web/cli.html in biointerchange-1.0.1 vs web/cli.html in biointerchange-1.0.2
- old
+ new
@@ -7,18 +7,17 @@
<meta name="description" content="">
<meta name="author" content="">
<!-- Le styles -->
<link href="bootstrap/css/bootstrap.css" rel="stylesheet">
+ <link href="bootstrap/css/bootstrapi-theme.min.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]-->
@@ -27,30 +26,26 @@
<!-- <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 class="container-fluid">
+ <a class="navbar-brand" href="index.html">BioInterchange</a>
+ <ul class="nav navbar-nav">
+ <li class="active"><a href="cli.html">Shell Tool</a></li>
+ <li><a href="ontologies.html">Ontologies</a></li>
+ <li><a href="about.html">About</a></li>
+ </ul>
</div>
</div>
-
<div class="container">
<!-- Example row of columns -->
<div class="row">
- <div class="span12">
+ <div class="col-md-12">
<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
@@ -58,11 +53,11 @@
</p>
<h4>Usage</h4>
<p>
Examples:
<pre>
-biointerchange --input biointerchange.gvf --rdf rdf.biointerchange.gvf --batchsize 100 --file examples/estd176_Banerjee_et_al_2011.2012-11-29.NCBI36.gvf
+biointerchange --input biointerchange.gvf --rdf rdf.biointerchange.gfvo --batchsize 100 --file examples/estd176_Banerjee_et_al_2011.2012-11-29.NCBI36.gvf
biointerchange --input dbcls.catanns.json --rdf rdf.bh12.sio --file examples/pubannotation.10096561.json --annotate_name 'Peter Smith' --annotate_name_id 'peter.smith@example.com'
biointerchange --input uk.ac.man.pdfx --rdf rdf.bh12.sio --file examples/gb-2007-8-3-R40.xml --annotate_name 'Peter Smith' --annotate_name_id 'peter.smith@example.com'
biointerchange --input phylotastic.newick --rdf rdf.phylotastic.newick --file examples/tree2.new --annotate_date '1 June 2006'
</pre>
Input formats:
@@ -73,12 +68,12 @@
<li><code>phylotastic.newick</code>: <a href="http://evolution.genetics.washington.edu/phylip/newicktree.html">Newick tree file format</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.biointerchange.gfvo</code>: RDFization of <code>biointerchange.gff3</code></li>
+ <li><code>rdf.biointerchange.gfvo</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>
<li><code>rdf.phylotastic.newick</code>: RDFization of <code>phylotastic.newick</code></li>
</ul>
</p>
<h4>Using a Triple Store</h4>
@@ -99,19 +94,10 @@
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> sparql select * where { ?s <http://www.biointerchange.org/gvf1o#GVF1_0004> ?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 <path-to-gff3o/gvf1o> <yourdata.n3> > 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>bininda_emonds_mammals.new</code>: Newick formatted Bininda-Emonds mammals tree (see <a href="http://www.ncbi.nlm.nih.gov/pubmed/17392779">The delayed rise of present-day mammals</a>). Downloaded from <a href="https://github.com/bendmorris/rdf-treestore/blob/master/trees/bininda_emonds_mammals.new">https://github.com/bendmorris/rdf-treestore/blob/master/trees/bininda_emonds_mammals.new</a></li>
@@ -126,10 +112,10 @@
</div>
<hr>
<footer>
- <p>© <a href="about.html">The BioInterchange Contributors</a> 2012–2013</p>
+ <p>© <a href="about.html">The BioInterchange Contributors</a> 2012–2014</p>
</footer>
</div> <!-- /container -->
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