simple_bioc 0.0.22 → 0.0.23

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: e2d799ecd6e81c5e5c2c615b9d264058c0906357
+  metadata.gz: 7d747ee4c88ad72429a1f73385d8a25d2c297260
+  data.tar.gz: 15d2973d3bfd51bdce07d67830c336755ef843d3
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+  data.tar.gz: 7743f9e0f76f5eb8935e0c36abd04cebfe2f3a79363b5b662344cf05e68397a0fa2426d61591796dbc407758145cf9a0838fb4ceac9392a2ad32a9ae15d1a151

data/README.md

@@ -42,7 +42,15 @@ Traverse & Manipulate Data. Data structure are almost the same as the DTD. Pleas
 Build XML text from data
 
     puts SimpleBioC::to_xml(collection)
-  
+
+Convert PubAnnotation JSON from data
+
+    puts SimpleBioC::to_pubann(collection, {
+      sourcedb: 'PubMed', 
+      target: 'http://pubannotation.org/docs/sourcedb/PubMed/sourceid/18034444', 
+      project: 'Ab3P-abbreviations'
+    }))
+
 ## Options
 
 ### Specify set of <document>s to parse

data/lib/simple_bioc.rb

@@ -2,6 +2,7 @@
 require "simple_bioc/version"
 require "simple_bioc/bioc_reader"
 require "simple_bioc/bioc_writer"
+require "simple_bioc/pub_ann_writer"
 
 # SimpleBioC main library
 module SimpleBioC
@@ -80,4 +81,8 @@ module SimpleBioC
   def to_xml(collection, options = {})
     BioCWriter.write(collection, options)
   end
+
+  def to_pubann(collection, options = {})
+    PubAnnWriter.write(collection, options)
+  end
 end

data/lib/simple_bioc/bioc_writer.rb

@@ -1,5 +1,4 @@
 require 'nokogiri'
-require 'json_builder'
 
 Dir[File.dirname(__FILE__) + '/*.rb'].each {|file| require file }
 

data/lib/simple_bioc/document.rb

@@ -34,5 +34,22 @@ module SimpleBioC
     def to_s
       "Document:#{@id}"
     end
+
+    def all_texts
+      @passages.map{|p| p.all_texts}.join(" ")
+    end
+
+    def all_annotations
+      ret = []
+      @passages.each{|p| p.all_annotations(ret)}
+      ret
+    end
+
+    def all_relations
+      ret = []
+      @relations.each{|r| ret << r}
+      @passages.each{|p| p.all_relations(ret)}
+      ret
+    end
   end
 end

data/lib/simple_bioc/passage.rb

@@ -28,5 +28,20 @@ module SimpleBioC
       @relations.each{|r| yield r}
       @sentences.each{|s| s.each_relation{|r| yield r}}
     end
+
+    def all_texts
+      return text unless self.text.nil?
+      @sentences.map{|s| s.text}.join(" ")
+    end
+
+    def all_annotations(ret)
+      @annotations.each{|a| ret << a}
+      @sentences.each{|s| s.all_annotations(ret)}
+    end
+
+    def all_relations(ret)
+      @relations.each{|r| ret << r}
+      @sentences.each{|s| s.all_relations(ret)}
+    end
   end
 end

data/lib/simple_bioc/pub_ann_writer.rb

@@ -0,0 +1,49 @@
+require 'jbuilder'
+
+Dir[File.dirname(__FILE__) + '/*.rb'].each {|file| require file }
+
+module PubAnnWriter
+  module_function
+  def write(collection, options = {})
+    Jbuilder.new do |json|
+      write_collection(json, collection, options)
+    end.target!
+  end
+
+  def write_collection(json, collection, options)
+    json.array! collection.documents do |d|
+      write_document(json, d, options)
+    end
+  end
+
+  def write_document(json, document, options)
+    json.sourceid document.id
+    json.sourcedb options[:sourcedb] || ""
+    json.project options[:project] || ""
+    json.target options[:target] || ""
+    json.text document.all_texts
+    json.denotations document.all_annotations do |a|
+      a.locations.each do |l|
+        json.span do 
+          json.begin l.offset
+          json.end l.offset + l.length
+        end
+        json.obj a.infons.map{|k,v| v}.join(",")
+        json.id a.id unless a.id.nil?
+      end
+    end
+    json.relations document.all_relations do |r|
+      json.pred r.infons.map{|k,v| v}.join(",")
+      first = true
+      r.nodes.each do |n|
+        if first 
+          json.obj n.refid
+          first = false
+        else
+          json.subj n.refid
+        end
+      end
+      json.id r.id unless r.id.nil?
+    end
+  end
+end

data/lib/simple_bioc/sentence.rb

@@ -19,6 +19,14 @@ module SimpleBioC
       @relations.each{|r| yield r}
     end
 
+    def all_annotations(ret)
+      @annotations.each{|a| ret << a}
+    end
+
+    def all_relations(ret)
+      @relations.each{|r| ret << r}
+    end
+
     def to_c
       "Sentence @#{@offset}: #{@text}"
     end

data/lib/simple_bioc/version.rb

@@ -1,3 +1,3 @@
 module SimpleBioC
-  VERSION = "0.0.22"
+  VERSION = "0.0.23"
 end

data/samples/convert_pubann.rb

@@ -0,0 +1,15 @@
+# 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])
+puts SimpleBioC::to_xml(collection, {
+  sourcedb: 'PubMed', 
+  target: 'http://pubannotation.org/docs/sourcedb/PubMed/sourceid/18034444', 
+  project: 'Ab3P-abbreviations'
+})

data/simple_bioc.gemspec

@@ -19,11 +19,13 @@ Gem::Specification.new do |spec|
   spec.require_paths = ["lib"]
 
   spec.add_dependency "nokogiri", "~> 1.6"
-  spec.add_dependency "json_builder", "~> 3.1"
+  spec.add_dependency "jbuilder", "~> 2.3"
 
   spec.add_development_dependency "bundler", "~> 1.3"
   spec.add_development_dependency "rake", "~> 10.3"
   spec.add_development_dependency "yard", "~> 0.8"
   spec.add_development_dependency "rspec", "~> 3.2"
   spec.add_development_dependency("test_xml", ["~> 0.1"])
+  spec.add_development_dependency "json-compare", "~> 0.1"
+  spec.add_development_dependency "yajl-ruby", "~> 1.2"
 end

data/spec/pubann_spec.rb

@@ -0,0 +1,16 @@
+require 'simple_bioc'
+require 'yajl'
+require 'json-compare'
+require 'test_xml/spec'
+
+describe "PubAnn" do
+  it "should convert file to pubann JSON" do
+    col1 = SimpleBioC.from_xml("./xml/pubann/18034444.xml")
+    output = SimpleBioC.to_pubann(col1, {
+      sourcedb: 'PubMed', 
+      target: 'http://pubannotation.org/docs/sourcedb/PubMed/sourceid/18034444', 
+      project: 'Ab3P-abbreviations'
+    })
+    puts output
+  end 
+end

data/xml/pubann/18034444.json

@@ -0,0 +1 @@
+{"denotations": [{"span": {"begin": 477, "end": 480}, "obj": "ABBR", "id": "SF0"}, {"span": {"begin": 461, "end": 475}, "obj": "ABBR", "id": "LF0"}, {"span": {"begin": 664, "end": 667}, "obj": "ABBR", "id": "SF1"}, {"span": {"begin": 648, "end": 662}, "obj": "ABBR", "id": "LF1"}, {"span": {"begin": 693, "end": 696}, "obj": "ABBR", "id": "SF2"}, {"span": {"begin": 673, "end": 691}, "obj": "ABBR", "id": "LF2"}, {"span": {"begin": 777, "end": 782}, "obj": "ABBR", "id": "SF3"}, {"span": {"begin": 784, "end": 832}, "obj": "ABBR", "id": "LF3"}, {"span": {"begin": 1351, "end": 1355}, "obj": "ABBR", "id": "SF4"}, {"span": {"begin": 1357, "end": 1389}, "obj": "ABBR", "id": "LF4"}], "target": "http://pubannotation.org/docs/sourcedb/PubMed/sourceid/18034444", "sourceid": "18034444", "sourcedb": "PubMed", "relations": [{"pred": "ShortForm", "obj": "SF0", "subj": "LF0", "id": "R0"}, {"pred": "ShortForm", "obj": "SF1", "subj": "LF1", "id": "R1"}, {"pred": "ShortForm", "obj": "SF2", "subj": "LF2", "id": "R2"}, {"pred": "ShortForm", "obj": "SF3", "subj": "LF3", "id": "R3"}, {"pred": "ShortForm", "obj": "SF4", "subj": "LF4", "id": "R4"}], "project": "Ab3P-abbreviations", "text": "The use of diolefin-containing rhodium precatalysts leads to induction periods in asymmetric hydrogenation of prochiral olefins. Consequently, the reaction rate increases in the beginning. The induction period is caused by the fact that some of the catalyst is blocked by the diolefin and thus not available for hydrogenation of the prochiral olefin. Therefore, the maximum reaction rate cannot be reached initially. Due to the relatively slow hydrogenation of cyclooctadiene (cod) the share of active catalysts increases at first, and this leads to typical induction periods. The aim of this work is to quantify the hydrogenation of the diolefins cyclooctadiene (cod) and norborna-2,5-diene (nbd) for cationic complexes of the type [Rh(ligand)(diolefin)]BF(4) for the ligands Binap (1,1'-binaphthalene-2,2'-diylbis(phenylphosphine)), Me-Duphos (1,2-bis(2,5-dimethylphospholano)benzene, and Catasium in the solvents methanol, THF, and propylene carbonate. Furthermore, an approach is presented to determine the desired rate constant and the resulting respective pre-hydrogenation time from stoichiometric hydrogenations of the diolefin complexes via UV/Vis spectroscopy. This method is especially useful for very slow diolefin hydrogenations (e.g., cod hydrogenation with the ligands Me-Duphos, Et-Duphos (1,2-bis(2,5-diethylphospholano)benzene), and dppe (1,2-bis(diphenylphosphino)ethane)."}

data/xml/pubann/18034444.xml

@@ -0,0 +1,104 @@
+<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE collection SYSTEM 'BioC.dtd'>
+<collection>
+  <source>Ab3P gold standard</source>
+  <date>20080529</date>
+  <key>Ab3P_gold.key</key>
+  <document>
+    <id>18034444</id>
+    <passage>
+      <infon key="type">title</infon>
+      <offset>0</offset>
+      <text>Rhodium-Complex-Catalyzed Asymmetric Hydrogenation: Transformation of Precatalysts into Active Species.</text>
+    </passage>
+    <passage>
+      <infon key="type">abstract</infon>
+      <offset>104</offset>
+      <text>The use of diolefin-containing rhodium precatalysts leads to induction periods in asymmetric hydrogenation of prochiral olefins. Consequently, the reaction rate increases in the beginning. The induction period is caused by the fact that some of the catalyst is blocked by the diolefin and thus not available for hydrogenation of the prochiral olefin. Therefore, the maximum reaction rate cannot be reached initially. Due to the relatively slow hydrogenation of cyclooctadiene (cod) the share of active catalysts increases at first, and this leads to typical induction periods. The aim of this work is to quantify the hydrogenation of the diolefins cyclooctadiene (cod) and norborna-2,5-diene (nbd) for cationic complexes of the type [Rh(ligand)(diolefin)]BF(4) for the ligands Binap (1,1'-binaphthalene-2,2'-diylbis(phenylphosphine)), Me-Duphos (1,2-bis(2,5-dimethylphospholano)benzene, and Catasium in the solvents methanol, THF, and propylene carbonate. Furthermore, an approach is presented to determine the desired rate constant and the resulting respective pre-hydrogenation time from stoichiometric hydrogenations of the diolefin complexes via UV/Vis spectroscopy. This method is especially useful for very slow diolefin hydrogenations (e.g., cod hydrogenation with the ligands Me-Duphos, Et-Duphos (1,2-bis(2,5-diethylphospholano)benzene), and dppe (1,2-bis(diphenylphosphino)ethane).</text>
+      <annotation id="SF0">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">ShortForm</infon>
+        <location offset="581" length="3"/>
+        <text>cod</text>
+      </annotation>
+      <annotation id="LF0">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">LongForm</infon>
+        <location offset="565" length="14"/>
+        <text>cyclooctadiene</text>
+      </annotation>
+      <annotation id="SF1">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">ShortForm</infon>
+        <location offset="768" length="3"/>
+        <text>cod</text>
+      </annotation>
+      <annotation id="LF1">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">LongForm</infon>
+        <location offset="752" length="14"/>
+        <text>cyclooctadiene</text>
+      </annotation>
+      <annotation id="SF2">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">ShortForm</infon>
+        <location offset="797" length="3"/>
+        <text>nbd</text>
+      </annotation>
+      <annotation id="LF2">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">LongForm</infon>
+        <location offset="777" length="18"/>
+        <text>norborna-2,5-diene</text>
+      </annotation>
+      <annotation id="SF3">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">ShortForm</infon>
+        <location offset="881" length="5"/>
+        <text>Binap</text>
+      </annotation>
+      <annotation id="LF3">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">LongForm</infon>
+        <location offset="888" length="48"/>
+        <text>1,1'-binaphthalene-2,2'-diylbis(phenylphosphine)</text>
+      </annotation>
+      <annotation id="SF4">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">ShortForm</infon>
+        <location offset="1455" length="4"/>
+        <text>dppe</text>
+      </annotation>
+      <annotation id="LF4">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">LongForm</infon>
+        <location offset="1461" length="32"/>
+        <text>1,2-bis(diphenylphosphino)ethane</text>
+      </annotation>
+      <relation id="R0">
+        <infon key="type">ABBR</infon>
+        <node refid="LF0" role="LongForm"/>
+        <node refid="SF0" role="ShortForm"/>
+      </relation>
+      <relation id="R1">
+        <infon key="type">ABBR</infon>
+        <node refid="LF1" role="LongForm"/>
+        <node refid="SF1" role="ShortForm"/>
+      </relation>
+      <relation id="R2">
+        <infon key="type">ABBR</infon>
+        <node refid="LF2" role="LongForm"/>
+        <node refid="SF2" role="ShortForm"/>
+      </relation>
+      <relation id="R3">
+        <infon key="type">ABBR</infon>
+        <node refid="LF3" role="LongForm"/>
+        <node refid="SF3" role="ShortForm"/>
+      </relation>
+      <relation id="R4">
+        <infon key="type">ABBR</infon>
+        <node refid="LF4" role="LongForm"/>
+        <node refid="SF4" role="ShortForm"/>
+      </relation>
+    </passage>
+  </document>
+</collection>

data/xml/pubann/18045413.json

@@ -0,0 +1 @@
+{"denotations": [{"span": {"begin": 59, "end": 62}, "obj": "ABBR", "id": "SF0"}, {"span": {"begin": 44, "end": 57}, "obj": "ABBR", "id": "LF0"}, {"span": {"begin": 86, "end": 89}, "obj": "ABBR", "id": "SF1"}, {"span": {"begin": 64, "end": 84}, "obj": "ABBR", "id": "LF1"}, {"span": {"begin": 867, "end": 872}, "obj": "ABBR", "id": "SF2"}, {"span": {"begin": 848, "end": 865}, "obj": "ABBR", "id": "LF2"}, {"span": {"begin": 928, "end": 936}, "obj": "ABBR", "id": "SF3"}, {"span": {"begin": 909, "end": 926}, "obj": "ABBR", "id": "LF3"}], "target": "http://pubannotation.org/docs/sourcedb/PubMed/sourceid/18045413", "sourceid": "18045413", "sourcedb": "PubMed", "relations": [{"pred": "ShortForm", "obj": "SF0", "subj": "LF0", "id": "R0"}, {"pred": "ShortForm", "obj": "SF1", "subj": "LF1", "id": "R1"}, {"pred": "ShortForm", "obj": "SF2", "subj": "LF2", "id": "R2"}, {"pred": "ShortForm", "obj": "SF3", "subj": "LF3", "id": "R3"}], "project": "Ab3P-abbreviations", "text": "Aim: To evaluate the ability of high-energy ultraviolet A (UVA) light-emitting diode (LED) to inactivate bacteria in water and investigate the inactivating mechanism of UVA irradiation. Methods and Results: We developed a new disinfection device equipped with high-energy UVA-LED. Inactivation of bacteria was determined by colony-forming assay. Vibrio parahaemolyticus, enteropathogenic Escherichia coli, Staphylococcus aureus and Escherichia coli DH5alpha were reduced by greater than 5-log(10) stages within 75 min at 315 J cm(-2) of UVA. Salmonella enteritidis was reduced greater than 4-log(10) stages within 160 min at 672 J cm(-2) of UVA. The formation of 8-hydroxy-2'-deoxyguanosine in UVA-LED irradiated bacteria was 2.6-fold higher than that of UVC-irradiated bacteria at the same inactivation level. Addition of mannitol, a scavenger of hydroxyl radicals (OH( )), or catalase, an enzyme scavenging hydrogen peroxide (H(2)O(2)) to bacterial suspensions significantly suppressed disinfection effect of UVA-LED. Conclusion: This disinfection system has enough ability to inactivate bacteria and OH( ) and H(2)O(2) participates in the disinfection mechanism of UVA irradiation. Significance and Impact of the Study: We newly developed UVA irradiation system and found that UVA alone was able to disinfect the water efficiently. This will become a useful disinfection system."}

data/xml/pubann/18045413.xml

@@ -0,0 +1,87 @@
+<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE collection SYSTEM 'BioC.dtd'>
+<collection>
+  <source>Ab3P gold standard</source>
+  <date>20080529</date>
+  <key>Ab3P_gold.key</key>
+  <document>
+    <id>18045413</id>
+    <passage>
+      <infon key="type">title</infon>
+      <offset>0</offset>
+      <text>New water disinfection system using UVA light-emitting diodes.</text>
+    </passage>
+    <passage>
+      <infon key="type">abstract</infon>
+      <offset>63</offset>
+      <text>Aim: To evaluate the ability of high-energy ultraviolet A (UVA) light-emitting diode (LED) to inactivate bacteria in water and investigate the inactivating mechanism of UVA irradiation. Methods and Results: We developed a new disinfection device equipped with high-energy UVA-LED. Inactivation of bacteria was determined by colony-forming assay. Vibrio parahaemolyticus, enteropathogenic Escherichia coli, Staphylococcus aureus and Escherichia coli DH5alpha were reduced by greater than 5-log(10) stages within 75 min at 315 J cm(-2) of UVA. Salmonella enteritidis was reduced greater than 4-log(10) stages within 160 min at 672 J cm(-2) of UVA. The formation of 8-hydroxy-2'-deoxyguanosine in UVA-LED irradiated bacteria was 2.6-fold higher than that of UVC-irradiated bacteria at the same inactivation level. Addition of mannitol, a scavenger of hydroxyl radicals (OH( )), or catalase, an enzyme scavenging hydrogen peroxide (H(2)O(2)) to bacterial suspensions significantly suppressed disinfection effect of UVA-LED. Conclusion: This disinfection system has enough ability to inactivate bacteria and OH( ) and H(2)O(2) participates in the disinfection mechanism of UVA irradiation. Significance and Impact of the Study: We newly developed UVA irradiation system and found that UVA alone was able to disinfect the water efficiently. This will become a useful disinfection system.</text>
+      <annotation id="SF0">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">ShortForm</infon>
+        <location offset="122" length="3"/>
+        <text>UVA</text>
+      </annotation>
+      <annotation id="LF0">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">LongForm</infon>
+        <location offset="107" length="13"/>
+        <text>ultraviolet A</text>
+      </annotation>
+      <annotation id="SF1">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">ShortForm</infon>
+        <location offset="149" length="3"/>
+        <text>LED</text>
+      </annotation>
+      <annotation id="LF1">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">LongForm</infon>
+        <location offset="127" length="20"/>
+        <text>light-emitting diode</text>
+      </annotation>
+      <annotation id="SF2">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">ShortForm</infon>
+        <location offset="930" length="5"/>
+        <text>OH( )</text>
+      </annotation>
+      <annotation id="LF2">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">LongForm</infon>
+        <location offset="911" length="17"/>
+        <text>hydroxyl radicals</text>
+      </annotation>
+      <annotation id="SF3">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">ShortForm</infon>
+        <location offset="991" length="8"/>
+        <text>H(2)O(2)</text>
+      </annotation>
+      <annotation id="LF3">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">LongForm</infon>
+        <location offset="972" length="17"/>
+        <text>hydrogen peroxide</text>
+      </annotation>
+      <relation id="R0">
+        <infon key="type">ABBR</infon>
+        <node refid="LF0" role="LongForm"/>
+        <node refid="SF0" role="ShortForm"/>
+      </relation>
+      <relation id="R1">
+        <infon key="type">ABBR</infon>
+        <node refid="LF1" role="LongForm"/>
+        <node refid="SF1" role="ShortForm"/>
+      </relation>
+      <relation id="R2">
+        <infon key="type">ABBR</infon>
+        <node refid="LF2" role="LongForm"/>
+        <node refid="SF2" role="ShortForm"/>
+      </relation>
+      <relation id="R3">
+        <infon key="type">ABBR</infon>
+        <node refid="LF3" role="LongForm"/>
+        <node refid="SF3" role="ShortForm"/>
+      </relation>
+    </passage>
+  </document>
+</collection>

data/xml/pubann/18060712.json

@@ -0,0 +1 @@
+{"denotations": [{"span": {"begin": 30, "end": 34}, "obj": "ABBR", "id": "SF0"}, {"span": {"begin": 14, "end": 28}, "obj": "ABBR", "id": "LF0"}, {"span": {"begin": 342, "end": 346}, "obj": "ABBR", "id": "SF1"}, {"span": {"begin": 312, "end": 340}, "obj": "ABBR", "id": "LF1"}, {"span": {"begin": 641, "end": 645}, "obj": "ABBR", "id": "SF2"}, {"span": {"begin": 599, "end": 639}, "obj": "ABBR", "id": "LF2"}], "target": "http://pubannotation.org/docs/sourcedb/PubMed/sourceid/18060712", "sourceid": "18060712", "sourcedb": "PubMed", "relations": [{"pred": "ShortForm", "obj": "SF0", "subj": "LF0", "id": "R0"}, {"pred": "ShortForm", "obj": "SF1", "subj": "LF1", "id": "R1"}, {"pred": "ShortForm", "obj": "SF2", "subj": "LF2", "id": "R2"}], "project": "Ab3P-abbreviations", "text": "Resting-state functional MRI (fMRI) could be an advantageous choice for clinical applications by virtue of its clinical convenience and non-invasiveness. Without explicit stimulus, resting-state brain activity patterns cannot be obtained using any model-driven method. In this study, we advanced a measure named resting-state activity index (RSAI) to evaluate the resting-state brain activities. Using RSAI, we first investigated the resting-state brain activity patterns in normal adolescents to test the validity of this RSAI measure. Then we compared the resting-state brain activity patterns of Attention deficit hyperactivity disorder (ADHD) patients to those of their matched controls. According to the resultant brain activity patterns, we suggest that RSAI could be an applicable measure to evaluate resting-state brain activities. As compared to the controls, the ADHD patients exhibited more significant resting-state activities in basic sensory and sensory-related cortices. This finding was in accordance with ADHD symptoms of inattention."}

data/xml/pubann/18060712.xml

@@ -0,0 +1,70 @@
+<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE collection SYSTEM 'BioC.dtd'>
+<collection>
+  <source>Ab3P gold standard</source>
+  <date>20080529</date>
+  <key>Ab3P_gold.key</key>
+  <document>
+    <id>18060712</id>
+    <passage>
+      <infon key="type">title</infon>
+      <offset>0</offset>
+      <text>Enhanced resting-state brain activities in ADHD patients: A fMRI study.</text>
+    </passage>
+    <passage>
+      <infon key="type">abstract</infon>
+      <offset>72</offset>
+      <text>Resting-state functional MRI (fMRI) could be an advantageous choice for clinical applications by virtue of its clinical convenience and non-invasiveness. Without explicit stimulus, resting-state brain activity patterns cannot be obtained using any model-driven method. In this study, we advanced a measure named resting-state activity index (RSAI) to evaluate the resting-state brain activities. Using RSAI, we first investigated the resting-state brain activity patterns in normal adolescents to test the validity of this RSAI measure. Then we compared the resting-state brain activity patterns of Attention deficit hyperactivity disorder (ADHD) patients to those of their matched controls. According to the resultant brain activity patterns, we suggest that RSAI could be an applicable measure to evaluate resting-state brain activities. As compared to the controls, the ADHD patients exhibited more significant resting-state activities in basic sensory and sensory-related cortices. This finding was in accordance with ADHD symptoms of inattention.</text>
+      <annotation id="SF0">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">ShortForm</infon>
+        <location offset="102" length="4"/>
+        <text>fMRI</text>
+      </annotation>
+      <annotation id="LF0">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">LongForm</infon>
+        <location offset="86" length="14"/>
+        <text>functional MRI</text>
+      </annotation>
+      <annotation id="SF1">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">ShortForm</infon>
+        <location offset="414" length="4"/>
+        <text>RSAI</text>
+      </annotation>
+      <annotation id="LF1">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">LongForm</infon>
+        <location offset="384" length="28"/>
+        <text>resting-state activity index</text>
+      </annotation>
+      <annotation id="SF2">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">ShortForm</infon>
+        <location offset="713" length="4"/>
+        <text>ADHD</text>
+      </annotation>
+      <annotation id="LF2">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">LongForm</infon>
+        <location offset="671" length="40"/>
+        <text>Attention deficit hyperactivity disorder</text>
+      </annotation>
+      <relation id="R0">
+        <infon key="type">ABBR</infon>
+        <node refid="LF0" role="LongForm"/>
+        <node refid="SF0" role="ShortForm"/>
+      </relation>
+      <relation id="R1">
+        <infon key="type">ABBR</infon>
+        <node refid="LF1" role="LongForm"/>
+        <node refid="SF1" role="ShortForm"/>
+      </relation>
+      <relation id="R2">
+        <infon key="type">ABBR</infon>
+        <node refid="LF2" role="LongForm"/>
+        <node refid="SF2" role="ShortForm"/>
+      </relation>
+    </passage>
+  </document>
+</collection>

data/xml/pubann/18077952.json

@@ -0,0 +1 @@
+{"denotations": [{"span": {"begin": 105, "end": 108}, "obj": "ABBR", "id": "SF0"}, {"span": {"begin": 76, "end": 103}, "obj": "ABBR", "id": "LF0"}, {"span": {"begin": 210, "end": 212}, "obj": "ABBR", "id": "SF1"}, {"span": {"begin": 188, "end": 208}, "obj": "ABBR", "id": "LF1"}], "target": "http://pubannotation.org/docs/sourcedb/PubMed/sourceid/18077952", "sourceid": "18077952", "sourcedb": "PubMed", "relations": [{"pred": "ShortForm", "obj": "SF0", "subj": "LF0", "id": "R0"}, {"pred": "ShortForm", "obj": "SF1", "subj": "LF1", "id": "R1"}], "project": "Ab3P-abbreviations", "text": "OBJECT: The purpose of this study was to evaluate the long-term efficacy of microvascular decompression (MVD) and to identify the factors affecting outcome in patients treated for primary trigeminal neuralgia (TN). Only the cases with a clear-cut neurovascular conflict (vascular contact and/or compression of the root entry zone of the trigeminal nerve) found at surgery and treated with \"pure\" MVD (decompression of the root without any additional lesioning or cutting of the adjacent rootlets) were retained. METHODS: The study included 362 patients who were followed up over a period of 1 to 18 years (median follow-up 7.2 years). A Kaplan-Meier survival analysis was generated at 1 and 15 years of follow-up for all of the considered factors. According to Kaplan-Meier analysis, the success rate (defined as pain-free patients without any medication) was 91% at 1 year and estimated to be 73.38% after 15 years of follow-up. RESULTS: None of the following patient-related factors played any significant role in prognosis: sex, patient age at surgery, history of systemic hypertension, duration of neuralgia before surgery, or history of failed trigeminal surgery. Patients with atypical neuralgia (a baseline of permanent pain) had the same outcome as those with a typical (purely spasmodic) presentation. In addition, the side and topography of the trigeminal nerve did not play a role, whereas involvement of all three divisions of the nerve had a negative effect on outcome. Concerning anatomical factors, neither the type of the compressive vessel nor its location along or around the root was found to be significant. However, the severity of compression was important-the more severe the degree of compression, the better the outcome (p = 0.002). The authors also found that presence of focal arachnoiditis had a negative influence on outcome (p = 0.002). CONCLUSIONS: Pure MVD can offer patients affected by a primary TN a 73.38% probability of long-term (15 years) cure of neuralgia. The presence of a clear-cut and marked vascular compression at surgery (and possibly-although not yet reliably--on preoperative magnetic resonance imaging) is the guarantee of a higher than 90% success rate."}

data/xml/pubann/18077952.xml

@@ -0,0 +1,53 @@
+<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE collection SYSTEM 'BioC.dtd'>
+<collection>
+  <source>Ab3P gold standard</source>
+  <date>20080529</date>
+  <key>Ab3P_gold.key</key>
+  <document>
+    <id>18077952</id>
+    <passage>
+      <infon key="type">title</infon>
+      <offset>0</offset>
+      <text>Microvascular decompression for primary trigeminal neuralgia: long-term effectiveness and prognostic factors in a series of 362 consecutive patients with clear-cut neurovascular conflicts who underwent pure decompression.</text>
+    </passage>
+    <passage>
+      <infon key="type">abstract</infon>
+      <offset>222</offset>
+      <text>OBJECT: The purpose of this study was to evaluate the long-term efficacy of microvascular decompression (MVD) and to identify the factors affecting outcome in patients treated for primary trigeminal neuralgia (TN). Only the cases with a clear-cut neurovascular conflict (vascular contact and/or compression of the root entry zone of the trigeminal nerve) found at surgery and treated with "pure" MVD (decompression of the root without any additional lesioning or cutting of the adjacent rootlets) were retained. METHODS: The study included 362 patients who were followed up over a period of 1 to 18 years (median follow-up 7.2 years). A Kaplan-Meier survival analysis was generated at 1 and 15 years of follow-up for all of the considered factors. According to Kaplan-Meier analysis, the success rate (defined as pain-free patients without any medication) was 91% at 1 year and estimated to be 73.38% after 15 years of follow-up. RESULTS: None of the following patient-related factors played any significant role in prognosis: sex, patient age at surgery, history of systemic hypertension, duration of neuralgia before surgery, or history of failed trigeminal surgery. Patients with atypical neuralgia (a baseline of permanent pain) had the same outcome as those with a typical (purely spasmodic) presentation. In addition, the side and topography of the trigeminal nerve did not play a role, whereas involvement of all three divisions of the nerve had a negative effect on outcome. Concerning anatomical factors, neither the type of the compressive vessel nor its location along or around the root was found to be significant. However, the severity of compression was important-the more severe the degree of compression, the better the outcome (p = 0.002). The authors also found that presence of focal arachnoiditis had a negative influence on outcome (p = 0.002). CONCLUSIONS: Pure MVD can offer patients affected by a primary TN a 73.38% probability of long-term (15 years) cure of neuralgia. The presence of a clear-cut and marked vascular compression at surgery (and possibly-although not yet reliably--on preoperative magnetic resonance imaging) is the guarantee of a higher than 90% success rate.</text>
+      <annotation id="SF0">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">ShortForm</infon>
+        <location offset="327" length="3"/>
+        <text>MVD</text>
+      </annotation>
+      <annotation id="LF0">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">LongForm</infon>
+        <location offset="298" length="27"/>
+        <text>microvascular decompression</text>
+      </annotation>
+      <annotation id="SF1">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">ShortForm</infon>
+        <location offset="432" length="2"/>
+        <text>TN</text>
+      </annotation>
+      <annotation id="LF1">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">LongForm</infon>
+        <location offset="410" length="20"/>
+        <text>trigeminal neuralgia</text>
+      </annotation>
+      <relation id="R0">
+        <infon key="type">ABBR</infon>
+        <node refid="LF0" role="LongForm"/>
+        <node refid="SF0" role="ShortForm"/>
+      </relation>
+      <relation id="R1">
+        <infon key="type">ABBR</infon>
+        <node refid="LF1" role="LongForm"/>
+        <node refid="SF1" role="ShortForm"/>
+      </relation>
+    </passage>
+  </document>
+</collection>

data/xml/pubann/18176205.json

@@ -0,0 +1 @@
+{"denotations": [{"span": {"begin": 673, "end": 676}, "obj": "ABBR", "id": "SF0"}, {"span": {"begin": 617, "end": 671}, "obj": "ABBR", "id": "LF0"}], "target": "http://pubannotation.org/docs/sourcedb/PubMed/sourceid/18176205", "sourceid": "18176205", "sourcedb": "PubMed", "relations": [{"pred": "ShortForm", "obj": "SF0", "subj": "LF0", "id": "R0"}], "project": "Ab3P-abbreviations", "text": "BACKGROUND:: Flap necrosis caused by inadequate blood supply is a common postoperative complication in reconstructive surgery. Because a putative stem cell population within the adipose tissue has been found to possess angiogenic potential, the authors sought to determine whether these cells might selectively induce neovascularization and increase the viability of random pattern skin flaps. METHODS:: Adipose-derived stem cells were isolated from the inguinal fat pads of ICR mice and expanded ex vivo for three passages. After the elevation of cranially based random pattern skin flaps (3 cm long and 1 cm wide), 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine (DiI)-labeled adipose-derived stem cells were then injected into the pedicle base (group A) or 1.5 cm distal to the pedicle (group B). Medium containing no adipose-derived stem cells, mature adipocytes, or basic fibroblast growth factor were injected in three other control groups separately. (n = 10 for each group). Millimetric measurements were taken at postoperative day 7 for evaluation of flap viability. Specimens were harvested for histologic analyses. RESULTS:: Adipose-derived stem cells led to a statistically significant increase in flap viability in both group A and group B compared with the control and the adipocyte groups. Histologic examination also demonstrated a statistically significant increase in capillary density in both group A and group B. Moreover, some of the endothelial cells were stained positively for DiI. CONCLUSIONS:: These findings suggest that adipose-derived stem cells have a potential for enhancing the blood supply of random pattern skin flaps. This mechanism might be both the direct differentiation of adipose-derived stem cells into endothelial cells and the indirect effect of angiogenic growth factor released from adipose-derived stem cells."}

data/xml/pubann/18176205.xml

@@ -0,0 +1,36 @@
+<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE collection SYSTEM 'BioC.dtd'>
+<collection>
+  <source>Ab3P gold standard</source>
+  <date>20080529</date>
+  <key>Ab3P_gold.key</key>
+  <document>
+    <id>18176205</id>
+    <passage>
+      <infon key="type">title</infon>
+      <offset>0</offset>
+      <text>Improved Viability of Random Pattern Skin Flaps through the Use of Adipose-Derived Stem Cells.</text>
+    </passage>
+    <passage>
+      <infon key="type">abstract</infon>
+      <offset>95</offset>
+      <text>BACKGROUND:: Flap necrosis caused by inadequate blood supply is a common postoperative complication in reconstructive surgery. Because a putative stem cell population within the adipose tissue has been found to possess angiogenic potential, the authors sought to determine whether these cells might selectively induce neovascularization and increase the viability of random pattern skin flaps. METHODS:: Adipose-derived stem cells were isolated from the inguinal fat pads of ICR mice and expanded ex vivo for three passages. After the elevation of cranially based random pattern skin flaps (3 cm long and 1 cm wide), 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine (DiI)-labeled adipose-derived stem cells were then injected into the pedicle base (group A) or 1.5 cm distal to the pedicle (group B). Medium containing no adipose-derived stem cells, mature adipocytes, or basic fibroblast growth factor were injected in three other control groups separately. (n = 10 for each group). Millimetric measurements were taken at postoperative day 7 for evaluation of flap viability. Specimens were harvested for histologic analyses. RESULTS:: Adipose-derived stem cells led to a statistically significant increase in flap viability in both group A and group B compared with the control and the adipocyte groups. Histologic examination also demonstrated a statistically significant increase in capillary density in both group A and group B. Moreover, some of the endothelial cells were stained positively for DiI. CONCLUSIONS:: These findings suggest that adipose-derived stem cells have a potential for enhancing the blood supply of random pattern skin flaps. This mechanism might be both the direct differentiation of adipose-derived stem cells into endothelial cells and the indirect effect of angiogenic growth factor released from adipose-derived stem cells.</text>
+      <annotation id="SF0">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">ShortForm</infon>
+        <location offset="768" length="3"/>
+        <text>DiI</text>
+      </annotation>
+      <annotation id="LF0">
+        <infon key="type">ABBR</infon>
+        <infon key="ABBR">LongForm</infon>
+        <location offset="712" length="54"/>
+        <text>1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine</text>
+      </annotation>
+      <relation id="R0">
+        <infon key="type">ABBR</infon>
+        <node refid="LF0" role="LongForm"/>
+        <node refid="SF0" role="ShortForm"/>
+      </relation>
+    </passage>
+  </document>
+</collection>

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: simple_bioc
 version: !ruby/object:Gem::Version
-  version: 0.0.22
+  version: 0.0.23
 platform: ruby
 authors:
 - Dongseop Kwon
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-02-09 00:00:00.000000000 Z
+date: 2016-08-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
@@ -25,19 +25,19 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '1.6'
 - !ruby/object:Gem::Dependency
-  name: json_builder
+  name: jbuilder
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.1'
+        version: '2.3'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.1'
+        version: '2.3'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -108,6 +108,34 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.1'
+- !ruby/object:Gem::Dependency
+  name: json-compare
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+- !ruby/object:Gem::Dependency
+  name: yajl-ruby
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.2'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.2'
 description: SimpleBioC is a simple parser / builder for BioC data format. BioC is
   a simple XML format to share text documents and annotations. You can find more information
   about BioC from the official BioC web site (http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/)
@@ -193,13 +221,16 @@ files:
 - lib/simple_bioc/node.rb
 - lib/simple_bioc/node_base.rb
 - lib/simple_bioc/passage.rb
+- lib/simple_bioc/pub_ann_writer.rb
 - lib/simple_bioc/relation.rb
 - lib/simple_bioc/sentence.rb
 - lib/simple_bioc/version.rb
+- samples/convert_pubann.rb
 - samples/print_annotation.rb
 - samples/sample1.rb
 - simple_bioc.gemspec
 - spec/file_check_spec.rb
+- spec/pubann_spec.rb
 - spec/simple_bioc_spec.rb
 - xml/10330397_gene.xml
 - xml/10330397_ppimention.xml
@@ -232,6 +263,16 @@ files:
 - xml/output.xml
 - xml/pos.key
 - xml/pos.xml
+- xml/pubann/18034444.json
+- xml/pubann/18034444.xml
+- xml/pubann/18045413.json
+- xml/pubann/18045413.xml
+- xml/pubann/18060712.json
+- xml/pubann/18060712.xml
+- xml/pubann/18077952.json
+- xml/pubann/18077952.xml
+- xml/pubann/18176205.json
+- xml/pubann/18176205.xml
 - xml/sentence.key
 - xml/sentence.xml
 homepage: https://github.com/dongseop/simple_bioc
@@ -260,5 +301,6 @@ specification_version: 4
 summary: Simple BioC parser/builder for ruby
 test_files:
 - spec/file_check_spec.rb
+- spec/pubann_spec.rb
 - spec/simple_bioc_spec.rb
 has_rdoc: