biointerchange 0.1.0 → 0.1.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/.travis.yml +3 -3
- data/Gemfile +2 -1
- data/README.md +192 -7
- data/Rakefile +1 -1
- data/VERSION +1 -1
- data/examples/vocabulary.rb +23 -0
- data/generators/javaify.rb +131 -0
- data/generators/pythonify.rb +67 -0
- data/generators/rdfxml.rb +152 -44
- data/lib/biointerchange/core.rb +2 -1
- data/lib/biointerchange/exceptions.rb +27 -0
- data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +21 -18
- data/lib/biointerchange/gff3o.rb +495 -0
- data/lib/biointerchange/gvf1o.rb +730 -0
- data/lib/biointerchange/registry.rb +2 -2
- data/lib/biointerchange/sio.rb +10951 -5845
- data/lib/biointerchange/sofa.rb +2171 -1300
- data/spec/exceptions_spec.rb +6 -0
- data/spec/gff3_rdfwriter_spec.rb +7 -1
- data/spec/text_mining_pdfx_xml_reader_spec.rb +6 -0
- data/spec/text_mining_pubannos_json_reader_spec.rb +6 -0
- data/spec/text_mining_rdfwriter_spec.rb +6 -0
- data/supplemental/java/biointerchange/pom.xml +45 -0
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/App.java +58 -0
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/AppSIO.java +49 -0
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java +647 -0
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java +946 -0
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SIO.java +15390 -0
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SOFA.java +2968 -0
- data/supplemental/java/biointerchange/src/test/java/org/biointerchange/AppTest.java +38 -0
- data/supplemental/python/biointerchange/__init__.py +4 -0
- data/supplemental/python/biointerchange/gff3o.py +581 -0
- data/supplemental/python/biointerchange/gvf1o.py +864 -0
- data/supplemental/python/biointerchange/sio.py +11772 -0
- data/supplemental/python/biointerchange/sofa.py +2422 -0
- data/supplemental/python/example.py +19 -0
- data/supplemental/python/setup.py +13 -0
- data/web/about.html +3 -0
- data/web/api.html +219 -0
- data/web/index.html +4 -3
- data/web/ontologies.html +109 -0
- data/web/webservices.html +1 -0
- metadata +144 -117
- data/docs/exceptions_readme.txt +0 -13
- data/lib/biointerchange/gff3.rb +0 -135
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import biointerchange
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from biointerchange import *
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# Get the URI of an ontology term by label:
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GFF3O.seqid()
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# Ambiguous labels will return an array of URIs:
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# "start" can refer to a sub-property of "feature_properties" or "target_properties"
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GFF3O.start()
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# "feature_properties" can be either a datatype or object property
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GFF3O.feature_properties()
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# Use build-in method "is_datatype_property" to resolve ambiguity:
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# (Note: there is exactly one item in the result set, so the selection of the first item is acceptable.)
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feature_properties = filter(lambda uri: GFF3O.is_datatype_property(uri), GFF3O.feature_properties())[0]
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# Use build-in method "with_parent" to pick properties based on their context:
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GFF3O.with_parent(GFF3O.start(), feature_properties)
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from setuptools import setup, find_packages
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setup(
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name = "biointerchange",
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version = "0.1.2",
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author = "Joachim Baran, Geraint Duck",
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description = ( "Wrapper for easy access to GFF3O, GVF1O, SIO and SOFA.",
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"Part of the BioInterchange project." ),
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license = "MIT",
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url = "http://www.biointerchange.org",
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packages = find_packages()
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)
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data/web/about.html
CHANGED
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<div class="nav-collapse collapse">
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<ul class="nav">
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<li><a href="index.html">Home</a></li>
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<li><a href="ontologies.html">Ontologies</a></li>
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<li class="active"><a href="about.html">About</a></li>
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<!--
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<li class="dropdown">
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<div class="span12">
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<h2>About BioInterchange</h2>
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<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>
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<h2>Contact</h2>
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<p><a href="http://joachimbaran.wordpress.com">Joachim Baran</a><br /><i>joachim.baran</i><b>@</b><i>gmail.com</i></p>
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</div>
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data/web/api.html
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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="BioInterchange ontologies page">
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<meta name="author" content="Joachim Baran">
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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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<!-- 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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<!-- 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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<body>
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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="ontologies.html">Ontologies</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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<div class="container">
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<!-- Example row of columns -->
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<div class="row">
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<div class="span12">
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<h2>Application Programming Interface</h2>
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<p>BioInterchange offers Application Programming Interfaces (APIs) for multiple programming languages, but only Ruby is supporting the full range of functinality that BioInterchange provides. For Python and Java, a subset of the Ruby API is available: vocabulary wrappers for convenient access to ontologies used in BioInterchange.</p>
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<h3>Ruby API</h3>
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<h4>The BioInterchange Framework</h4>
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<em>TODO... sorry.</em>
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<h4>Vocabulary Wrappers</h4>
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<h3>Python API</h3>
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<pre>
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sudo easy_install rdflib
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sudo easy_install http://www.biointerchange.org/eggs/biointerchange-0.1.2-py2.7.egg
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</pre>
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Usage example (see also <a href="https://github.com/BioInterchange/BioInterchange/blob/master/supplemental/python/example.py">example.py</a>):
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<pre>
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import biointerchange
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from biointerchange import *
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# Get the URI of an ontology term by label:
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GFF3O.seqid()
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# Ambiguous labels will return an array of URIs:
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# "start" can refer to a sub-property of "feature_properties" or "target_properties"
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GFF3O.start()
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# "feature_properties" can be either a datatype or object property
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GFF3O.feature_properties()
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# Use build-in method "is_datatype_property" to resolve ambiguity:
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# (Note: there is exactly one item in the result set, so the selection of the first item is acceptable.)
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feature_properties = filter(lambda uri: GFF3O.is_datatype_property(uri), GFF3O.feature_properties())[0]
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# Use build-in method "with_parent" to pick properties based on their context:
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GFF3O.with_parent(GFF3O.start(), feature_properties)
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</pre>
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<h3>Java API</h3>
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<pre>
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<repositories>
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<repository>
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<id>biointerchange</id>
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<name>BioInterchange</name>
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<url>http://www.biointerchange.org/artifacts</url>
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</repository>
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</repositories>
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<dependencies>
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<dependency>
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<groupId>org.biointerchange</groupId>
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<artifactId>vocabularies</artifactId>
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<version>0.1.2</version>
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</dependency>
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</dependencies>
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</pre>
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Usage example (see also <a href="https://github.com/BioInterchange/BioInterchange/blob/master/supplemental/java/biointerchange/src/main/java/org/biointerchange/App.java">App.java</a>):
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<pre>
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package org.biointerchange;
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import com.hp.hpl.jena.rdf.model.*;
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import com.hp.hpl.jena.vocabulary.*;
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import org.apache.commons.collections.CollectionUtils;
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import org.apache.commons.collections.Predicate;
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import java.util.Set;
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import org.biointerchange.vocabulary.*;
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/**
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* Demo on how to make use of BioInterchange's vocabulary classes.
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*
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* @author Joachim Baran
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*/
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public class App
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{
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public static void main(String[] args) {
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Resource seqid = GFF3O.seqid();
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System.out.println("'seqid' property:");
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printResource(seqid);
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System.out.println("'start' properties:");
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Set<Resource> start = GFF3O.start();
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for (Resource startSynonym : start)
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printResource(startSynonym);
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System.out.println("'feature_properties' properties:");
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Set<Resource> featureProperties = GFF3O.feature_properties();
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for (Resource featurePropertiesSynonym : featureProperties)
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printResource(featurePropertiesSynonym);
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System.out.println("'feature_properties' properties, which are a datatype property:");
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CollectionUtils.filter(featureProperties, new Predicate() {
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public boolean evaluate(Object o) {
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return GFF3O.isDatatypeProperty((Resource)o);
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}
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});
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for (Resource featurePropertiesSynonym : featureProperties)
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printResource(featurePropertiesSynonym);
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System.out.println("'start' property with parent datatype property 'feature_properties':");
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Set<Resource> startUnderDatatypeFeatureProperties = GFF3O.withParent(start, featureProperties.iterator().next());
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for (Resource startSynonym : startUnderDatatypeFeatureProperties)
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printResource(startSynonym);
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}
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private static void printResource(Resource resource) {
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System.out.println(" " + resource.toString());
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System.out.println(" Namespace: " + resource.getNameSpace());
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System.out.println(" Local name: " + resource.getLocalName());
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System.out.println(" Jena Property (rather than Resource): " + (resource instanceof Property));
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System.out.println(" Ontology class: " + GFF3O.isClass(resource));
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System.out.println(" Ontology object property: " + GFF3O.isObjectProperty(resource));
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System.out.println(" Ontology datatype property: " + GFF3O.isDatatypeProperty(resource));
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}
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}
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</pre>
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<h3>BioInterchange Ontologies</h3>
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Ontologies specifically designed and implemented for BioInterchange are available via their <a href="http://biointerchange.github.com/Ontologies">GitHub project pages</a>.
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<h4>Generic Feature Format Version 3 Ontology</h4>
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<p>The Generic Feature Format Version 3 Ontology (GFF3O) has been closely modelled on the <a href="http://www.sequenceontology.org/resources/gff3.html">Generic Feature Format Version 3</a> (GFF3) specification.</p>
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<p><i>A more detailed description has yet to be written...</i></p>
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<ul>
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<li><a href="http://biointerchange.github.com/Ontologies">Generic Feature Format Version 3 Ontology</a> (GFF3O)</li>
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</ul>
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<h4>Genome Variation Format Version 1 Ontology</h4>
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<p>The Genome Variation Format Version 1 Ontology (GVF1O) has been closely modelled on the <a href="http://www.sequenceontology.org/resources/gvf.html">Genomic Variation Format</a> (GVF) specification.</p>
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<p><i>A more detailed description has yet to be written...</i></p>
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<ul>
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<li><a href="http://biointerchange.github.com/Ontologies">Genome Variation Format Version 1 Ontology</a> (GVF1O)</li>
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</ul>
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<h3>External Ontologies</h3>
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<ul>
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<li><a href="http://xmlns.com/foaf/spec">Friend of a Friend</a> (FOAF)</li>
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<li><a href="http://code.google.com/p/semanticscience/wiki/SIO">Semanticscience Integrated Ontology</a> (SIO)</li>
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<p>© <a href="https://github.com/BioInterchange/BioInterchange#contributors">The BioInterchange Contributors</a> 2012</p>
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|
data/web/index.html
CHANGED
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<h1>BioInterchange</h1>
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<p>Interchange data using the Resource Description Framework (RDF) and let BioInterchange automagically create RDF triples from your TSV, XML, GFF3, GVF and other files. BioInterchange helps you transform your data sets into linked data for sharing and data integration via command line, web-service, or API.</p>
|
|
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|
<!-- <p><a class="btn btn-primary btn-large">Learn more »</a></p> -->
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@@ -77,7 +78,7 @@
|
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|
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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 »</a> --><em>
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|
|
@@ -87,7 +88,7 @@
|
|
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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"
|
|
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|
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<p><a class="btn" href="api.html">View details »</a></p>
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|
<p><a class="btn" href="../doc/BioInterchange.html">View Ruby docs »</a></p>
|
|
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|
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|
|
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|
data/web/ontologies.html
ADDED
|
@@ -0,0 +1,109 @@
|
|
|
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|
+
<!DOCTYPE html>
|
|
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|
+
<html lang="en">
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|
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<head>
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<title>BioInterchange</title>
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|
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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|
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<meta name="description" content="BioInterchange ontologies page">
|
|
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|
+
<meta name="author" content="Joachim Baran">
|
|
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+
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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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|
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|
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|
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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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|
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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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+
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|
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|
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|
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|
|
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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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|
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<li><a href="index.html">Home</a></li>
|
|
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<li class="active"><a href="ontologies.html">Ontologies</a></li>
|
|
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|
+
<li><a href="about.html">About</a></li>
|
|
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|
+
<!--
|
|
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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>
|
|
50
|
+
<li><a href="#">Be</a></li>
|
|
51
|
+
<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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|
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<li><a href="#">API usage information</a></li>
|
|
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|
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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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|
+
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|
|
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|
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|
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|
|
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|
|
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|
|
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|
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<!-- Example row of columns -->
|
|
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|
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|
|
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|
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|
|
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|
+
<h2>Ontologies</h2>
|
|
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|
+
<p>BioInterchange makes use of external ontologies, i.e. ontologies that were developed outside the scope of the BioInterchange project, and ontologies that we designed and implemented for specific file format conversion purposes. We are always happy to hear about ontologies that we should consider incorporating into BioInterchange and contributions of ontologies that permit including more file formats for RDF conversion are most welcome.</p>
|
|
73
|
+
<h3>BioInterchange Ontologies</h3>
|
|
74
|
+
Ontologies specifically designed and implemented for BioInterchange are available via their <a href="http://biointerchange.github.com/Ontologies">GitHub project pages</a>.
|
|
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|
+
<h4>Generic Feature Format Version 3 Ontology</h4>
|
|
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|
+
<p>The Generic Feature Format Version 3 Ontology (GFF3O) has been closely modelled on the <a href="http://www.sequenceontology.org/resources/gff3.html">Generic Feature Format Version 3</a> (GFF3) specification.</p>
|
|
77
|
+
<p><i>A more detailed description has yet to be written...</i></p>
|
|
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|
+
<ul>
|
|
79
|
+
<li><a href="http://biointerchange.github.com/Ontologies">Generic Feature Format Version 3 Ontology</a> (GFF3O)</li>
|
|
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|
+
</ul>
|
|
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|
+
<h4>Genome Variation Format Version 1 Ontology</h4>
|
|
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<p>The Genome Variation Format Version 1 Ontology (GVF1O) has been closely modelled on the <a href="http://www.sequenceontology.org/resources/gvf.html">Genomic Variation Format</a> (GVF) specification.</p>
|
|
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|
+
<p><i>A more detailed description has yet to be written...</i></p>
|
|
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|
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<ul>
|
|
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|
+
<li><a href="http://biointerchange.github.com/Ontologies">Genome Variation Format Version 1 Ontology</a> (GVF1O)</li>
|
|
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|
+
</ul>
|
|
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|
+
<h3>External Ontologies</h3>
|
|
88
|
+
<ul>
|
|
89
|
+
<li><a href="http://xmlns.com/foaf/spec">Friend of a Friend</a> (FOAF)</li>
|
|
90
|
+
<li><a href="http://code.google.com/p/semanticscience/wiki/SIO">Semanticscience Integrated Ontology</a> (SIO)</li>
|
|
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|
|
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|
|
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|
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<footer>
|
|
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|
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<p>© <a href="https://github.com/BioInterchange/BioInterchange#contributors">The BioInterchange Contributors</a> 2012</p>
|
|
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|
|
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|
|
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</div> <!-- /container -->
|
|
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|
|
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|
|
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================================================== -->
|
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|
|
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|
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|
|
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|
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</html>
|
data/web/webservices.html
CHANGED
metadata
CHANGED
|
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|
|
|
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|
-
--- !ruby/object:Gem::Specification
|
|
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|
+
--- !ruby/object:Gem::Specification
|
|
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|
name: biointerchange
|
|
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version: 0.1.2
|
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|
platform: ruby
|
|
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|
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authors:
|
|
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|
+
authors:
|
|
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12
|
- Joachim Baran
|
|
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|
- Kevin B. Cohen
|
|
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|
- Geraint Duck
|
|
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|
- Michel Dumontier
|
|
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|
-
|
|
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|
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- Jin-Dong Kim
|
|
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|
+
autorequire:
|
|
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|
bindir: bin
|
|
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|
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|
|
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|
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|
|
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|
+
|
|
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|
+
date: 2012-11-27 00:00:00 -05:00
|
|
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|
default_executable: biointerchange
|
|
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|
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dependencies:
|
|
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|
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|
|
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|
+
dependencies:
|
|
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|
+
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|
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|
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|
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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requirements:
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|
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segments:
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version: 1.6.4
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type: :runtime
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