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<h1>Haplotype Mapping Project Use Cases </h1>
<h2><A NAME= Linkage> Name:</a> Linkage</h2>
<P><B>Scenario Reference: </B><A HREF='fc_hapmap_scenarios.html'>
Linkage</a></P>
<P><B>Problem:</B> Determine which genes are on the same haplotype block as the query.</P>
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<h2> Background Knowledge: </h2>
<p>Haplotypes blocks are ancestral segments of chromosomes that contain many single letter genetic variations inherited together as a set or a block. They are areas of low recombination and high linkage disequilibrium. Genes on the same haplotype block will normally be inherited together throughout successive generations.
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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>
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<h2>Other Actors: </h2>
<P>Depending on how the haplotype databases develop, it may be necessary to use another service for this query where you could enter a gene range, and it would return all known genes located in that range.</P>
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<h2>Initial State and Preconditions: </h2>
<p> The biologist has the name of a gene, STS marker, SNP name, SNP position or genomic position. He wishes to know to which genes and SNPs it is linked.</p>
<p> The haplotype data provider has a database of haplotype blocks, their mapping position, and boundaries in different populations. This information should be integrated with the current SNP data.</p>
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<h2> End Result: </h2>
<p>Biologist gets a list of genes/SNPs that are linked to the query position. </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 CGI form to search using the correct criteria (e.g. by gene name, chromosomal positions, STS markers etc).</li>
<li>The web page is returned with a list of blocks in different populations where the markers are located.</li>
<li>The researcher must find the boundaries of the block(s) where the query position is located in order to see which genes and SNPs are linked to the query position.</li>
<li>A search must then be made to find all genes/SNPs/markers which fall in the genome within this range. Maybe the haplotype database will provide this facility, but maybe the biologist would have to look to another service provider.</li>
<li>Maybe the biologist will be able to browse the information graphically to see the pattern of distribution of SNPs, genes and markers observed in the block, or download the results in bulk.</li>
</ol>
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<h2> Existing Workflow Limitations: </h2>
<p> The biologist must know the names of the haplotype databases and where they reside, or do a Google, PubMed or similar search, to find them. Once such a database is found, it may take some time to determine whether it is possible to do a query of this nature.</p>
<p> It may be necessary to use a second service provider to complete the 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 are the known haplotype databases.</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 </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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