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<h1>Wormbase Use Cases </h1>
<h2><A NAME= Wormbase>Name: </a>Wormbase sequence information.</h2>
<P><B>Scenario Reference: </B><A HREF='fc_wb_scenarios.html#ScenarioWBseq'> Wormbase sequence information. </a></P>
<P><B>Problem: </B>Retrieve information about a locus. </P>
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<h2> Background Knowledge: </h2>
<p>Wormbase is an online database for the genome and biology of C. elegans <A HREF="http://www.wormbase.org">(www.wormbase.org)</A></p>
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<h2> Primary Actors: </h2>
<ol>
<li>A biologist</li>
<li>A worm sequence data provider such as Wormbase
e.g. <a HREF='http://www.wormbase.org'>(http://www.wormbase.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 (3 letter) gene locus name.</p>
<p> The service provider must have C.elegans genome and protein information.</p>
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<h2> End Result: </h2>
<p>
Success: The biologist receives the sequence and other information requested.
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Fail: The biologist fails to find the information required. Either the biologist cannot find the correct data provider, the data provider does not have the information or the biologist cannot formulate his query correctly. </p>
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<h2> Current Workflow: </h2>
<ol>
<li>The biologist browses to find a database containing C. elegans genome information.</li>
<li>Biologist finds the link to the relevant search page.</li>
<li>Biologist reads the literature on the search page to determine whether he can do the query he wants.</li>
<li>Biologist enters his locus name in the search box.</li>
<li>The data provider returns a list of hits.</li>
<li>Biologist selects the most relevant hit for the locus page.</li>
<li>From the locus page the corresponding sequence names and proteins are listed.</li>
<li>The biologist can navigate to the protein page to scroll and find the protein sequence. From here the amino acid sequence can be retrieved by copy and paste.</li>
<li>The biologist can navigate to the corresponding sequence pages.</li>
<li>From the sequence page it is possible to scroll and select either the spliced sequence or the unspliced DNA with exon regions highlighted.</li>
<li>In order to retrieve the bases upstream of the first exon, the biologist must read the literature on the more advanced searches offered by the database provider and navigate the to page providing the correct searching capabilities.</li>
<li>The biologist then fills out the correct criteria to get a certain number of bases upstream of the first exon. </li>
<li>The search tool returns the sequence. </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> Different sections of the query require different search pages in Wormbase. This can be confusing and time consuming. </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 locus name.</li>
<li>MOBY directs the biologist straight to the search page and informs the biologist which format the input data must have.</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>
Wormbase <a HREF='http://www.wormbase.org/'>(http://www.wormbase.org/) </A></p>
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