biointerchange 0.1.0

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Files changed (57) hide show
  1. data/.document +5 -0
  2. data/.rspec +1 -0
  3. data/.travis.yml +12 -0
  4. data/Gemfile +17 -0
  5. data/LICENSE.txt +8 -0
  6. data/README.md +166 -0
  7. data/Rakefile +50 -0
  8. data/VERSION +1 -0
  9. data/bin/biointerchange +6 -0
  10. data/docs/exceptions_readme.txt +13 -0
  11. data/examples/BovineGenomeChrX.gff3.gz +0 -0
  12. data/examples/gb-2007-8-3-R40.xml +243 -0
  13. data/examples/pubannotation.json +1 -0
  14. data/generators/rdfxml.rb +104 -0
  15. data/lib/biointerchange/core.rb +195 -0
  16. data/lib/biointerchange/exceptions.rb +38 -0
  17. data/lib/biointerchange/genomics/gff3_feature.rb +82 -0
  18. data/lib/biointerchange/genomics/gff3_feature_set.rb +37 -0
  19. data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +107 -0
  20. data/lib/biointerchange/genomics/gff3_reader.rb +86 -0
  21. data/lib/biointerchange/gff3.rb +135 -0
  22. data/lib/biointerchange/reader.rb +25 -0
  23. data/lib/biointerchange/registry.rb +29 -0
  24. data/lib/biointerchange/sio.rb +7124 -0
  25. data/lib/biointerchange/sofa.rb +1566 -0
  26. data/lib/biointerchange/textmining/content.rb +69 -0
  27. data/lib/biointerchange/textmining/document.rb +36 -0
  28. data/lib/biointerchange/textmining/pdfx_xml_reader.rb +161 -0
  29. data/lib/biointerchange/textmining/process.rb +57 -0
  30. data/lib/biointerchange/textmining/pubannos_json_reader.rb +72 -0
  31. data/lib/biointerchange/textmining/text_mining_rdf_ntriples.rb +197 -0
  32. data/lib/biointerchange/textmining/text_mining_reader.rb +41 -0
  33. data/lib/biointerchange/writer.rb +23 -0
  34. data/lib/biointerchange.rb +3 -0
  35. data/spec/exceptions_spec.rb +27 -0
  36. data/spec/gff3_rdfwriter_spec.rb +67 -0
  37. data/spec/text_mining_pdfx_xml_reader_spec.rb +89 -0
  38. data/spec/text_mining_pubannos_json_reader_spec.rb +71 -0
  39. data/spec/text_mining_rdfwriter_spec.rb +57 -0
  40. data/web/about.html +89 -0
  41. data/web/biointerchange.js +133 -0
  42. data/web/bootstrap/css/bootstrap-responsive.css +1040 -0
  43. data/web/bootstrap/css/bootstrap-responsive.min.css +9 -0
  44. data/web/bootstrap/css/bootstrap.css +5624 -0
  45. data/web/bootstrap/css/bootstrap.min.css +9 -0
  46. data/web/bootstrap/img/glyphicons-halflings-white.png +0 -0
  47. data/web/bootstrap/img/glyphicons-halflings.png +0 -0
  48. data/web/bootstrap/js/bootstrap.js +2027 -0
  49. data/web/bootstrap/js/bootstrap.min.js +6 -0
  50. data/web/bootstrap/js/jquery-1.8.1.min.js +2 -0
  51. data/web/css/rdoc-style.css +5786 -0
  52. data/web/css/rdoc.css +716 -0
  53. data/web/images/BioInterchange300.png +0 -0
  54. data/web/index.html +109 -0
  55. data/web/service/rdfizer.fcgi +68 -0
  56. data/web/webservices.html +123 -0
  57. metadata +240 -0
data/web/index.html ADDED
@@ -0,0 +1,109 @@
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+ <!DOCTYPE html>
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+ <html lang="en">
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+ <head>
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+ <meta charset="utf-8">
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+ <title>BioInterchange</title>
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+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
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+ <meta name="description" content="">
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+ <meta name="author" content="">
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+
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+ <!-- Le styles -->
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+ <link href="bootstrap/css/bootstrap.css" rel="stylesheet">
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+ <style type="text/css">
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+ body {
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+ padding-top: 60px;
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+ padding-bottom: 40px;
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+ }
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+ </style>
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+ <link href="bootstrap/css/bootstrap-responsive.css" rel="stylesheet">
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+
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+ <!-- Le HTML5 shim, for IE6-8 support of HTML5 elements -->
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+ <!--[if lt IE 9]>
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+ <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
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+ <![endif]-->
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+
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+ <!-- Le fav and touch icons -->
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+ <!-- <link rel="shortcut icon" href="../assets/ico/favicon.ico"> -->
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+ </head>
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+
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+ <body>
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+ <a href="https://github.com/BioInterchange/BioInterchange"><img style="z-index: 5000; position: fixed; top: 0; right: 0; border: 0;" src="https://s3.amazonaws.com/github/ribbons/forkme_right_gray_6d6d6d.png" alt="Fork me on GitHub"></a>
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+ <div class="navbar navbar-inverse navbar-fixed-top">
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+ <div class="navbar-inner">
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+ <div class="container">
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+ <a class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
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+ <span class="icon-bar"></span>
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+ <span class="icon-bar"></span>
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+ <span class="icon-bar"></span>
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+ </a>
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+ <a class="brand" href="index.html">BioInterchange</a>
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+ <div class="nav-collapse collapse">
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+ <ul class="nav">
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+ <li class="active"><a href="index.html">Home</a></li>
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+ <li><a href="about.html">About</a></li>
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+ <!--
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+ <li class="dropdown">
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+ <a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation <b class="caret"></b></a>
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+ <ul class="dropdown-menu">
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+ <li><a href="#">To</a></li>
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+ <li><a href="#">Be</a></li>
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+ <li><a href="#">Done</a></li>
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+ <li><a href="#">Dude</a></li>
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+ <li class="divider"></li>
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+ <li class="nav-header">API</li>
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+ <li><a href="#">API usage information</a></li>
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+ <li><a href="#">Implementing new readers/writers</a></li>
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+ </ul>
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+ </li>
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+ -->
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+ </ul>
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+ </div><!--/.nav-collapse -->
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+ </div>
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+ </div>
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+ </div>
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+
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+ <div class="container">
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+
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+ <!-- Main hero unit for a primary marketing message or call to action -->
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+ <div class="hero-unit">
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+ <div style="float: left; margin-right: 24px;"><a href="http://www.biointerchange.org"><img width=150 height=150 src="images/BioInterchange300.png" /></a></div>
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+ <h1>BioInterchange</h1>
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+ <p>Interchanging data using the Resource Description Framework (RDF) is simple, but creating RDF resources can be rather hard. BioInterchange automatically creates RDF from your TSV, XML, and other files.</p>
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+ <!-- <p><a class="btn btn-primary btn-large">Learn more &raquo;</a></p> -->
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+ </div>
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+
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+ <!-- Example row of columns -->
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+ <div class="row">
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+ <div class="span4">
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+ <h2>Shell Tool</h2>
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+ <p>Create RDF files from large data sets using the BioInterchange shell tool. It is installed as a Ruby gem that works with Mac OS X, Linux and Windows.</p>
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+ <p><!-- <a class="btn" href="#">View details &raquo;</a> --><em>Work in progress...</em></p>
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+ </div>
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+ <div class="span4">
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+ <h2>Web-Services</h2>
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+ <p>Quickly RDFize small data snippets with BioInterchange's web-service. Either copy/paste your data into an interactive web-site, or use the RESTful web-service.</p>
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+ <p><a class="btn" href="webservices.html">View details &raquo;</a></em></p>
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+ </div>
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+ <div class="span4">
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+ <h2>API</h2>
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+ <p>Integrate BioInterchange into your Ruby programs as a gem. The small footprint API makes it possible to create RDF from simple data structures in a few lines.</p>
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+ <p><a class="btn" disabled="disabled" href="#">View details &raquo; <em>(Well, work in progress too...)</em></a></p>
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+ <p><a class="btn" href="../doc/BioInterchange.html">View Ruby docs &raquo;</a></p>
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+ </div>
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+ </div>
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+
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+ <hr>
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+
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+ <footer>
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+ <p>&copy; <a href="https://github.com/BioInterchange/BioInterchange#contributors">The BioInterchange Contributors</a> 2012</p>
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+ </footer>
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+
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+ </div> <!-- /container -->
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+
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+ <!-- Le javascript
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+ ================================================== -->
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+ <!-- Placed at the end of the document so the pages load faster -->
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+ <!-- <script src="bootstrap/js/jquery-1.8.1.min.js"></script> -->
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+ <script src="bootstrap/js/bootstrap.min.js"></script>
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+ </body>
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+ </html>
data/web/service/rdfizer.fcgi ADDED
@@ -0,0 +1,68 @@
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+ #!/usr/bin/ruby
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+
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+ require 'rubygems'
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+ require 'net/http'
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+ require 'uri'
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+ require 'cgi'
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+ require 'fcgi'
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+
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+ # This will be obsolete once BioInterchange has been turned into a gem:
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+ load '../../lib/biointerchange/core.rb'
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+ load '../../lib/biointerchange/gff3.rb'
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+ load '../../lib/biointerchange/sio.rb'
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+ load '../../lib/biointerchange/sofa.rb'
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+ load '../../lib/biointerchange/reader.rb'
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+ load '../../lib/biointerchange/writer.rb'
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+ load '../../lib/biointerchange/textmining/text_mining_reader.rb'
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+ load '../../lib/biointerchange/textmining/pubannos_json_reader.rb'
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+ load '../../lib/biointerchange/textmining/pdfx_xml_reader.rb'
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+ load '../../lib/biointerchange/textmining/text_mining_rdf_ntriples.rb'
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+ load '../../lib/biointerchange/textmining/content.rb'
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+ load '../../lib/biointerchange/textmining/document.rb'
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+ load '../../lib/biointerchange/textmining/process.rb'
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+ load '../../lib/biointerchange/genomics/gff3_feature.rb'
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+ load '../../lib/biointerchange/genomics/gff3_feature_set.rb'
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+ load '../../lib/biointerchange/genomics/gff3_reader.rb'
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+ load '../../lib/biointerchange/genomics/gff3_rdf_ntriples.rb'
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+
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+ input_formats = {}
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+ input_formats['dbcls.catanns.json'] = [ BioInterchange::TextMining::PubannosJsonReader, 'name', 'name_id', 'date', [ Proc.new { |*args| BioInterchange::TextMining::TMReader::determine_process(*args) }, 'name_id' ], 'version' ]
30
+ input_formats['uk.ac.man.pdfx'] = [ BioInterchange::TextMining::PdfxXmlReader, 'name', 'name_id', 'date', [ Proc.new { |*args| BioInterchange::TextMining::TMReader::determine_process(*args) }, 'name_id' ], 'version' ]
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+ input_formats['biointerchange.gff3'] = [ BioInterchange::Genomics::GFF3Reader, 'name', 'name_uri', 'date' ]
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+
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+ output_formats = {}
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+ output_formats['rdf.bh12.sio'] = BioInterchange::TextMining::RDFWriter
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+ output_formats['rdf.biointerchange.gff3'] = BioInterchange::Genomics::RDFWriter
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+
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+ FCGI.each { |fcgi|
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+ request = fcgi.in.read
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+
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+ fcgi.out.print("Content-Type: text/plain\r\n")
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+ fcgi.out.print("\r\n")
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+
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+ begin
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+ request = JSON.parse(request)
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+ parameters = JSON.parse(URI.decode(request['parameters']))
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+ data = URI.decode(request['data'])
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+
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+ raise ArgumentError, 'An input format must be given in the meta-data using the key "input".' unless parameters['input']
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+ raise ArgumentError, "Unknown input format \"#{parameters['input']}\"." unless input_formats[parameters['input']]
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+ raise ArgumentError, 'An output format must be given in the meta-data using the key "output".' unless parameters['output']
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+ raise ArgumentError, "Unknown output format \"#{parameters['output']}\"." unless output_formats[parameters['output']]
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+
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+ reader_class, *args = input_formats[parameters['input']]
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+ reader = reader_class.new(*BioInterchange::get_parameters(parameters, args))
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+ istream, ostream = IO.pipe
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+ ostream.print(data)
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+ ostream.close
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+ model = reader.deserialize(istream)
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+ istream, ostream = IO.pipe
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+ output_formats[parameters['output']].new(ostream).serialize(model)
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+ ostream.close
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+ fcgi.out.print(istream.read)
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+ rescue => e
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+ fcgi.out.print("#{e.backtrace}\n")
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+ end
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+ fcgi.finish
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+ }
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+
data/web/webservices.html ADDED
@@ -0,0 +1,123 @@
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+ <!DOCTYPE html>
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+ <html lang="en">
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+ <head>
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+ <meta charset="utf-8">
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+ <title>BioInterchange</title>
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+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
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+ <meta name="description" content="">
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+ <meta name="author" content="">
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+
10
+ <!-- Le styles -->
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+ <link href="bootstrap/css/bootstrap.css" rel="stylesheet">
12
+ <style type="text/css">
13
+ body {
14
+ padding-top: 60px;
15
+ padding-bottom: 40px;
16
+ }
17
+ </style>
18
+ <link href="bootstrap/css/bootstrap-responsive.css" rel="stylesheet">
19
+ <script src="bootstrap/js/jquery-1.8.1.min.js"></script>
20
+
21
+ <!-- Le HTML5 shim, for IE6-8 support of HTML5 elements -->
22
+ <!--[if lt IE 9]>
23
+ <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
24
+ <![endif]-->
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+
26
+ <!-- Le fav and touch icons -->
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+ <!-- <link rel="shortcut icon" href="../assets/ico/favicon.ico"> -->
28
+ </head>
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+
30
+ <body>
31
+ <a href="https://github.com/BioInterchange/BioInterchange"><img style="z-index: 5000; position: fixed; top: 0; right: 0; border: 0;" src="https://s3.amazonaws.com/github/ribbons/forkme_right_gray_6d6d6d.png" alt="Fork me on GitHub"></a>
32
+ <div class="navbar navbar-inverse navbar-fixed-top">
33
+ <div class="navbar-inner">
34
+ <div class="container">
35
+ <a class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
36
+ <span class="icon-bar"></span>
37
+ <span class="icon-bar"></span>
38
+ <span class="icon-bar"></span>
39
+ </a>
40
+ <a class="brand" href="index.html">BioInterchange</a>
41
+ <div class="nav-collapse collapse">
42
+ <ul class="nav">
43
+ <li class="active"><a href="index.html">Home</a></li>
44
+ <li><a href="about.html">About</a></li>
45
+ <!--
46
+ <li class="dropdown">
47
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation <b class="caret"></b></a>
48
+ <ul class="dropdown-menu">
49
+ <li><a href="#">To</a></li>
50
+ <li><a href="#">Be</a></li>
51
+ <li><a href="#">Done</a></li>
52
+ <li><a href="#">Dude</a></li>
53
+ <li class="divider"></li>
54
+ <li class="nav-header">API</li>
55
+ <li><a href="#">API usage information</a></li>
56
+ <li><a href="#">Implementing new readers/writers</a></li>
57
+ </ul>
58
+ </li>
59
+ -->
60
+ </ul>
61
+ </div><!--/.nav-collapse -->
62
+ </div>
63
+ </div>
64
+ </div>
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+
66
+ <div class="container">
67
+
68
+ <!-- Example row of columns -->
69
+ <div class="row">
70
+ <div class="span12">
71
+ <h1>Web-Services</h1>
72
+ <p>Two query points to access BioInterchange are provided on the internet:
73
+ <ol>
74
+ <li>an interactive web-interface</li>
75
+ <li>a RESTful web-service</li>
76
+ </ol>
77
+ </p>
78
+ <h3>Interactive Web-Interface</h3>
79
+ <p>Select the input format of the data:<br />
80
+ <select id="inputformat" style="min-width: 50%;" onchange="selectDbclsCatannsJson();">
81
+ <option value="dbcls.catanns.json" selected>DBCLS PubAnnotation's Category Annotations (catanns) JSON</option>
82
+ <option value="biointerchange.gff3">GFF3</option>
83
+ <option value="uk.ac.man.pdfx">PDFx XML</option>
84
+ </select><br />
85
+ Select the RDF serialization method (output format):<br />
86
+ <span class="muted">Not all output format are supported for a given input format. Invalid choices are disabled automatically here.</span><br />
87
+ <select id="outputformat" style="min-width: 50%;">
88
+ <option id="output.rdf.bh12.sio" value="rdf.bh12.sio" selected>RDF using SIO and FOAF ontologies</option>
89
+ <option id="output.rdf.biointerchange.gff3" value="rdf.biointerchange.gff3" disabled>RDF using GFF3 ontology</option>
90
+ </select><br />
91
+ <a class="btn btn-info" onclick="pasteExample();">Paste Input-Specific Example</a>
92
+ </p>
93
+ <p>Input format specific parameters:<br />
94
+ <span class="muted">These parameters add meta-data to the data below. This meta-data says something about the data that is not represented in the data structure itself. For example, it could be a version number or date of when the data was created.</span><br />
95
+ <textarea id="metainput" style="font-size: 75%; width: 100%; min-height: 200px; font-family: Monaco, Menlo, Consolas, 'Courier New', monospace;"></textarea>
96
+ Paste data for RDFization below:
97
+ <textarea id="maininput" style="font-size: 75%; width: 100%; min-height: 200px; font-family: Monaco, Menlo, Consolas, 'Courier New', monospace;"></textarea>
98
+ <br /><br />
99
+ RDF output:<br />
100
+ <a class="btn btn-primary" onclick="generateRDF();">Generate RDF</a>
101
+ <pre id="output" style="font-size: 75%; width: 100%; min-height: 50px;"><i>RDF output will be <b>concatenated</b> here...</i></pre>
102
+ <a class="btn" onclick="$('#output').empty();">Clear RDF</a>
103
+ </p>
104
+ <h3>RESTful Web-Service</h3>
105
+ <p>TODO</p>
106
+ </div>
107
+ </div>
108
+
109
+ <hr>
110
+
111
+ <footer>
112
+ <p>&copy; <a href="https://github.com/BioInterchange/BioInterchange#contributors">The BioInterchange Contributors</a> 2012</p>
113
+ </footer>
114
+
115
+ </div> <!-- /container -->
116
+
117
+ <!-- Le javascript
118
+ ================================================== -->
119
+ <!-- Placed at the end of the document so the pages load faster -->
120
+ <script src="bootstrap/js/bootstrap.min.js"></script>
121
+ <script src="biointerchange.js"></script>
122
+ </body>
123
+ </html>
metadata ADDED
@@ -0,0 +1,240 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: biointerchange
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.1.0
5
+ segments:
6
+ - 0
7
+ - 1
8
+ - 0
9
+ prerelease: false
10
+ platform: ruby
11
+ authors:
12
+ - Joachim Baran
13
+ - Kevin B. Cohen
14
+ - Geraint Duck
15
+ - Michel Dumontier
16
+ autorequire: !!null
17
+ bindir: bin
18
+ cert_chain: []
19
+ date: 2012-10-11 00:00:00.000000000 -04:00
20
+ default_executable: biointerchange
21
+ dependencies:
22
+ - !ruby/object:Gem::Dependency
23
+ name: rdf
24
+ requirement: &70317163090000 !ruby/object:Gem::Requirement
25
+ none: false
26
+ requirements:
27
+ - - ! '>='
28
+ - !ruby/object:Gem::Version
29
+ version: 0.3.4.1
30
+ segments:
31
+ - 0
32
+ - 3
33
+ - 4
34
+ - 1
35
+ type: :runtime
36
+ prerelease: false
37
+ version_requirements: *70317163090000
38
+ - !ruby/object:Gem::Dependency
39
+ name: json
40
+ requirement: &70317163083460 !ruby/object:Gem::Requirement
41
+ none: false
42
+ requirements:
43
+ - - ! '>='
44
+ - !ruby/object:Gem::Version
45
+ version: 1.6.4
46
+ segments:
47
+ - 1
48
+ - 6
49
+ - 4
50
+ type: :runtime
51
+ prerelease: false
52
+ version_requirements: *70317163083460
53
+ - !ruby/object:Gem::Dependency
54
+ name: getopt
55
+ requirement: &70317163081140 !ruby/object:Gem::Requirement
56
+ none: false
57
+ requirements:
58
+ - - ! '>='
59
+ - !ruby/object:Gem::Version
60
+ version: 1.4.1
61
+ segments:
62
+ - 1
63
+ - 4
64
+ - 1
65
+ type: :runtime
66
+ prerelease: false
67
+ version_requirements: *70317163081140
68
+ - !ruby/object:Gem::Dependency
69
+ name: rspec
70
+ requirement: &70317163079560 !ruby/object:Gem::Requirement
71
+ none: false
72
+ requirements:
73
+ - - ~>
74
+ - !ruby/object:Gem::Version
75
+ version: 2.8.0
76
+ segments:
77
+ - 2
78
+ - 8
79
+ - 0
80
+ type: :development
81
+ prerelease: false
82
+ version_requirements: *70317163079560
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+ - !ruby/object:Gem::Dependency
84
+ name: bundler
85
+ requirement: &70317163060340 !ruby/object:Gem::Requirement
86
+ none: false
87
+ requirements:
88
+ - - ~>
89
+ - !ruby/object:Gem::Version
90
+ version: 1.2.1
91
+ segments:
92
+ - 1
93
+ - 2
94
+ - 1
95
+ type: :development
96
+ prerelease: false
97
+ version_requirements: *70317163060340
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+ - !ruby/object:Gem::Dependency
99
+ name: jeweler
100
+ requirement: &70317163057220 !ruby/object:Gem::Requirement
101
+ none: false
102
+ requirements:
103
+ - - ~>
104
+ - !ruby/object:Gem::Version
105
+ version: 1.8.4
106
+ segments:
107
+ - 1
108
+ - 8
109
+ - 4
110
+ type: :development
111
+ prerelease: false
112
+ version_requirements: *70317163057220
113
+ - !ruby/object:Gem::Dependency
114
+ name: bio
115
+ requirement: &70317163046060 !ruby/object:Gem::Requirement
116
+ none: false
117
+ requirements:
118
+ - - ! '>='
119
+ - !ruby/object:Gem::Version
120
+ version: 1.4.2
121
+ segments:
122
+ - 1
123
+ - 4
124
+ - 2
125
+ type: :development
126
+ prerelease: false
127
+ version_requirements: *70317163046060
128
+ - !ruby/object:Gem::Dependency
129
+ name: rdoc
130
+ requirement: &70317163030160 !ruby/object:Gem::Requirement
131
+ none: false
132
+ requirements:
133
+ - - ~>
134
+ - !ruby/object:Gem::Version
135
+ version: '3.12'
136
+ segments:
137
+ - 3
138
+ - 12
139
+ type: :development
140
+ prerelease: false
141
+ version_requirements: *70317163030160
142
+ description: BioInterchange is a Ruby gem, command-line tool, web-service for turning
143
+ heterogeneous data formats such as JSON, XML, GFF3, etc., into RDF."
144
+ email: joachim.baran@gmail.com
145
+ executables:
146
+ - biointerchange
147
+ extensions: []
148
+ extra_rdoc_files:
149
+ - LICENSE.txt
150
+ - README.md
151
+ files:
152
+ - .document
153
+ - .rspec
154
+ - .travis.yml
155
+ - Gemfile
156
+ - LICENSE.txt
157
+ - README.md
158
+ - Rakefile
159
+ - VERSION
160
+ - bin/biointerchange
161
+ - docs/exceptions_readme.txt
162
+ - examples/BovineGenomeChrX.gff3.gz
163
+ - examples/gb-2007-8-3-R40.xml
164
+ - examples/pubannotation.json
165
+ - generators/rdfxml.rb
166
+ - lib/biointerchange.rb
167
+ - lib/biointerchange/core.rb
168
+ - lib/biointerchange/exceptions.rb
169
+ - lib/biointerchange/genomics/gff3_feature.rb
170
+ - lib/biointerchange/genomics/gff3_feature_set.rb
171
+ - lib/biointerchange/genomics/gff3_rdf_ntriples.rb
172
+ - lib/biointerchange/genomics/gff3_reader.rb
173
+ - lib/biointerchange/gff3.rb
174
+ - lib/biointerchange/reader.rb
175
+ - lib/biointerchange/registry.rb
176
+ - lib/biointerchange/sio.rb
177
+ - lib/biointerchange/sofa.rb
178
+ - lib/biointerchange/textmining/content.rb
179
+ - lib/biointerchange/textmining/document.rb
180
+ - lib/biointerchange/textmining/pdfx_xml_reader.rb
181
+ - lib/biointerchange/textmining/process.rb
182
+ - lib/biointerchange/textmining/pubannos_json_reader.rb
183
+ - lib/biointerchange/textmining/text_mining_rdf_ntriples.rb
184
+ - lib/biointerchange/textmining/text_mining_reader.rb
185
+ - lib/biointerchange/writer.rb
186
+ - spec/exceptions_spec.rb
187
+ - spec/gff3_rdfwriter_spec.rb
188
+ - spec/text_mining_pdfx_xml_reader_spec.rb
189
+ - spec/text_mining_pubannos_json_reader_spec.rb
190
+ - spec/text_mining_rdfwriter_spec.rb
191
+ - web/about.html
192
+ - web/biointerchange.js
193
+ - web/bootstrap/css/bootstrap-responsive.css
194
+ - web/bootstrap/css/bootstrap-responsive.min.css
195
+ - web/bootstrap/css/bootstrap.css
196
+ - web/bootstrap/css/bootstrap.min.css
197
+ - web/bootstrap/img/glyphicons-halflings-white.png
198
+ - web/bootstrap/img/glyphicons-halflings.png
199
+ - web/bootstrap/js/bootstrap.js
200
+ - web/bootstrap/js/bootstrap.min.js
201
+ - web/bootstrap/js/jquery-1.8.1.min.js
202
+ - web/css/rdoc-style.css
203
+ - web/css/rdoc.css
204
+ - web/images/BioInterchange300.png
205
+ - web/index.html
206
+ - web/service/rdfizer.fcgi
207
+ - web/webservices.html
208
+ has_rdoc: true
209
+ homepage: http://www.biointerchange.org
210
+ licenses:
211
+ - MIT
212
+ post_install_message: !!null
213
+ rdoc_options: []
214
+ require_paths:
215
+ - lib
216
+ required_ruby_version: !ruby/object:Gem::Requirement
217
+ none: false
218
+ requirements:
219
+ - - ! '>='
220
+ - !ruby/object:Gem::Version
221
+ version: '0'
222
+ segments:
223
+ - 0
224
+ hash: -1636007082743393289
225
+ required_rubygems_version: !ruby/object:Gem::Requirement
226
+ none: false
227
+ requirements:
228
+ - - ! '>='
229
+ - !ruby/object:Gem::Version
230
+ version: '0'
231
+ segments:
232
+ - 0
233
+ requirements: []
234
+ rubyforge_project: !!null
235
+ rubygems_version: 1.3.7
236
+ signing_key: !!null
237
+ specification_version: 3
238
+ summary: An open source framework for transforming heterogeneous data formats into
239
+ RDF.
240
+ test_files: []