biointerchange 0.2.1 → 0.2.2

data/supplemental/python/setup.py

@@ -2,9 +2,9 @@ from setuptools import setup, find_packages
  
 setup(
     name = "biointerchange",
-    version = "0.2.1",
+    version = "0.2.2",
     author = "Joachim Baran, Geraint Duck",
-    description = ( "Wrapper for easy access to GFF3O, GVF1O, SIO, SO and SOFA.",
+    description = ( "Wrapper for easy access to FALDO, GFF3O, GVF1O, SIO, SO and SOFA.",
                     "Part of the BioInterchange project." ),
     license = "MIT",
     url = "http://www.biointerchange.org",

data/web/about.html

@@ -31,34 +31,14 @@
     <div class="navbar navbar-inverse navbar-fixed-top">
       <div class="navbar-inner">
         <div class="container">
-          <a class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
-            <span class="icon-bar"></span>
-            <span class="icon-bar"></span>
-            <span class="icon-bar"></span>
-          </a>
           <a class="brand" href="index.html">BioInterchange</a>
-          <div class="nav-collapse collapse">
-            <ul class="nav">
-              <li><a href="index.html">Home</a></li>
-              <li><a href="ontologies.html">Ontologies</a></li>
-              <li class="active"><a href="about.html">About</a></li>
-              <!--
-              <li class="dropdown">
-                <a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation <b class="caret"></b></a>
-                <ul class="dropdown-menu">
-                  <li><a href="#">To</a></li>
-                  <li><a href="#">Be</a></li>
-                  <li><a href="#">Done</a></li>
-                  <li><a href="#">Dude</a></li>
-                  <li class="divider"></li>
-                  <li class="nav-header">API</li>
-                  <li><a href="#">API usage information</a></li>
-                  <li><a href="#">Implementing new readers/writers</a></li>
-                </ul>
-              </li>
-              -->
-            </ul>
-          </div><!--/.nav-collapse -->
+          <ul class="nav">
+            <li><a href="cli.html">Shell Tool</a></li>
+            <li><a href="webservices.html">Web-Services</a></li>
+            <li><a href="api.html">API</a></li>
+            <li><a href="ontologies.html">Ontologies</a></li>
+            <li class="active"><a href="about.html">About</a></li>
+          </ul>
         </div>
       </div>
     </div>
@@ -69,7 +49,7 @@
       <div class="row">
         <div class="span12">
           <h2>About BioInterchange</h2>
-          <p>BioInterchange was conceived and designed during <a href="http://biosciencedbc.jp">NBDC</a>/<a href="http://dbcls.rois.ac.jp">DBCLS</a>'s <a href="http://2012.biohackathon.org">BioHackathon 2012</a>. Architecture and RDF serialization implementations were provided by <a href="http://joachimbaran.wordpress.com">Joachim Baran</a>, <a href="http://www.cs.man.ac.uk/~duckg">Geraint Duck</a> provided JSON and XML deserialization implementations and contributed to architecture decisions, guidance on ontology use and applications were given by <a href="http://compbio.ucdenver.edu/Hunter_lab/Cohen/index.shtml">Kevin B. Cohen</a> and <a href="http://dumontierlab.com">Michel Dumontier</a>, where Michel brought forward and extended the <a href="http://code.google.com/p/semanticscience/wiki/SIO">Semanticscience Integrated Ontology</a> (SIO).</p>
+          <p>BioInterchange was conceived and designed during <a href="http://biosciencedbc.jp">NBDC</a>/<a href="http://dbcls.rois.ac.jp">DBCLS</a>'s <a href="http://2012.biohackathon.org">BioHackathon 2012</a>. Architecture and RDF serialization implementations were provided by <a href="http://joachimbaran.wordpress.com">Joachim Baran</a>, <a href="http://www.cs.man.ac.uk/~duckg">Geraint Duck</a> provided JSON and XML deserialization implementations and contributed to architecture decisions, guidance on ontology use and applications were given by <a href="http://compbio.ucdenver.edu/Hunter_lab/Cohen/index.shtml">Kevin B. Cohen</a> and <a href="http://dumontierlab.com">Michel Dumontier</a>, where Michel brought forward and extended the <a href="http://code.google.com/p/semanticscience/wiki/SIO">Semanticscience Integrated Ontology</a> (SIO). <a href="http://dbcls.rois.ac.jp/~jdkim">Jin-Dong Kim</a> helped to define ontology relationships for RDFizing DBCLS' PubAnnotation category annotations.</p>
           <h2>Contact</h2>
           <p><a href="http://joachimbaran.wordpress.com">Joachim Baran</a><br /><i>joachim.baran</i><b>&#64;</b><i>gmail.com</i></p>
         </div>
@@ -78,7 +58,7 @@
       <hr>
 
       <footer>
-        <p>&copy; <a href="https://github.com/BioInterchange/BioInterchange#contributors">The BioInterchange Contributors</a> 2012</p>
+        <p>&copy; <a href="about.html">The BioInterchange Contributors</a> 2012&ndash;2013</p>
       </footer>
 
     </div> <!-- /container -->

data/web/api.html

@@ -31,34 +31,14 @@
     <div class="navbar navbar-inverse navbar-fixed-top">
       <div class="navbar-inner">
         <div class="container">
-          <a class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
-            <span class="icon-bar"></span>
-            <span class="icon-bar"></span>
-            <span class="icon-bar"></span>
-          </a>
           <a class="brand" href="index.html">BioInterchange</a>
-          <div class="nav-collapse collapse">
-            <ul class="nav">
-              <li class="active"><a href="index.html">Home</a></li>
-              <li><a href="ontologies.html">Ontologies</a></li>
-              <li><a href="about.html">About</a></li>
-              <!--
-              <li class="dropdown">
-                <a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation <b class="caret"></b></a>
-                <ul class="dropdown-menu">
-                  <li><a href="#">To</a></li>
-                  <li><a href="#">Be</a></li>
-                  <li><a href="#">Done</a></li>
-                  <li><a href="#">Dude</a></li>
-                  <li class="divider"></li>
-                  <li class="nav-header">API</li>
-                  <li><a href="#">API usage information</a></li>
-                  <li><a href="#">Implementing new readers/writers</a></li>
-                </ul>
-              </li>
-              -->
-            </ul>
-          </div><!--/.nav-collapse -->
+          <ul class="nav">
+            <li><a href="cli.html">Shell Tool</a></li>
+            <li><a href="webservices.html">Web-Services</a></li>
+            <li class="active"><a href="api.html">API</a></li>
+            <li><a href="ontologies.html">Ontologies</a></li>
+            <li><a href="about.html">About</a></li>
+          </ul>
         </div>
       </div>
     </div>
@@ -105,7 +85,7 @@ GFF3O.with_parent(GFF3O.start(), feature_properties)
             <p>Vocabulary wrappers in Python are available as an egg, that can be installed via <a href="http://pypi.python.org/pypi/setuptools">easy_install</a>:</p>
 <pre>
 sudo easy_install rdflib
-sudo easy_install http://www.biointerchange.org/eggs/biointerchange-0.1.2-py2.7.egg
+sudo easy_install http://www.biointerchange.org/eggs/biointerchange-0.2.2-py2.7.egg
 </pre>
             <p>Usage example (see also <a href="https://github.com/BioInterchange/BioInterchange/blob/master/supplemental/python/example.py">example.py</a>):</p>
 <pre>
@@ -143,7 +123,7 @@ GFF3O.with_parent(GFF3O.start(), feature_properties)
   &lt;dependency&gt;
     &lt;groupId&gt;org.biointerchange&lt;/groupId&gt;
     &lt;artifactId&gt;vocabularies&lt;/artifactId&gt;
-    &lt;version&gt;0.1.2&lt;/version&gt;
+    &lt;version&gt;0.2.2&lt;/version&gt;
   &lt;/dependency&gt;
 &lt;/dependencies&gt;
 </pre>
@@ -212,7 +192,7 @@ public class App
       <hr>
 
       <footer>
-        <p>&copy; <a href="https://github.com/BioInterchange/BioInterchange#contributors">The BioInterchange Contributors</a> 2012</p>
+        <p>&copy; <a href="about.html">The BioInterchange Contributors</a> 2012&ndash;2013</p>
       </footer>
 
     </div> <!-- /container -->

data/web/biointerchange.js

@@ -1,5 +1,11 @@
+/* Generates RDF from provided data according to additionally given parameters.
+ *
+ * '#inputformat': select box that determines the type of input data that should be converted into RDF
+ * '#metainput': a text field that contains parameters for the RDF conversion in JSON format
+ * '#output': text field to which the RDF output is appended to
+ */
 function generateRDF() {
-  if ($('#inputformat').val() == 'biointerchange.gff3' || $('#inputformat').val() == 'dbcls.catanns.json' || $('#inputformat').val() == 'uk.ac.man.pdfx') {
+  if ($('#inputformat').val() == 'biointerchange.gff3' || $('#inputformat').val() == 'biointerchange.gvf' || $('#inputformat').val() == 'dbcls.catanns.json' || $('#inputformat').val() == 'uk.ac.man.pdfx') {
     request = '{ "parameters" : "' + escape($('#metainput').val()) + '", "data" : "' + escape($('#maininput').val()) + '" }'
     $.ajax({
       type: 'POST',
@@ -16,38 +22,57 @@ function generateRDF() {
   }
 }
 
+/* Determines valid RDF output converters ("writers" or serializers) based on the chosen input data type/format.
+ *
+ * '#inputformat': select box that determines the input format type
+ * '#outputformat': select box with all available output formats -- some of which might be disabled (based on selected input format)
+ */
 function selectDbclsCatannsJson() {
   var outputFormats = $('#outputformat')[0];
   for (var i = 0; i < outputFormats.length; i++)
-  if ($('#inputformat').val() == 'biointerchange.gff3') {
-    if (outputFormats[i].value == 'rdf.biointerchange.gff3') {
-      outputFormats[i].selected = true;
-      outputFormats[i].disabled = false;
+    if ($('#inputformat').val() == 'biointerchange.gff3') {
+      if (outputFormats[i].value == 'rdf.biointerchange.gff3') {
+        outputFormats[i].selected = true;
+        outputFormats[i].disabled = false;
+      } else {
+        outputFormats[i].selected = false;
+        outputFormats[i].disabled = true;
+      }
+    } else if ($('#inputformat').val() == 'biointerchange.gvf') {
+      if (outputFormats[i].value == 'rdf.biointerchange.gvf') {
+        outputFormats[i].selected = true;
+        outputFormats[i].disabled = false;
+      } else {
+        outputFormats[i].selected = false;
+        outputFormats[i].disabled = true;
+      }
+    } else if ($('#inputformat').val() == 'dbcls.catanns.json') {
+      if (outputFormats[i].value == 'rdf.bh12.sio') {
+        outputFormats[i].selected = true;
+        outputFormats[i].disabled = false;
+      } else {
+        outputFormats[i].selected = false;
+        outputFormats[i].disabled = true;
+      }
+    } else if ($('#inputformat').val() == 'uk.ac.man.pdfx') {
+      if (outputFormats[i].value == 'rdf.bh12.sio') {
+        outputFormats[i].selected = true;
+        outputFormats[i].disabled = false;
+      } else {
+        outputFormats[i].selected = false;
+        outputFormats[i].disabled = true;
+      }
     } else {
-      outputFormats[i].selected = false;
-      outputFormats[i].disabled = true;
+     // Woopsie.
     }
-  } else if ($('#inputformat').val() == 'dbcls.catanns.json') {
-    if (outputFormats[i].value == 'rdf.bh12.sio') {
-      outputFormats[i].selected = true;
-      outputFormats[i].disabled = false;
-    } else {
-      outputFormats[i].selected = false;
-      outputFormats[i].disabled = true;
-    }
-  } else if ($('#inputformat').val() == 'uk.ac.man.pdfx') {
-    if (outputFormats[i].value == 'rdf.bh12.sio') {
-      outputFormats[i].selected = true;
-      outputFormats[i].disabled = false;
-    } else {
-      outputFormats[i].selected = false;
-      outputFormats[i].disabled = true;
-    }
-  } else {
-    // Woopsie.
-  }
 }
 
+/* Pastes an example into the web form.
+ *
+ * '#inputformat': a select box determining the input data format
+ * '#metainput': text field that is being populated with example parameters in JSON format
+ * '#maininput': text field that is being populated with a data example
+ */
 function pasteExample() {
   if ($('#inputformat').val() == 'biointerchange.gff3') {
     $('#metainput').val(
@@ -60,11 +85,37 @@ function pasteExample() {
       "}\n"
     );
     $('#maininput').val(
+      "##gff-version 3\n" +
+      "##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9913\n" +
+      "##sequence-region ChrX.38 1 88516663\n" +
       "ChrX.38\tbovine_complete_cds_gmap_perfect\tgene\t15870\t16254\t.\t+\t.\tID=BC109609_ChrX.38\n" +
-      "ChrX.38\tbovine_complete_cds_gmap_perfect\tRNA\t15870\t16254\t.\t+\t.\tID=bovine_complete_cds_gmap_perfect_BC109609_ChrX.38;Parent=BC109609_ChrX.38\n" +
+      "ChrX.38\tbovine_complete_cds_gmap_perfect\tmRNA\t15870\t16254\t.\t+\t.\tID=bovine_complete_cds_gmap_perfect_BC109609_ChrX.38;Parent=BC109609_ChrX.38\n" +
       "ChrX.38\tbovine_complete_cds_gmap_perfect\tCDS\t15870\t16254\t.\t+\t0\tParent=bovine_complete_cds_gmap_perfect_BC109609_ChrX.38\n" +
       "ChrX.38\tbovine_complete_cds_gmap_perfect\texon\t15870\t16254\t.\t+\t0\tParent=bovine_complete_cds_gmap_perfect_BC109609_ChrX.38\n"
     );
+  } else if ($('#inputformat').val() == 'biointerchange.gvf') {
+    $('#metainput').val(
+      "{\n" +
+      "  \"input\" : \"biointerchange.gvf\",\n" +
+      "  \"output\" : \"rdf.biointerchange.gvf\",\n" +
+      "  \"name\" : \"Peter Smith\",\n" +
+      "  \"name_id\" : \"peter.smith@some.example.domain\",\n" +
+      "  \"date\" : \"2012-07-19\"\n" +
+      "}\n"
+    );
+    $('#maininput').val(
+      "##gff-version 3\n" +
+      "##gvf-version 1.06\n" +
+      "##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=4932\n" +
+      "##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/so.obo?revision=1.283\n" +
+      "##data-source Source=ensembl;version=71;url=http://e71.ensembl.org/Saccharomyces_cerevisiae\n" +
+      "##sequence-region I 1 230218\n" +
+      "I\tSGRP\tSNV\t84\t84\t.\t+\t.\tID=1;Variant_seq=A;Variant_effect=upstream_gene_variant 0 transcript YAL067W-A,upstream_gene_variant 0 transcript YAL069W,upstream_gene_variant 0 transcript YAL068W-A,downstream_gene_variant 0 transcript YAL068C;Dbxref=SGRP:s01-84;Reference_seq=G\n" +
+      "I\tSGRP\tSNV\t109\t109\t.\t+\t.\tID=2;Variant_seq=C;Variant_effect=upstream_gene_variant 0 transcript YAL067W-A,upstream_gene_variant 0 transcript YAL068W-A,upstream_gene_variant 0 transcript YAL069W,downstream_gene_variant 0 transcript YAL068C;Dbxref=SGRP:s01-109;Reference_seq=G\n" +
+      "I\tSGRP\tSNV\t111\t111\t.\t+\t.\tID=3;Variant_seq=T;Variant_effect=upstream_gene_variant 0 transcript YAL067W-A,upstream_gene_variant 0 transcript YAL069W,upstream_gene_variant 0 transcript YAL068W-A,downstream_gene_variant 0 transcript YAL068C;Dbxref=SGRP:s01-111;Reference_seq=C\n" +
+      "I\tSGRP\tSNV\t114\t114\t.\t+\t.\tID=4;Variant_seq=C;Variant_effect=upstream_gene_variant 0 transcript YAL067W-A,upstream_gene_variant 0 transcript YAL068W-A,upstream_gene_variant 0 transcript YAL069W,downstream_gene_variant 0 transcript YAL068C;Dbxref=SGRP:s01-114;Reference_seq=T\n" +
+      "I\tSGRP\tSNV\t115\t115\t.\t+\t.\tID=5;Variant_seq=G;Variant_effect=upstream_gene_variant 0 transcript YAL067W-A,upstream_gene_variant 0 transcript YAL068W-A,upstream_gene_variant 0 transcript YAL069W,downstream_gene_variant 0 transcript YAL068C;Dbxref=SGRP:s01-115;Reference_seq=C\n"
+    );
   } else if ($('#inputformat').val() == 'dbcls.catanns.json') {
     $('#metainput').val(
       "{\n" +

data/web/cli.html

@@ -0,0 +1,137 @@
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8">
+    <title>BioInterchange</title>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <meta name="description" content="">
+    <meta name="author" content="">
+
+    <!-- Le styles -->
+    <link href="bootstrap/css/bootstrap.css" rel="stylesheet">
+    <style type="text/css">
+      body {
+        padding-top: 60px;
+        padding-bottom: 40px;
+      }
+    </style>
+    <link href="bootstrap/css/bootstrap-responsive.css" rel="stylesheet">
+    <script src="bootstrap/js/jquery-1.8.1.min.js"></script>
+
+    <!-- Le HTML5 shim, for IE6-8 support of HTML5 elements -->
+    <!--[if lt IE 9]>
+      <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
+    <![endif]-->
+
+    <!-- Le fav and touch icons -->
+    <!-- <link rel="shortcut icon" href="../assets/ico/favicon.ico"> -->
+  </head>
+
+  <body>
+    <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>
+    <div class="navbar navbar-inverse navbar-fixed-top">
+      <div class="navbar-inner">
+        <div class="container">
+          <a class="brand" href="index.html">BioInterchange</a>
+          <ul class="nav">
+            <li class="active"><a href="cli.html">Shell Tool</a></li>
+            <li><a href="webservices.html">Web-Services</a></li>
+            <li><a href="api.html">API</a></li>
+            <li><a href="ontologies.html">Ontologies</a></li>
+            <li><a href="about.html">About</a></li>
+          </ul>
+        </div>
+      </div>
+    </div>
+
+    <div class="container">
+
+      <!-- Example row of columns -->
+      <div class="row">
+        <div class="span12">
+          <h1>Shell Tool</h1>
+          <p>
+            BioInterchange's command-line tool <code>biointerchange</code> can be installed as a command line tools as follows:
+<pre>
+gem install biointerchange
+</pre>
+          </p>
+          <h4>Usage</h4>
+          <p>
+            Examples:
+<pre>
+biointerchange --input dbcls.catanns.json --rdf rdf.bh12.sio --file examples/pubannotation.10096561.json --name 'Peter Smith' --name_id 'peter.smith@example.com'
+biointerchange --input uk.ac.man.pdfx --rdf rdf.bh12.sio --file examples/gb-2007-8-3-R40.xml --name 'Peter Smith' --name_id 'peter.smith@example.com'
+</pre>
+            Input formats:
+            <ul>
+              <li><code>biointerchange.gff3</code>: <a href="http://www.sequenceontology.org/resources/gff3.html">Generic Feature Format Version 3</a></li>
+              <li><code>biointerchange.gvf</code>: <a href="http://www.sequenceontology.org/resources/gvf.html">Genome Variation Format</a></li>
+              <li><code>dbcls.catanns.json</code>: <a href="http://pubannotation.dbcls.jp">PubAnnotation categorical annotations</a></li>
+              <li><code>uk.ac.man.pdfx</code>: <a href=http://pdfx.cs.man.ac.uk">PDFx</a></li>
+            </ul>
+            Output formats:
+            <ul>
+              <li><code>rdf.biointerchange.gff3</code>: RDFization of <code>biointerchange.gff3</code></li>
+              <li><code>rdf.biointerchange.gvf</code>: RDFization of <code>biointerchange.gvf</code></li>
+              <li><code>rdf.bh12.sio</code>: RDFization of <code>dbcls.catanns.json</code> or <code>uk.ac.man.pdfx</code></li>
+            </ul>
+          </p>
+          <h4>Using a Triple Store</h4>
+          <p>
+            RDF data produced by BioInterchange can be directly loaded into a triple store. The following gives an example about loading and querying RDF data using <a href="http://www.openrdf.org">Sesame</a>]; the commands are entered via Sesame's <code>bin/console.sh</code>:
+<pre>
+&gt; create memory.
+Please specify values for the following variables:
+Repository ID [memory]: testrepo
+Repository title [Memory store]: Test Repository
+Persist (true|false) [true]: false
+Sync delay [0]:
+Repository created
+&gt; open testrepo.
+testrepo&gt; load <path-to-your-rdf-data> .
+testrepo&gt; sparql select * where { ?s ?p ?o } .
+</pre>
+            To list all <code>seqid</code> entries from a GFF3/GVF-file conversion in the store, the following SPARQL query can be used:
+<pre>
+testrepo&gt; sparql select * where { ?s &lt;http://www.biointerchange.org/gvf1o#GVF1_0004&gt; ?o } .
+</pre>
+          </p>
+          <h4>Data Consistency Verification</h4>
+          <p>
+            Data consistency is verifyable for the output formats <code>rdf.biointerchange.gff3</code> and <code>rdf.biointerchange.gvf</code> using the BioInterchange <a href="ontologies.html">ontologies</a> GFF3O and GVF1O. The following is an example of how <a href="http://jena.apache.org">Jena</a>'s command line tools and the <a href="http://hermit-reasoner.com">HermiT reasoner</a> can be used for conistency verification:
+<pre>
+rdfcat &lt;path-to-gff3o/gvf1o&gt; &lt;yourdata.n3&gt; &gt; merged.xml
+java -d64 -Xmx4G -jar HermiT.jar -k -v merged.xml
+</pre>
+            Another approach is to load the data and its related GFF3O/GVF1O ontology into <a href="http://protege.stanford.edu">Protege</a>, merge them, and then use the "Explain inconsistent ontology" menu item to inspect possible data inconsistencies.
+          </p>
+          <h4>Example Data Provenance</h4>
+          <p>
+            The following list provides information on the origin of the example-data files in the <code>examples</code> directory:
+            <ul>
+              <li><code>BovineGenomeChrX.gff3.gz</code>: Gzipped GFF3 file describing a Bos taurus chromosome X. Downloaded from <a href="http://bovinegenome.org/?q=download_chromosome_gff3">http://bovinegenome.org/?q=download_chromosome_gff3</a></li>
+              <li><code>chromosome_BF.gff</code>: GFF3 file of floating contigs from the Baylor Sequencing Centre. Downloaded from <a href="http://dictybase.org/Downloads">http://dictybase.org/Downloads</a></li>
+              <li><code>estd176_Banerjee_et_al_2011.2012-11-29.NCBI36.gvf</code>: GVF file of EBI's <a href="http://www.ebi.ac.uk/dgva/database-genomic-variants-archive">DGVa</a>. Downloaded from <a href="ftp://ftp.ebi.ac.uk/pub/databases/dgva/estd176_Banerjee_et_al_2011/gvf/estd176_Banerjee_et_al_2011.2012-11-29.NCBI36.gvf">ftp://ftp.ebi.ac.uk/pub/databases/dgva/estd176_Banerjee_et_al_2011/gvf/estd176_Banerjee_et_al_2011.2012-11-29.NCBI36.gvf</a></li>
+              <li><code>gb-2007-8-3-R40.xml</code>: Generated by <a href="http://pdfx.cs.man.ac.uk">PDFx</a> from open-access source PDF <a href="http://genomebiology.com/content/pdf/gb-2007-8-3-r40.pdf">Sense-antisense pairs in mammals: functional and evolutionary considerations</a></li>
+              <li><code>Saccharomyces_cerevisiae_incl_consequences.gvf.gz</code>: Downloaded from <a href="ftp://ftp.ensembl.org/pub/release-71/variation/gvf/saccharomyces_cerevisiae/Saccharomyces_cerevisiae_incl_consequences.gvf.gz">ftp://ftp.ensembl.org/pub/release-71/variation/gvf/saccharomyces_cerevisiae/Saccharomyces_cerevisiae_incl_consequences.gvf.gz</a></li>
+            </ul>
+          </p>
+        </div>
+      </div>
+
+      <hr>
+
+      <footer>
+        <p>&copy; <a href="about.html">The BioInterchange Contributors</a> 2012&ndash;2013</p>
+      </footer>
+
+    </div> <!-- /container -->
+
+    <!-- Le javascript
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+    <!-- Placed at the end of the document so the pages load faster -->
+    <script src="bootstrap/js/bootstrap.min.js"></script>
+    <script src="biointerchange.js"></script>
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+</html>

data/web/index.html

@@ -31,41 +31,20 @@
     <div class="navbar navbar-inverse navbar-fixed-top">
       <div class="navbar-inner">
         <div class="container">
-          <a class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
-            <span class="icon-bar"></span>
-            <span class="icon-bar"></span>
-            <span class="icon-bar"></span>
-          </a>
           <a class="brand" href="index.html">BioInterchange</a>
-          <div class="nav-collapse collapse">
-            <ul class="nav">
-              <li class="active"><a href="index.html">Home</a></li>
-              <li><a href="ontologies.html">Ontologies</a></li>
-              <li><a href="about.html">About</a></li>
-              <!--
-              <li class="dropdown">
-                <a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation <b class="caret"></b></a>
-                <ul class="dropdown-menu">
-                  <li><a href="#">To</a></li>
-                  <li><a href="#">Be</a></li>
-                  <li><a href="#">Done</a></li>
-                  <li><a href="#">Dude</a></li>
-                  <li class="divider"></li>
-                  <li class="nav-header">API</li>
-                  <li><a href="#">API usage information</a></li>
-                  <li><a href="#">Implementing new readers/writers</a></li>
-                </ul>
-              </li>
-              -->
-            </ul>
-          </div><!--/.nav-collapse -->
+          <ul class="nav">
+            <li><a href="cli.html">Shell Tool</a></li>
+            <li><a href="webservices.html">Web-Services</a></li>
+            <li><a href="api.html">API</a></li>
+            <li><a href="ontologies.html">Ontologies</a></li>
+            <li><a href="about.html">About</a></li>
+          </ul>
         </div>
       </div>
     </div>
 
     <div class="container">
 
-      <!-- Main hero unit for a primary marketing message or call to action -->
       <div class="hero-unit">
         <div style="float: left; margin-right: 24px;"><a href="http://www.biointerchange.org"><img width=150 height=150 src="images/BioInterchange300.png" /></a></div>
         <h1>BioInterchange</h1>
@@ -73,30 +52,36 @@
         <!-- <p><a class="btn btn-primary btn-large">Learn more &raquo;</a></p> -->
       </div>
 
-      <!-- Example row of columns -->
       <div class="row">
-        <div class="span4">
+        <div class="span6" style="text-align: justify;">
           <h2>Shell Tool</h2>
           <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>
-          <p><!-- <a class="btn" href="#">View details &raquo;</a> --><em>It's there, just this page isn't...</em></p>
+          <p><a class="btn" href="cli.html">View details &raquo;</a></p>
         </div>
-        <div class="span4">
+        <div class="span6" style="text-align: justify;">
           <h2>Web-Services</h2>
           <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>
           <p><a class="btn" href="webservices.html">View details &raquo;</a></em></p>
        </div>
-        <div class="span4">
+      </div>
+      <div class="row">
+        <div class="span6" style="text-align: justify;">
           <h2>API</h2>
           <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>
           <p><a class="btn" href="api.html">View details &raquo;</a></p>
           <p><a class="btn" href="../doc/BioInterchange.html">View Ruby docs &raquo;</a></p>
         </div>
+        <div class="span6" style="text-align: justify;">
+          <h2>Ontologies</h2>
+          <p>Reuse ontologies that we specifically developed to tackle some RDFizations. External ontologies that are used by BioInterchange are listed here too.
+          <p><a class="btn" href="ontologies.html">View details &raquo;</a></p>
+        </div>
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       <footer>
-        <p>&copy; <a href="https://github.com/BioInterchange/BioInterchange#contributors">The BioInterchange Contributors</a> 2012</p>
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