simple_bioc 0.0.1 → 0.0.2

data/lib/simple_bioc/relation.rb

@@ -1,14 +1,19 @@
 require 'simple_bioc/node_base'
+module SimpleBioC
+  class Relation < NodeBase
+    attr_accessor :nodes
 
-class Relation < NodeBase
-  attr_accessor :nodes
+    def initialize(parent)
+      super(parent)
+      @nodes = []
+    end
 
-  def initialize(parent)
-    super(parent)
-    @nodes = []
-  end
+    def adjust_ref
+      nodes.each{|n| n.adjust_ref}
+    end
 
-  def adjust_ref
-    nodes.each{|n| n.adjust_ref}
+    def to_c
+      "Relation:#{id}"
+    end
   end
 end

data/lib/simple_bioc/sentence.rb

@@ -1,20 +1,26 @@
-class Sentence
-  attr_accessor :offset, :text, :infons, :annotations, :relations
-  attr_reader :passage
+module SimpleBioC
+  class Sentence
+    attr_accessor :offset, :text, :infons, :annotations, :relations
+    attr_reader :passage
 
-  def initialize(parent)
-    @infons = {}
-    @annotations = []
-    @relations = []
-    @passage = parent
-  end
+    def initialize(parent)
+      @infons = {}
+      @annotations = []
+      @relations = []
+      @passage = parent
+    end
 
-  def find_node(id)
-    (relations+annotations).each{|n| return n if n.id == id}
-    nil
-  end
+    def find_node(id)
+      (relations+annotations).each{|n| return n if n.id == id}
+      nil
+    end
+
+    def each_relation
+      relations.each{|r| yield r}
+    end
 
-  def each_relation
-    relations.each{|r| yield r}
+    def to_c
+      "Sentence @#{offset}: #{text}"
+    end
   end
 end

data/lib/simple_bioc/version.rb

@@ -1,3 +1,3 @@
-module SimpleBioc
-  VERSION = "0.0.1"
+module SimpleBioC
+  VERSION = "0.0.2"
 end

data/samples/print_annotation.rb

@@ -0,0 +1,18 @@
+# print_annotation: print all annotations in the given file
+
+require 'simple_bioc'
+
+if ARGF.argv.size < 1
+  puts "usage: ruby print_annotation.rb {filepath}"
+  exit
+end
+
+collection = SimpleBioC::from_xml(ARGF.argv[0])
+collection.documents.each do |d|
+  d.passages.each do |p|
+    p.sentences.each do |s|
+      s.annotations.each{|a| puts "#{d} #{a}"}
+    end
+    p.annotations.each{|a| puts "#{d} #{a}"}
+  end
+end

data/samples/sample1.rb

@@ -0,0 +1,31 @@
+# Sample1: parse, traverse, manipulate, and build BioC data
+require 'simple_bioc'
+
+# parse BioC file
+collection = SimpleBioC.from_xml("../xml/everything.xml")
+
+# the returned object contains all the information in the BioC file
+# traverse & read information
+collection.documents.each do |document|
+  puts document
+  document.passages.each do |passage|
+    puts passage
+  end
+end
+
+# manipulate 
+doc = SimpleBioC::Document.new(collection)
+doc.id = "23071747"
+doc.infons["journal"] = "PLoS One"
+collection.documents << doc
+
+p = SimpleBioC::Passage.new(doc)
+p.offset = 0
+p.text = "TRIP database 2.0: a manually curated information hub for accessing TRP channel interaction network."
+p.infons["type"] = "title"
+doc.passages << p
+
+
+# build BioC document from data
+xml = SimpleBioC.to_xml(collection)
+puts xml

data/simple_bioc.gemspec

@@ -5,7 +5,7 @@ require 'simple_bioc/version'
 
 Gem::Specification.new do |spec|
   spec.name          = "simple_bioc"
-  spec.version       = SimpleBioc::VERSION
+  spec.version       = SimpleBioC::VERSION
   spec.authors       = ["Dongseop Kwon"]
   spec.email         = ["dongseop@gmail.com"]
   spec.description   = "Simple BioC parser/builder for ruby. BioC is a 'A Minimalist Approach to Interoperability for Biomedical Text Processing' (http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/BioCHome.html)"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: simple_bioc
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
 platform: ruby
 authors:
 - Dongseop Kwon
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-12-04 00:00:00.000000000 Z
+date: 2013-12-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
@@ -94,6 +94,54 @@ files:
 - LICENSE.txt
 - README.md
 - Rakefile
+- html/BioCReader.html
+- html/BioCWriter.html
+- html/README_md.html
+- html/SimpleBioC.html
+- html/SimpleBioC/Annotation.html
+- html/SimpleBioC/Collection.html
+- html/SimpleBioC/Document.html
+- html/SimpleBioC/Location.html
+- html/SimpleBioC/Node.html
+- html/SimpleBioC/NodeBase.html
+- html/SimpleBioC/Passage.html
+- html/SimpleBioC/Relation.html
+- html/SimpleBioC/Sentence.html
+- html/created.rid
+- html/images/add.png
+- html/images/arrow_up.png
+- html/images/brick.png
+- html/images/brick_link.png
+- html/images/bug.png
+- html/images/bullet_black.png
+- html/images/bullet_toggle_minus.png
+- html/images/bullet_toggle_plus.png
+- html/images/date.png
+- html/images/delete.png
+- html/images/find.png
+- html/images/loadingAnimation.gif
+- html/images/macFFBgHack.png
+- html/images/package.png
+- html/images/page_green.png
+- html/images/page_white_text.png
+- html/images/page_white_width.png
+- html/images/plugin.png
+- html/images/ruby.png
+- html/images/tag_blue.png
+- html/images/tag_green.png
+- html/images/transparent.png
+- html/images/wrench.png
+- html/images/wrench_orange.png
+- html/images/zoom.png
+- html/index.html
+- html/js/darkfish.js
+- html/js/jquery.js
+- html/js/navigation.js
+- html/js/search.js
+- html/js/search_index.js
+- html/js/searcher.js
+- html/rdoc.css
+- html/table_of_contents.html
 - lib/simple_bioc.rb
 - lib/simple_bioc/annotation.rb
 - lib/simple_bioc/bioc_reader.rb
@@ -107,6 +155,8 @@ files:
 - lib/simple_bioc/relation.rb
 - lib/simple_bioc/sentence.rb
 - lib/simple_bioc/version.rb
+- samples/print_annotation.rb
+- samples/sample1.rb
 - simple_bioc.gemspec
 - spec/simple_bioc_spec.rb
 - xml/BioC.dtd