biointerchange 0.1.2 → 0.1.3

data/web/api.html

@@ -71,16 +71,43 @@
           <h2>Application Programming Interface</h2>
           <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>
           <h3>Ruby API</h3>
+            <p>The Ruby API &mdash; including vocabulary wrapper classes &mdash; are available via <a href="http://rubygems.org/gems/biointerchange">RubyGems</a>:</p>
+<pre>
+sudo gem install biointerchange
+</pre>
             <h4>The BioInterchange Framework</h4>
               <em>TODO... sorry.</em>
             <h4>Vocabulary Wrappers</h4>
+              <p>Usage example (see also <a href="https://github.com/BioInterchange/BioInterchange/blob/master/examples/vocabulary.rb">vocabulary.rb</a>):</p>
+<pre>
+require 'rubygems'
+require 'biointerchange'
 
+include BioInterchange
+
+# Get the URI of an ontology term by label:
+GFF3O.seqid()
+
+# Ambiguous labels will return an array of URIs:
+# "start" can refer to a sub-property of "feature_properties" or "target_properties"
+GFF3O.start()
+# "feature_properties" can be either a datatype or object property
+GFF3O.feature_properties()
+
+# Use build-in method "is_datatype_property" to resolve ambiguity:
+# (Note: there is exactly one item in the result set, so the selection of the first item is acceptable.)
+feature_properties = GFF3O.feature_properties().select { |uri| GFF3O.is_datatype_property(uri) }[0]
+
+# Use build-in method "with_parent" to pick properties based on their context:
+GFF3O.with_parent(GFF3O.start(), feature_properties)
+</pre>
           <h3>Python API</h3>
+            <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
 </pre>
-Usage example (see also <a href="https://github.com/BioInterchange/BioInterchange/blob/master/supplemental/python/example.py">example.py</a>):
+            <p>Usage example (see also <a href="https://github.com/BioInterchange/BioInterchange/blob/master/supplemental/python/example.py">example.py</a>):</p>
 <pre>
 import biointerchange
 from biointerchange import *
@@ -102,6 +129,7 @@ feature_properties = filter(lambda uri: GFF3O.is_datatype_property(uri), GFF3O.f
 GFF3O.with_parent(GFF3O.start(), feature_properties)
 </pre>
           <h3>Java API</h3>
+            <p>Vocabulary wrappers in Java are available as a Maven artifact. Add the following repository and dependency setting to your Project Object Model (POM) file:</p>
 <pre>
 &lt;repositories&gt;
   &lt;repository&gt;
@@ -119,7 +147,7 @@ GFF3O.with_parent(GFF3O.start(), feature_properties)
   &lt;/dependency&gt;
 &lt;/dependencies&gt;
 </pre>
-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>):
+            <p>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>):</p>
 <pre>
 package org.biointerchange;
 
@@ -180,27 +208,6 @@ public class App
     }
 }
 </pre>
-          <h3>BioInterchange Ontologies</h3>
-          Ontologies specifically designed and implemented for BioInterchange are available via their <a href="http://biointerchange.github.com/Ontologies">GitHub project pages</a>.
-          <h4>Generic Feature Format Version 3 Ontology</h4>
-          <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>
-          <p><i>A more detailed description has yet to be written...</i></p>
-          <ul>
-            <li><a href="http://biointerchange.github.com/Ontologies">Generic Feature Format Version 3 Ontology</a> (GFF3O)</li>
-          </ul>
-          <h4>Genome Variation Format Version 1 Ontology</h4>
-          <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>
-          <p><i>A more detailed description has yet to be written...</i></p>
-          <ul>
-            <li><a href="http://biointerchange.github.com/Ontologies">Genome Variation Format Version 1 Ontology</a> (GVF1O)</li>
-          </ul>
-          <h3>External Ontologies</h3>
-          <ul>
-            <li><a href="http://xmlns.com/foaf/spec">Friend of a Friend</a> (FOAF)</li>
-            <li><a href="http://code.google.com/p/semanticscience/wiki/SIO">Semanticscience Integrated Ontology</a> (SIO)</li>
-          </ul>
-        </div>
-      </div>
 
       <hr>
 

metadata

@@ -1,14 +1,10 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: biointerchange
-version: !ruby/object:Gem::Version 
-  prerelease: false
-  segments: 
-  - 0
-  - 1
-  - 2
-  version: 0.1.2
+version: !ruby/object:Gem::Version
+  version: 0.1.3
+  prerelease: 
 platform: ruby
-authors: 
+authors:
 - Joachim Baran
 - Kevin B. Cohen
 - Geraint Duck
@@ -17,146 +13,162 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2012-11-27 00:00:00 -05:00
-default_executable: biointerchange
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2013-01-05 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: rdf
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 0
-        - 3
-        - 4
-        - 1
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 0.3.4.1
   type: :runtime
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: json
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 1
-        - 6
-        - 4
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.3.4.1
+- !ruby/object:Gem::Dependency
+  name: json
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 1.6.4
   type: :runtime
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: getopt
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 1
-        - 4
-        - 1
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.6.4
+- !ruby/object:Gem::Dependency
+  name: getopt
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 1.4.1
   type: :runtime
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  name: addressable
   prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 2
-        - 3
-        - 2
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.1
+- !ruby/object:Gem::Dependency
+  name: addressable
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 2.3.2
   type: :runtime
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
-  name: rspec
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
-    requirements: 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.3.2
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 2
-        - 8
-        - 0
+      - !ruby/object:Gem::Version
         version: 2.8.0
   type: :development
-  version_requirements: *id005
-- !ruby/object:Gem::Dependency 
-  name: bundler
   prerelease: false
-  requirement: &id006 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 1
-        - 1
-        - 5
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 1.1.5
   type: :development
-  version_requirements: *id006
-- !ruby/object:Gem::Dependency 
-  name: jeweler
   prerelease: false
-  requirement: &id007 !ruby/object:Gem::Requirement 
-    requirements: 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.1.5
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 1
-        - 8
-        - 4
+      - !ruby/object:Gem::Version
         version: 1.8.4
   type: :development
-  version_requirements: *id007
-- !ruby/object:Gem::Dependency 
-  name: bio
   prerelease: false
-  requirement: &id008 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 1
-        - 4
-        - 2
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 1.4.2
   type: :development
-  version_requirements: *id008
-- !ruby/object:Gem::Dependency 
-  name: rdoc
   prerelease: false
-  requirement: &id009 !ruby/object:Gem::Requirement 
-    requirements: 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 3
-        - 12
-        version: "3.12"
+      - !ruby/object:Gem::Version
+        version: '3.12'
   type: :development
-  version_requirements: *id009
-description: BioInterchange is a Ruby gem, command-line tool, web-service for turning heterogeneous data formats such as JSON, XML, GFF3, etc., into RDF."
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+description: BioInterchange is a Ruby gem, command-line tool, web-service for turning
+  heterogeneous data formats such as JSON, XML, GFF3, etc., into RDF."
 email: joachim.baran@gmail.com
-executables: 
+executables:
 - biointerchange
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE.txt
 - README.md
-files: 
+files:
 - .document
 - .rspec
 - .travis.yml
@@ -167,8 +179,12 @@ files:
 - VERSION
 - bin/biointerchange
 - examples/BovineGenomeChrX.gff3.gz
+- examples/chromosome_BF.gff
+- examples/estd176_Banerjee_et_al_2011.2012-11-29.NCBI36.gvf
 - examples/gb-2007-8-3-R40.xml
-- examples/pubannotation.json
+- examples/pubannotation.10096561.json
+- examples/pubannotation.10096561.json.old
+- examples/pubannotation.2626671.json
 - examples/vocabulary.rb
 - generators/javaify.rb
 - generators/pythonify.rb
@@ -178,8 +194,13 @@ files:
 - lib/biointerchange/exceptions.rb
 - lib/biointerchange/genomics/gff3_feature.rb
 - lib/biointerchange/genomics/gff3_feature_set.rb
+- lib/biointerchange/genomics/gff3_pragmas.rb
 - lib/biointerchange/genomics/gff3_rdf_ntriples.rb
 - lib/biointerchange/genomics/gff3_reader.rb
+- lib/biointerchange/genomics/gvf_feature.rb
+- lib/biointerchange/genomics/gvf_feature_set.rb
+- lib/biointerchange/genomics/gvf_pragmas.rb
+- lib/biointerchange/genomics/gvf_reader.rb
 - lib/biointerchange/gff3o.rb
 - lib/biointerchange/gvf1o.rb
 - lib/biointerchange/reader.rb
@@ -187,6 +208,7 @@ files:
 - lib/biointerchange/sio.rb
 - lib/biointerchange/sofa.rb
 - lib/biointerchange/textmining/content.rb
+- lib/biointerchange/textmining/content_connection.rb
 - lib/biointerchange/textmining/document.rb
 - lib/biointerchange/textmining/pdfx_xml_reader.rb
 - lib/biointerchange/textmining/process.rb
@@ -196,6 +218,7 @@ files:
 - lib/biointerchange/writer.rb
 - spec/exceptions_spec.rb
 - spec/gff3_rdfwriter_spec.rb
+- spec/gvf_rdfwriter_spec.rb
 - spec/text_mining_pdfx_xml_reader_spec.rb
 - spec/text_mining_pubannos_json_reader_spec.rb
 - spec/text_mining_rdfwriter_spec.rb
@@ -233,35 +256,30 @@ files:
 - web/ontologies.html
 - web/service/rdfizer.fcgi
 - web/webservices.html
-has_rdoc: true
 homepage: http://www.biointerchange.org
-licenses: 
+licenses:
 - MIT
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      segments: 
-      - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      segments: 
-      - 0
-      version: "0"
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.3.6
+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
-summary: An open source framework for transforming heterogeneous data formats into RDF.
+summary: An open source framework for transforming heterogeneous data formats into
+  RDF.
 test_files: []
-