<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>MOBY Use Case Haplotypes</title>
<meta http-equiv="content-type"
content="text/html; charset=ISO-8859-1">
<meta name="author" content="Fiona Cunningham">
</head>
<body>
<br>
<h1>Haplotype Mapping Project Use Cases </h1>
<h2><A NAME= HapBlock> Name:</a> Haplotypes</h2>
<P><B>Scenario Reference: </B><A HREF='fc_hapmap_scenarios.html'>
Haplotypes</a></P>
<P><B>Problem: </B>Find a set of haplotypes, given a gene or SNP.</P>
<hr width="10%" align="left">
<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 can be used to decipher the genetic differences that make some people more susceptible to disease than others. </p>
<hr width="10%" align="left">
<h2> Primary Actors: </h2>
<ol>
<li>A biologist</li>
<li>A known haplotype data provider such as The SNP Consortium IN THE FUTURE!! <a HREF='http://snp.cshl.org/'>(http://snp.cshl.org/)</a>
</li>
</ol>
<hr width="10%" align="left">
<h2>Other Actors: </h2>
<an exhaustive list of other entities which must participate in
the flow of events to achieve this result>
<p> </p>
<hr width="10%" align="left">
<h2>Initial State and Preconditions: </h2>
<p> The biologist has a the name of one or two genes, STS markers, SNP names, SNP positions or genomic positions. </p>
<p> The Haplotype data provider has a database of haplotype blocks, their mapping position, sizes and boundaries in different populations. For each block the database also contains the possible haplotypes and their frequencies in each population studied. This information will be integrated with the current SNP data.</p>
<hr width="10%" align="left">
<h2> End Result: </h2>
<p>Biologist gets a list of haplotypes for the block where his query gene or SNP resides. </p>
<hr width="10%" align="left">
<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 that contain the marker submitted.</li>
<li>The user can then look at a list of relevant haplotypes and frequencies associated with each block. Each block links up to a page with further information on the position of the block on the genome and the markers that define that block. </li>
<li>Maybe the biologist will be able to select a subset of the haplotypes and request a table dump of the information or he could browse the information graphically to see the pattern of distribution of SNPs, genes and markers observed in the block.</li>
</ol>
<br>
<hr width="10%" align="left">
<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. </p>
<p> The other limitations will have to be assessed once the project is nearer completion. </p>
<hr width="10%" align="left"><br>
<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>
<br>
<hr width="10%" align="left">
<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>
<hr width="10%" align="left">
<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>
<hr width="10%" align="left">
<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> <br>
<hr width="10%" align="left">
<h2> Discussion: </h2>
<hr width="10%" align="left">
<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>
<hr width="10%" align="left">
<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>
<hr>
</body>
</html>