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<h1>Haplotype Mapping Project Use Cases </h1>
<h2><A NAME= Blocks> Name: </a>Block size</h2>
<P><B>Scenario Reference: </B><A HREF='fc_hapmap_scenarios.html#ScenarioBlocks'>
Block Size</a></P>
<P><B>Problem: </B>Download block sizes for different populations and their positions, given the default or a specified stringency. </P>
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<h2> Background Knowledge: </h2>
<p> Haplotype blocks are areas associated with little recombination. In general the size of haplotype blocks are smaller in African populations than Caucasian and Asian populations.</p>
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<h2> Primary Actors: </h2>
<ol>
<li>A biologist</li>
<li>A known haplotype data provider such as The SNP Consortium IN THE FUTURE!! 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 service provider must have block size data, i.e the information satisfying the query must exist in one of the haplotype databases. </p>
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<h2> End Result: </h2>
<p>Biologist gets a download of all the block sizes and their positions for various stringencies. </p>
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<h2> Hypothetical Mobyless Workflow: </h2>
<P><B>PLEASE NOTE: THIS PROJECT IS NOT YET COMPLETE SO THIS QUERY IS NOT POSSIBLE AT THE CURRENT TIME</B></P>
<ol>
<li>The biologist browses to a known haplotype database.</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>Biologist works out how to fill in the query form to search using two SNP names or positions. He indicates on the form that he wants to download all block sizes and positions for each population studied.</li>
<li>The biologist specifies the default or more stringent criteria for the block sizes.</li>
<li>The service provider returns a dump of the required information</li>
</ol>
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<h2> Existing Workflow Limitations: </h2>
<p> The biologist must know the names of the haplotype linkage databases and where they reside, or do a Google, PubMed or similar search, to find them. It is possible he finds an existing haplotype database but that it does not provide the facility to do his query.</p>
<p> The other limitations will have to be assessed once the project is nearer completion. </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 haplotype databases have linkage disequilibrium values.</li>
<li>Biologist asks MOBY which of the databases can perform a query given his input data.</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 haplotype database. This is likely to change relatively quickly as this is a developing project. </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 the haplotype databases, 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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