>Types of SNPs in a panel.</h2>
<P><B>Scenario Reference: </B><A HREF= 'fc_hapmap_scenarios.html#ScenarioPanelSNP'>Types of SNP in a panel.</a></P>
<P><B>Problem: </B>Retrieve information about the genotypes of each SNP in a panel. </P>
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<h2> Background Knowledge: </h2>
<p>
A panel is a collection of immortilised cells that come from a group of individuals. The cells with each individual's genome are placed in wells so that at every location on the genome there is DNA corresponding to two chromosomes. In SNP genotyping experiments, a single SNP is assayed against all the wells in the panel tray.
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<h2> Primary Actors: </h2>
<ol>
<li>A biologist</li>
<li>A panel information data provider such as The SNP Consortium
e.g.<a HREF='http://snp.cshl.org/'>(http://snp.cshl.org/)</a>
</li>
</ol>
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<h2>Other Actors: </h2>
<an exhaustive list of other entities which must participate in
the flow of events to achieve this result>
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<h2>Initial State and Preconditions: </h2>
<p> The biologist must have a valid panel ID and SNP ID.</p>
<p> The service provider must have panel and genotype information. </p>
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<h2> End Result: </h2>
<p>
The biologist receives information about the genotypes for a particular panel and SNP.</p>
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<h2> Current Workflow: </h2>
<ol>
<li>The biologist browses to a database containing panel genotype information.</li>
<li>Biologist finds the link to the relevant search page.</li>
<li>Biologist reads literature on the search page to determine whether he can do the query he wants.</li>
<li>There is no currently way to select specific information from a panel. The biologist must download an entire panel to get information on the genotypes of the assayed SNPs.</li>
</ol>
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<h2> Existing Workflow Limitations: </h2>
<p> The biologist must know the names of the appropriate databases and where they reside, or do a Google, PubMed or similar search, to find them. It is possible he finds an existing database but that it does not provide the facility to do his query.</p>
<p> There are no mechanisms to do more powerful queries on the panel data. </p>
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<h2>Existing Workflow Exemplars: </h2>
<P>The web-based nature of the data means that the information is kept up to date and the biologist does not need to maintain the UI.</p>
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<h2> MOBY Workflow: </h2>
<ol>
<li>The biologist asks MOBY which are the known service providers that could answer his query, given an input of a panel ID and SNP ID.</li>
<li>MOBY directs the biologist straight to the search page and informs the biologist which format the input data must have.</li>
<li>The rest of the query proceeds as before.</li>
</ol>
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<h2>MOBY Workflow Limitations: </h2>
<p>MOBY must keep up to date with changes in the UI and data presented by the database. </p>
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<h2> MOBY Workflow Exemplars: </h2>
<P>The advantage of having MOBY here is it that the user would no longer have to search for a service provider, hunt and digest the search pages, work out if there is away to formulate his query. All this could be done at the MOBY level.</P>
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<h2> Discussion: </h2>
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<h2> Priority:</h2>
<p>Mandatory. Moby should have an index and a description of each possible database site and be able to direct the biologist straight to the search page that best fits his/her needs.</P>
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<h2> Key References: </h2>
<p>
The SNP Consortium: <a HREF='http://snp.cshl.org/'>(http://snp.cshl.org/) </A></p>
<p>The National Human Genome Research Institute: <a HREF=' http://www.genome.gov/page.cfm?pageID=10005336'> (http://www.genome.gov/page.cfm?pageID=10005336)</a></p>
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