simple_bioc 0.0.1 → 0.0.2
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- checksums.yaml +4 -4
- data/README.md +73 -3
- data/Rakefile +5 -0
- data/html/BioCReader.html +657 -0
- data/html/BioCWriter.html +556 -0
- data/html/README_md.html +231 -0
- data/html/SimpleBioC.html +255 -0
- data/html/SimpleBioC/Annotation.html +279 -0
- data/html/SimpleBioC/Collection.html +316 -0
- data/html/SimpleBioC/Document.html +426 -0
- data/html/SimpleBioC/Location.html +288 -0
- data/html/SimpleBioC/Node.html +334 -0
- data/html/SimpleBioC/NodeBase.html +281 -0
- data/html/SimpleBioC/Passage.html +418 -0
- data/html/SimpleBioC/Relation.html +301 -0
- data/html/SimpleBioC/Sentence.html +399 -0
- data/html/created.rid +15 -0
- data/html/images/add.png +0 -0
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- data/html/images/zoom.png +0 -0
- data/html/index.html +212 -0
- data/html/js/darkfish.js +155 -0
- data/html/js/jquery.js +18 -0
- data/html/js/navigation.js +142 -0
- data/html/js/search.js +94 -0
- data/html/js/search_index.js +1 -0
- data/html/js/searcher.js +228 -0
- data/html/rdoc.css +595 -0
- data/html/table_of_contents.html +199 -0
- data/lib/simple_bioc.rb +4 -0
- data/lib/simple_bioc/annotation.rb +10 -6
- data/lib/simple_bioc/bioc_reader.rb +2 -2
- data/lib/simple_bioc/collection.rb +13 -11
- data/lib/simple_bioc/document.rb +31 -22
- data/lib/simple_bioc/location.rb +13 -7
- data/lib/simple_bioc/node.rb +14 -8
- data/lib/simple_bioc/node_base.rb +13 -10
- data/lib/simple_bioc/passage.rb +26 -23
- data/lib/simple_bioc/relation.rb +13 -8
- data/lib/simple_bioc/sentence.rb +21 -15
- data/lib/simple_bioc/version.rb +2 -2
- data/samples/print_annotation.rb +18 -0
- data/samples/sample1.rb +31 -0
- data/simple_bioc.gemspec +1 -1
- metadata +52 -2
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<li><a href="#label-SimpleBioc">SimpleBioc</a>
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<li><a href="#label-Feature%3A">Feature:</a>
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<li><a href="#label-Installation">Installation</a>
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<li><a href="#label-Sample">Sample</a>
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<li><a href="./SimpleBioC.html">SimpleBioC</a>
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<li><a href="./SimpleBioC/Annotation.html">SimpleBioC::Annotation</a>
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<h1 id="label-SimpleBioc">SimpleBioc<span><a href="#label-SimpleBioc">¶</a> <a href="#documentation">↑</a></span></h1>
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<p><a href="SimpleBioC.html">SimpleBioC</a> is a simple parser / builder for
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BioC data format. BioC is a simple XML format to share text documents and
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annotations. You can find more information about BioC from the official
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BioC web site (<a
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href="http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/">www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/</a>)</p>
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<h2 id="label-Feature%3A">Feature:<span><a href="#label-Feature%3A">¶</a> <a href="#documentation">↑</a></span></h2>
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<ul><li>
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<p>Parse & convert a BioC document to an object instance compatible to
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BioC DTD</p>
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</li><li>
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<p>Use plain ruby objects for simplicity</p>
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</li><li>
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<p>Build a BioC document from an object instance</p>
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</li></ul>
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<h2 id="label-Installation">Installation<span><a href="#label-Installation">¶</a> <a href="#documentation">↑</a></span></h2>
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<p>Add this line to your application's Gemfile:</p>
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<pre>gem 'simple_bioc'</pre>
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<p>And then execute:</p>
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<pre>$ bundle</pre>
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<p>Or install it yourself as:</p>
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<pre>$ gem install simple_bioc</pre>
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<h2 id="label-Usages">Usages<span><a href="#label-Usages">¶</a> <a href="#documentation">↑</a></span></h2>
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<p>Include library</p>
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<pre class="ruby"><span class="ruby-identifier">require</span> <span class="ruby-string">'simple_bioc'</span>
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</pre>
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<p>Parse with a file name (path)</p>
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<pre>collection = SimpleBioC::from_xml(filename)</pre>
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<p>Traverse & Manipulate Data. Data structure are almost the same as the
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DTD. Please refer <a href="http://">library documents</a>.</p>
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<pre>puts collection.documents[2].passages[0].text</pre>
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<p>Build XML text from data</p>
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<pre>puts SimpleBioC::to_xml(collection)</pre>
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<h2 id="label-Sample">Sample<span><a href="#label-Sample">¶</a> <a href="#documentation">↑</a></span></h2>
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<p>More samples can be found in Samples directory</p>
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<pre class="ruby"><span class="ruby-identifier">require</span> <span class="ruby-string">'simple_bioc'</span>
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<span class="ruby-comment"># Sample1: parse, traverse, manipulate, and build BioC data</span>
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<span class="ruby-identifier">require</span> <span class="ruby-string">'simple_bioc'</span>
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<span class="ruby-comment"># parse BioC file</span>
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<span class="ruby-identifier">collection</span> = <span class="ruby-constant">SimpleBioC</span>.<span class="ruby-identifier">from_xml</span>(<span class="ruby-string">"../xml/everything.xml"</span>)
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<span class="ruby-comment"># the returned object contains all the information in the BioC file</span>
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<span class="ruby-comment"># traverse & read information</span>
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<span class="ruby-identifier">collection</span>.<span class="ruby-identifier">documents</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">document</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">puts</span> <span class="ruby-identifier">document</span>
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<span class="ruby-identifier">document</span>.<span class="ruby-identifier">passages</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">passage</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">puts</span> <span class="ruby-identifier">passage</span>
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<span class="ruby-keyword">end</span>
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<span class="ruby-keyword">end</span>
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<span class="ruby-comment"># manipulate </span>
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<span class="ruby-identifier">doc</span> = <span class="ruby-constant">SimpleBioC</span><span class="ruby-operator">::</span><span class="ruby-constant">Document</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">collection</span>)
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<span class="ruby-identifier">doc</span>.<span class="ruby-identifier">id</span> = <span class="ruby-string">"23071747"</span>
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<span class="ruby-identifier">doc</span>.<span class="ruby-identifier">infons</span>[<span class="ruby-string">"journal"</span>] = <span class="ruby-string">"PLoS One"</span>
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<span class="ruby-identifier">collection</span>.<span class="ruby-identifier">documents</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">doc</span>
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<span class="ruby-identifier">p</span> = <span class="ruby-constant">SimpleBioC</span><span class="ruby-operator">::</span><span class="ruby-constant">Passage</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">doc</span>)
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<span class="ruby-identifier">p</span>.<span class="ruby-identifier">offset</span> = <span class="ruby-value">0</span>
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<span class="ruby-identifier">p</span>.<span class="ruby-identifier">text</span> = <span class="ruby-string">"TRIP database 2.0: a manually curated information hub for accessing TRP channel interaction network."</span>
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<span class="ruby-identifier">p</span>.<span class="ruby-identifier">infons</span>[<span class="ruby-string">"type"</span>] = <span class="ruby-string">"title"</span>
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<span class="ruby-identifier">doc</span>.<span class="ruby-identifier">passages</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">p</span>
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<span class="ruby-comment"># build BioC document from data</span>
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<span class="ruby-identifier">xml</span> = <span class="ruby-constant">SimpleBioC</span>.<span class="ruby-identifier">to_xml</span>(<span class="ruby-identifier">collection</span>)
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<span class="ruby-identifier">puts</span> <span class="ruby-identifier">xml</span>
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</pre>
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<h2 id="label-Contributing">Contributing<span><a href="#label-Contributing">¶</a> <a href="#documentation">↑</a></span></h2>
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<ol><li>
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<p>Fork it</p>
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</li><li>
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<p>Create your feature branch (<code>git checkout -b my-new-feature</code>)</p>
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</li><li>
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<p>Commit your changes (<code>git commit -am 'Add some
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feature'</code>)</p>
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<p>Push to the branch (<code>git push origin my-new-feature</code>)</p>
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<p>Create new Pull Request</p>
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</li></ol>
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<h2 id="label-LICENSE">LICENSE<span><a href="#label-LICENSE">¶</a> <a href="#documentation">↑</a></span></h2>
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<p>Copyright © 2013, Dongseop Kwon</p>
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<p>Released under the MIT License.</p>
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<p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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<p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 4.0.0.
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<title>module SimpleBioC - RDoc Documentation</title>
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<h3 class="section-header">Defined In</h3>
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<ul>
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<li>lib/simple_bioc.rb
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<li>lib/simple_bioc/annotation.rb
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<li ><a href="#method-i-from_xml">#from_xml</a>
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<h3 class="section-header">Class and Module Index</h3>
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<li><a href="./BioCReader.html">BioCReader</a>
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<li><a href="./SimpleBioC.html">SimpleBioC</a>
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<li><a href="./SimpleBioC/Annotation.html">SimpleBioC::Annotation</a>
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<h1 class="module">module SimpleBioC</h1>
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<p><a href="SimpleBioC.html">SimpleBioC</a> main library</p>
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<span class="method-name">from_xml</span><span
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class="method-args">(file_path)</span>
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<p>parse a BioC XML file in the given path and convert it into a collection
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">from_xml</span>(<span class="ruby-identifier">file_path</span>)
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<p>convert a collection instance to a BioC XML text</p>
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<pre><span class="ruby-comment"># File lib/simple_bioc.rb, line 15</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">to_xml</span>(<span class="ruby-identifier">collection</span>)
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