2016-03-10 02:26:59 +00:00
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File: README
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— Documentation by YARD 0.8.7.6
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<a href="_index.html">Index</a> »
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<span class="title">File: README</span>
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<div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
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href="class_list.html">
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Class List
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Method List
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<div id="content"><div id='filecontents'>
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<p><a href="http://classyfire.wishartlab.com">ClassyFire</a> is a resource
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that allows you to automatically classify any chemical compound based on
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its structure. This is the repository for the ClassyFire API allows you to
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send requests to and pull information from the ClassyFire web server.</p>
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<h1 id="label-What+is+this+repository+for-3F"><strong>What is this repository for?</strong></h1>
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<ul><li>
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<p>Quick summary</p>
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</li><li>
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<p>Version</p>
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</li><li>
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<p><a href="https://bitbucket.org/tutorials/markdowndemo">Learn Markdown</a></p>
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</li></ul>
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<h1 id="label-How+do+I+get+set+up-3F"><strong>How do I get set up?</strong></h1>
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<ul><li>
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<p>Summary of set up</p>
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</li><li>
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<p>Configuration</p>
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</li><li>
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<p>Dependencies</p>
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</li><li>
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<p>Database configuration</p>
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</li><li>
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<p>How to run tests</p>
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</li><li>
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<p>Deployment instructions</p>
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</li></ul>
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<h1 id="label-Contribution+guidelines"><strong>Contribution guidelines</strong></h1>
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<ul><li>
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<p>Writing tests</p>
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</li><li>
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<p>Code review</p>
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</li><li>
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<p>Other guidelines</p>
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</li></ul>
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<h1 id="label-Endpoints"><strong>Endpoints</strong></h1>
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<blockquote>
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<h2 id="label-1.+Entity">1. Entity</h2>
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<blockquote>
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<p>Chemical compounds are represented by the Entity model, through which one
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can access the compound's structure-based classification.</p>
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<h3 id="label-GET">GET</h3>
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<p><strong>/entities/entityInchikey</strong></p>
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<p>A chemical compound's classification can be retrieved in the JSON or
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XML format. The compound's information is accessed via the InChIkey as
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show in the following examples. In this example, the entity has the
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InChIKey=LABTWGUMFABVFG-ONEGZZNKSA-N.</p>
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<blockquote>
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<p>ClassyFireAPI.get_entity_classification(“BDAGIHXWWSANSR-UHFFFAOYSA-N”,“json”)</p>
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</blockquote>
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<p>Where:</p>
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<blockquote>
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<p>The entity's InChIKey is “BDAGIHXWWSANSR-UHFFFAOYSA-N”,</p>
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<p>The output format is “json” (JSON).</p>
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</blockquote>
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</blockquote>
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2016-03-10 02:50:36 +00:00
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<h2 id="label-2.+Sequence">2. Sequence</h2>
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<blockquote>
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<p>Sequences are represented by the Sequence model, through which one can
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access the compound's structure-based classification.</p>
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<h3 id="label-GET">GET</h3>
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<p><strong>/sequence/fingerprint</strong></p>
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<p>A (FASTA) sequence's classification can be retrieved in the JSON. In
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this example, the sequence has the fingerprint =
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“8bf70c23ac100cd2c3955081d8613325”</p>
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<blockquote>
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<p>ClassyFireAPI.get_sequence_classification(“8bf70c23ac100cd2c3955081d8613325”,“json”)</p>
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</blockquote>
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<p>Where:</p>
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<blockquote>
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<p>The sequence's fingerprint is “8bf70c23ac100cd2c3955081d8613325”,</p>
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2016-03-10 02:55:54 +00:00
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<blockquote>
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<p>The fingerprint is generate by Digest::MD5 from the peptide sequence
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“APDVQDCPECTLQENPFFSQPGAPILQCMGCCFSRAYPTPLRSKKTMLVQKNVTSESTCCVAKSYNRVTVMGGFKVENHTACHCSTCYYHKS”</p>
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</blockquote>
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2016-03-10 02:50:36 +00:00
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<p>The output format is “json” (JSON).</p>
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</blockquote>
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</blockquote>
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<h2 id="label-3.+Query">3. Query</h2>
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<blockquote>
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<p>The Query model represents the chemical structure to be classified. Its
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attributes are the query label and the query input.</p>
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<blockquote>
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<p>The query label is an identifier</p>
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<p>The query input contains the compound's identifier (optional) and its
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structural representation, separated by a tab. The chemical structure is
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represented either in the <a
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href="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html">Daylight
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SMILES</a> format, the <a
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href="http://www.iupac.org/home/publications/e-resources/inchi.html">InChI</a>
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format. Moreover, the compound can be represented with its <a
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href="http://www.chem.qmul.ac.uk/iupac/">IUPAC name</a>. The input can also
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be of type <a href="https://en.wikipedia.org/wiki/FASTA_format">FASTA</a>,
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which contains peptide or nucleotide sequences.</p>
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</blockquote>
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<h3 id="label-POST">POST</h3>
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<p>A query can be submitted using the POST method as demonstrated in the
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following example.</p>
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<blockquote>
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<p>ClassyFireAPI.submit_query(“curl_test”,“MOL1tCCCOCCnMOL2tCOCC=CCCC”,“STRUCTURE”)
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where the parameters are:</p>
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<p>The query label: curl_test,</p>
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<p>The entity identifiers: MOL1,MOL2</p>
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<p>The entity's structure represented in the SMILES format: CCCOCC and
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COCC=CCCC.</p>
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<p>The query is of type 'STRUCTURE'</p>
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</blockquote>
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<h3 id="label-GET">GET</h3>
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<p><strong>/queries/queryId</strong></p>
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<p>The classification results can be retrieved via a GET method in the JSON or
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XML format.</p>
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<blockquote>
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<p>ClassyFireAPI.get_query(443431,“json”)</p>
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</blockquote>
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<p>where:</p>
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<blockquote>
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<p>The query id is 443431, The output format is “json” (JSON)</p>
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</blockquote>
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</blockquote>
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</blockquote>
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<h1 id="label-Directory+Structure"><strong>Directory Structure</strong></h1>
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<ul><li>
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<p>lib</p>
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</li></ul>
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<h1 id="label-Who+do+I+talk+to-3F"><strong>Who do I talk to?</strong></h1>
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<ul><li>
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<p>Yannick Djoumbou Feunang: djoumbou@ualberta.ca</p>
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</li><li>
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<p>Other community or team contact</p>
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</li></ul>
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</div></div>
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<div id="footer">
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2016-06-28 22:52:27 +01:00
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Generated on Tue Jun 28 15:46:59 2016 by
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<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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2016-06-28 22:52:27 +01:00
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0.8.7.6 (ruby-2.4.0).
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</div>
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