taxonifi 0.1.0 → 0.2.0

data/lib/models/collection.rb

@@ -2,12 +2,27 @@ module Taxonifi
   class CollectionError < StandardError; end
   module Model
 
+    require File.expand_path(File.join(File.dirname(__FILE__), 'shared_class_methods'))
+
     # The base class that all collection classes are derived from.
     class Collection
+      include Taxonifi::Model::SharedClassMethods
+
+      # A Hash indexing object by id like {Integer => SomeBaseSubclass} 
       attr_accessor :by_id_index
+
+      # A Integer representing the current free id to be used for an accessioned a collection object. Not used in non-indexed collections.
       attr_accessor :current_free_id
+
+      # An Array, the collection.
       attr_accessor :collection 
 
+      # Returns an array of (downcased) strings representing the prefixes of the Collection based subclasses, like
+      # ['name', 'geog', 'ref'] etc.
+      def self.subclass_prefixes
+        self.subclasses.collect{|c| c.to_s.split("::").last}.collect{|n| n.gsub(/Collection/, "").downcase}
+      end
+
       def initialize(options = {})
         opts = {
           :initial_id => 0
@@ -15,6 +30,7 @@ module Taxonifi
         raise CollectionError, "Can not start with an initial_id of nil." if opts[:initial_id].nil?
         @collection = []
         @by_id_index = {} 
+        # @by_row_index = {}
         @current_free_id = opts[:initial_id]
         true
       end 
@@ -50,7 +66,6 @@ module Taxonifi
         return obj
       end
 
-
       # Return an array of ancestor (parent) ids.
       # TODO: deprecate?
       # More or less identical to Taxonifi::Name.ancestor_ids except

data/lib/models/name.rb

@@ -6,25 +6,27 @@ module Taxonifi
 
     # String
     attr_accessor  :name      
+   
     # String 
     attr_accessor  :rank   
+  
+    # String
+    attr_accessor  :author        
+ 
     # String, authors as originally read 
     attr_accessor  :year         
+
     # Boolean, true if parens present (i.e. _not_ in original combination) 
     attr_accessor  :parens       
+
     # A Taxonifi::Model::Name 
     attr_accessor  :parent      
-    # String
-    attr_accessor  :author        
-    # General purpose relationship, typically used to indicate synonymy.  A Taxonifi::Model::Name 
+
+    #  A Taxonifi::Model::Name General purpose relationship, typically used to indicate synonymy.
     attr_accessor  :related_name 
 
     # Array, contains properties assignable in Taxonifi::Model::Name#new()
-    ATTRIBUTES = [:name, :rank, :year, :parens, :parent, :author, :related_name]
-
-    ATTRIBUTES.each do |a|
-      attr_accessor a
-    end
+    @@ATTRIBUTES = [:name, :rank, :year, :parens, :parent, :author, :related_name]
 
     # optionally parsed/index
     attr_accessor :authors                    
@@ -33,11 +35,13 @@ module Taxonifi
     attr_accessor :author_year_index    
 
     def initialize(options = {})
+      super
       opts = {
         id: nil
       }.merge!(options)
+
       @parent = nil
-      build(ATTRIBUTES, opts)
+      build(@@ATTRIBUTES, opts)
       add_author_year(opts[:author_year]) if !opts[:author_year].nil? && opts[:author_year].size > 0
       @parent = opts[:parent] if (!opts[:parent].nil? && opts[:parent].class == Taxonifi::Model::Name)
       @id = opts[:id] # if !opts[:id].nil? && opts[:id].size != 0
@@ -67,6 +71,22 @@ module Taxonifi
       @rank = r
     end
 
+    # Return a string indicating at what level this name 
+    # is indexed within a NameCollection.
+    # TODO: Family group extension; ICZN specific 
+    def index_rank
+      case rank
+      when 'species', 'subspecies'
+        'species_group'
+      when 'genus', 'subgenus'
+        'genus_group'
+      when nil, ""
+        'unknown'
+      else
+        rank.downcase
+      end
+    end
+
     # Set the parent (a Taxonifi::Model::Name) 
     def parent=(parent)
       if @rank.nil?
@@ -89,16 +109,30 @@ module Taxonifi
     # TODO: rename to reflect parens
     def author_year
       au = author_year_string
-      if self.parens == false
-        "(#{au})"        
-      else
-        au.size == 0 ? nil : au
-      end
+      return nil if au.nil?
+      (self.parens == true) ? "(#{au})" : au
     end
 
     # Return the author year string. 
     def author_year_string
       au = [self.author, self.year].compact.join(", ")
+      return nil if au.size == 0
+      au
+    end
+
+    # Return a Taxonifi::Model::Name representing the finest genus_group_parent.
+    # TODO: ICZN specific(?)
+    def genus_group_parent
+      [ parent_at_rank('subgenus'), parent_at_rank('genus')].compact.first
+    end
+  
+    # Returns just the name and author year, no parens, no parents. 
+    # Like:
+    #   foo Smith, 1927
+    #   Foo Smith, 1927
+    #   Fooidae
+    def name_author_year_string
+      [name, author_year_string].compact.join(" ")
     end
 
     # Return the name of a parent at a given rank.
@@ -139,7 +173,7 @@ module Taxonifi
     def nomenclator_name 
       case @rank
       when 'species', 'subspecies'
-        [parent_name_at_rank('genus'), (parent_name_at_rank('subgenus') ? "({parent_name_at_rank('subgenus')})" : nil), parent_name_at_rank('species'), @name].compact.join(" ")
+        [parent_name_at_rank('genus'), (parent_name_at_rank('subgenus') ? "(#{parent_name_at_rank('subgenus')})" : nil), parent_name_at_rank('species'),  parent_name_at_rank('subspecies')].compact.join(" ")
       when 'subgenus'
         [parent_name_at_rank('genus'), "(#{@name})"].compact.join(" ")
       else
@@ -150,6 +184,7 @@ module Taxonifi
     # Return a dashed "vector" of ids representing the ancestor parent closure, like:
     #  0-1-14-29g-45s-99-100.
     #  Postfixed g means "genus", postifed s means "subgenus.  As per SpecieFile usage.
+    #  TODO: !! malformed because the valid name is not injected.  Note that this can be generated internally post import.
     def parent_ids_sf_style
       ids = [] 
       (ancestors.push self).each do |a|
@@ -176,6 +211,12 @@ module Taxonifi
       @author_year_index = Taxonifi::Model::AuthorYear.new(people: @authors, year: @year).compact_index
     end
 
+    # Return a String of Prolog rules representing this Name
+    def prologify
+      "false"
+
+    end
+
   end 
 
   # ICZN specific sublassing of a taxonomic name.

data/lib/models/name_collection.rb

@@ -5,16 +5,25 @@ module Taxonifi
     # A collection of taxonomic names. 
     class NameCollection < Taxonifi::Model::Collection
 
+      # A by-name (string index) 
       attr_accessor :by_name_index
+     
+      # A Taxonifi::Model::RefCollection, optionally generated from Author/Year strings 
       attr_accessor :ref_collection
 
+      # An optional collection of existing combinations of species names, as represented by 
+      # individual arrays of Taxonifi::Model::Names.  Note you can not use a Taxonifi::Model::SpeciesName 
+      # for this purpose because getting/setting names therin will affect other combinations
+      attr_accessor :combinations
+
       def initialize(options = {})
         super 
-        @collection = []
-        @by_name_index = {}             # "foo => [1,2,3]"
-        Taxonifi::RANKS.inject(@by_name_index){|hsh, v| hsh.merge!(v => {})}
+        @by_name_index = {'genus_group' => {}, 'species_group' => {} }                 # "foo => [1,2,3]"
+         Taxonifi::RANKS[0..-5].inject(@by_name_index){|hsh, v| hsh.merge!(v => {})}  # Lumping species and genus group names 
+
         @by_name_index['unknown'] = {} # unranked names get dumped in here
         @ref_collection = nil
+        @combinations = [] 
         true
       end 
 
@@ -33,7 +42,7 @@ module Taxonifi
         RANKS[highest - 1]
       end 
 
-      # The names objects in the collection at a rank. 
+      # Returns an Array of the names objects in the collection at a rank. 
       # TODO: Should index this on add_object
       def names_at_rank(rank)
         raise if !RANKS.include?(rank)
@@ -45,18 +54,27 @@ module Taxonifi
       end
 
       # Returns id of matching existing name
-      # or false if there i s no match.
-      # Matches against name (string) and parents ("identity")
+      # or false if there is no match.
+      # !! assumes parent is set
+      # Matches against name, year, and all parents (by id).
+      # 
+      # !! nominotypic names are considered to be the same (species and generic).  See 
+      #   @combinations to instantiate these
+      #
+      # TODO: This is likely already overly ICZN flavoured.
       def name_exists?(name = Taxonifi::Model::Name) 
-        # Does the name (string) exist? 
-        rank = name.rank.downcase 
-        rank ||= 'unknown'
-        if by_name_index[rank][name.name]
-          # Yes, check to see if parents match
-          by_name_index[rank][name.name].each do |id|
+        # species/genus group names are indexed for indexing purposes 
+        rank = name.index_rank
+
+        if by_name_index[rank][name.name_author_year_string]
+          by_name_index[rank][name.name_author_year_string].each do |id|
+            full_parent_vector = parent_id_vector(name.parent.id) 
+            return id if full_parent_vector == parent_id_vector(id)  # this hits species/genus group names
+            
             vector = parent_id_vector(id)
-            vector.pop
-            if vector == parent_id_vector(name.parent.id)
+            next if vector.last != name.parent.id                    # can stop looking at this possiblity
+            vector.pop                                               # compare just parents
+            if vector == full_parent_vector 
               exists = true
               return id
             end
@@ -108,6 +126,12 @@ module Taxonifi
         end
       end
 
+      # Return an array of the names in the collection
+      def name_string_array
+        collection.collect{|n| n.display_name}
+      end 
+   
+
       # Take the author/years of these names and generate a reference collection.
       # Start the ids assigned to the references with initial_id.
       def generate_ref_collection(initial_id = 0)
@@ -131,19 +155,46 @@ module Taxonifi
       def ref_collection=(ref_collection)
         @ref_collection = ref_collection if ref_collection.class == Taxonifi::Model::RefCollection
       end
+     
+      # Return an Array of "homonyms" within the rank
+      # provided.  Useful for finding missmatched upper heirarchies,
+      # if nc is a name_collection:
+      #
+      #  homonyms = nc.homonyms_at_rank('genus')
+      #  homonyms.keys.sort.each do |n|
+      #    puts "#{n} (#{homonyms[n].size}) :"
+      #    homonyms[n].each do |p|
+      #      puts "  #{p.ancestors.collect{|i| i.name}.join(",")}"
+      #    end
+      #  end 
+      #
+      def homonyms_at_rank(rank) 
+       raise if !RANKS.include?(rank)
+        uniques = {}
+        names_at_rank(rank).each do |n|
+          uniques.merge!(n.name => []) if !uniques[n.name]
+          uniques[n.name].push n
+        end
+        uniques.delete_if{|k| uniques[k].size < 2}
+        uniques
+      end
 
       protected
 
       # Index the object by name into the
       # @by_name_index variable (this looks like:
       #  {"Foo bar" => [1,2,93]})
-      def index_by_name(obj)
-        rank = obj.rank
+      #  Pass a Taxonifi::Name
+      def index_by_name(name)
+        rank = name.rank
+        rank = 'species_group' if %w{species subspecies variety}.include?(rank)
+        rank = 'genus_group' if %w{genus subgenus}.include?(rank)
         rank ||= 'unknown'
-        by_name_index[rank][obj.name] ||= [] 
-        by_name_index[rank][obj.name].push obj.id 
-      end
 
+        by_name_index[rank][name.name_author_year_string] ||= [] 
+        by_name_index[rank][name.name_author_year_string].push name.id 
+      end
     end
+
   end
 end

data/lib/models/ref.rb

@@ -48,6 +48,7 @@ module Taxonifi
 
       # If :author_year is passed it is broken down into People + year. 
       def initialize(options = {})
+        super
         opts = {
         }.merge!(options)
         @parent = nil
@@ -80,6 +81,22 @@ module Taxonifi
         @author_year_index = Taxonifi::Model::AuthorYear.new(people: @authors, year: @year).compact_index
       end
 
+      # Return a single String value representing the page
+      # data available for this reference.
+      def page_string
+        str = '' 
+        if @pg_start.nil?
+          str = [@pages].compact.join
+        else
+          if @pg_end.nil?
+            str = [@pg_start, @pages].compact.join("; ")
+          else
+            str = ["#{@pg_start}-#{@pg_end}", @pages].compact.join("; ")
+          end
+        end
+        str.strip
+      end
+
     end
   end
 end

data/lib/models/ref_collection.rb

@@ -28,11 +28,12 @@ module Taxonifi
       # The object at a given row.
       # TODO: inherit from Collection? 
       def object_from_row(row_number)
+        return nil if row_number.nil?
         @row_index[row_number]
       end
 
       # Incrementally (re-)assigns the id of every associated author (Person) 
-      # This is only really useful if you assume every author is unique.
+      # This is only useful if you assume every author is unique.
       def enumerate_authors(initial_id = 0)
         i = initial_id 
         collection.each do |r|

data/lib/models/shared_class_methods.rb

@@ -0,0 +1,29 @@
+module Taxonifi::Model::SharedClassMethods
+  def self.included(base)
+    base.class_eval do
+
+      # Return an array of the classes derived from the base class.
+      # TODO: DRY with collection code.
+      def self.subclasses
+        classes = []
+        ObjectSpace.each_object do |klass|
+          next unless Module === klass
+          classes << klass if self > klass
+        end
+        classes
+      end
+
+      # Determines identity base ONLY
+      # on attributes in ATTRIBUTES.
+      def identical?(obj)
+        raise Taxonifi::ModelError, "Objects are not comparible." if obj.class != self.class
+        self.class::ATTRIBUTES.each do |a|
+          next if a == :id # don't compare
+          return false if obj.send(a) != self.send(a)
+        end
+        return true
+      end
+
+    end
+  end
+end

data/lib/models/species_name.rb

@@ -65,20 +65,22 @@ module Taxonifi
       end
 
       # Return a string representation of the species name.
+      # Becuase we build parent relationships on setters
+      # this is the same as the last names display_name
       def display_name
-        strs = [] 
-        self.names.each do |n|
-          case n.rank
-          when 'subgenus'
-            strs.push "(#{n.name})"
-          else
-            strs.push n.name 
-          end
-        end
-        strs.push self.names.last.author_year
-        txt = strs.compact.join(" ")  
-        txt
+        names.last.display_name 
+      end
+
+      # Returns true if this combination contains a nominotypic subspecies name 
+      def nominotypical_species
+        names.species && names.subspecies && (names.species.name == names.subspecies.name)
       end
+
+      # Returns true if this combinations contains a nominotypic subgenus 
+      def nominotypical_genus
+        names.genus && names.subgenus && (names.genus.name == names.subgenus.name)
+      end
+
     end
   end
 end

data/lib/splitter/parser.rb

@@ -34,7 +34,6 @@ class Taxonifi::Splitter::Parser
     t = @lexer.pop(Taxonifi::Splitter::Tokens::Quadrinomial)
     ranks = %w{genus subgenus species subspecies}
     names = {} 
-    last_parent = nil
     ranks.each do |r|
       names.merge!(r: nil)
       @builder.send("#{r}=", Taxonifi::Model::Name.new(:name => t.send(r), rank: r) ) if t.send(r)
@@ -44,7 +43,7 @@ class Taxonifi::Splitter::Parser
       t = @lexer.pop(Taxonifi::Splitter::Tokens::AuthorYear)
       @builder.names.last.author = t.authors
       @builder.names.last.year = t.year
-      @builder.names.last.parens = !t.parens
+      @builder.names.last.parens = t.parens
       @builder.names.last.derive_authors_year
     end
   

data/lib/splitter/tokens.rb

@@ -241,7 +241,7 @@ module Taxonifi::Splitter::Tokens
       str =~ /\A\s*(\d+)\s*[-]?\s*(\d+)?\)?\s*[\.\,]?(.*)?/i
       @pg_start = $1 
       @pg_end = $2
-      @remainder = $3
+      @remainder = $3.strip
     end
   end
 

data/lib/taxonifi.rb

@@ -1,4 +1,5 @@
 require 'csv'
+require 'fileutils'
 
 # Everything in Taxonifi is in here.
 module Taxonifi
@@ -7,8 +8,12 @@ module Taxonifi
   RANKS = %w{
       kingdom
       phylum
+      superclass
       class
+      subclass
       infraclass
+      cohort
+      superorder
       order 
       suborder
       infraorder
@@ -21,6 +26,7 @@ module Taxonifi
       subgenus
       species
       subspecies
+      variety
   }
 
 
@@ -33,4 +39,10 @@ module Taxonifi
     require file
   end
 
+  Dir.glob( File.expand_path(File.join(File.dirname(__FILE__), "utils/*.rb") )) do |file|
+    require file
+  end
+
+
+
 end

data/lib/utils/array.rb

@@ -0,0 +1,17 @@
+require File.expand_path(File.join(File.dirname(__FILE__), '../taxonifi'))
+
+# Generic Array methods
+module Taxonifi::Utils
+  module Array
+
+    # Return an Array of length size of black Arrays
+    def self.build_array_of_empty_arrays(size)
+      a = []
+      (0..(size-1)).each do |i|
+        a[i] = []
+      end
+      a
+    end
+
+  end # end Taxonifi::Utils::Array Module 
+end 

data/lib/utils/hash.rb

@@ -0,0 +1,17 @@
+require File.expand_path(File.join(File.dirname(__FILE__), '../taxonifi'))
+
+# Generic Array methods
+module Taxonifi::Utils
+  module Hash 
+
+    # Return an Array of length size of black Arrays
+    def self.build_hash_of_hashes_with_keys(keys)
+      h = {} 
+      keys.each do |k|
+        h[k] = {}
+      end
+      h
+    end
+
+  end # end Taxonifi::Utils::Array Module 
+end 

data/taxonifi.gemspec

@@ -0,0 +1,116 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = "taxonifi"
+  s.version = "0.2.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["mjy"]
+  s.date = "2013-03-27"
+  s.description = "Taxonifi contains simple models and utilties of use in for parsing lists of taxonomic name (life) related metadata"
+  s.email = "diapriid@gmail.com"
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "lib/assessor/assessor.rb",
+    "lib/assessor/base.rb",
+    "lib/assessor/row_assessor.rb",
+    "lib/export/export.rb",
+    "lib/export/format/base.rb",
+    "lib/export/format/obo_nomenclature.rb",
+    "lib/export/format/prolog.rb",
+    "lib/export/format/species_file.rb",
+    "lib/lumper/clump.rb",
+    "lib/lumper/lumper.rb",
+    "lib/lumper/lumps/parent_child_name_collection.rb",
+    "lib/models/author_year.rb",
+    "lib/models/base.rb",
+    "lib/models/collection.rb",
+    "lib/models/generic_object.rb",
+    "lib/models/geog.rb",
+    "lib/models/geog_collection.rb",
+    "lib/models/name.rb",
+    "lib/models/name_collection.rb",
+    "lib/models/person.rb",
+    "lib/models/ref.rb",
+    "lib/models/ref_collection.rb",
+    "lib/models/shared_class_methods.rb",
+    "lib/models/species_name.rb",
+    "lib/splitter/builder.rb",
+    "lib/splitter/lexer.rb",
+    "lib/splitter/parser.rb",
+    "lib/splitter/splitter.rb",
+    "lib/splitter/tokens.rb",
+    "lib/taxonifi.rb",
+    "lib/utils/array.rb",
+    "lib/utils/hash.rb",
+    "taxonifi.gemspec",
+    "test/file_fixtures/Fossil.csv",
+    "test/file_fixtures/Lygaeoidea.csv",
+    "test/file_fixtures/names.csv",
+    "test/helper.rb",
+    "test/test_export_prolog.rb",
+    "test/test_exporter.rb",
+    "test/test_lumper_clump.rb",
+    "test/test_lumper_geogs.rb",
+    "test/test_lumper_hierarchical_collection.rb",
+    "test/test_lumper_names.rb",
+    "test/test_lumper_parent_child_name_collection.rb",
+    "test/test_lumper_refs.rb",
+    "test/test_obo_nomenclature.rb",
+    "test/test_parser.rb",
+    "test/test_splitter.rb",
+    "test/test_splitter_tokens.rb",
+    "test/test_taxonifi.rb",
+    "test/test_taxonifi_accessor.rb",
+    "test/test_taxonifi_base.rb",
+    "test/test_taxonifi_geog.rb",
+    "test/test_taxonifi_name.rb",
+    "test/test_taxonifi_name_collection.rb",
+    "test/test_taxonifi_ref.rb",
+    "test/test_taxonifi_ref_collection.rb",
+    "test/test_taxonifi_species_name.rb"
+  ]
+  s.homepage = "http://github.com/SpeciesFile/taxonifi"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.25"
+  s.summary = "A general purpose framework for scripted handling of taxonomic names"
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_development_dependency(%q<bundler>, ["> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
+      s.add_development_dependency(%q<activerecord>, ["= 3.2.8"])
+      s.add_development_dependency(%q<debugger>, [">= 0"])
+    else
+      s.add_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_dependency(%q<bundler>, ["> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
+      s.add_dependency(%q<activerecord>, ["= 3.2.8"])
+      s.add_dependency(%q<debugger>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<rdoc>, ["~> 3.12"])
+    s.add_dependency(%q<bundler>, ["> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
+    s.add_dependency(%q<activerecord>, ["= 3.2.8"])
+    s.add_dependency(%q<debugger>, [">= 0"])
+  end
+end
+

data/test/file_fixtures/Fossil.csv

@@ -0,0 +1,11 @@
+Phylum,Superclass,Class,Subclass,Infraclass,Cohort,Superorder,Order,Suborder,Infraorder,Superfamily,Family,Subfamily,Genus,Subgenus,Species,Subspecies,Variety,Author_Date,Authors,Year,Title,Publication,Volume_Number,Pages,Cited_Page,Litho_Age_Range,Stage,Epoch,Subperiod,Period,Era,Fossil_Preservation,Group,Formation,Member,Locality,County,State,Country,Continent,Synonyms,Synonym_Notes,In_Carpenter?
+Arthropoda,Hexapoda,Insecta,Pterygota,Neoptera,Polyneoptera,Orthopterida,Orthoptera,Ensifera,,Grylloidea,Gryllidae,Trigonidiinae,Abanaxipha,,incongrua,,,"Vickery & Poinar, 1994","Vickery, V.R., & Poinar, Jr., G.O.",1994,Crickets (Grylloptera: Grylloidea) in Dominican amber.,The Canadian Entomologist,126(1),13-22.,17,20.5 - 16.4,Burdigalian,Miocene Early,Neogene,Tertiary,Cenozoic,Amber,Wealden,Wessex,,Dominica,,,Dominican Republic,South America,,,
+Arthropoda,Hexapoda,Insecta,Pterygota,Neoptera,Polyneoptera,Orthopterida,Orthoptera,Ensifera,,Grylloidea,Gryllidae,Trigonidiinae,Abanaxipha,,longispina,,,"Vickery & Poinar, 1994","Vickery, V.R., & Poinar, Jr., G.O.",1994,Crickets (Grylloptera: Grylloidea) in Dominican amber.,The Canadian Entomologist,126(1),13-22.,17,20.5 - 16.4,Burdigalian,Miocene Early,Neogene,Tertiary,Cenozoic,Amber,Wealden,Wessex,,Dominica,,,Dominican Republic,South America,,,
+Arthropoda,Hexapoda,Insecta,Pterygota,,Metapterygota,Palaeodictyopterida,Palaeodictyoptera,,,,Spilapteridae,,Abaptilon,,sibericum $,,,"Zalessky, 1946","Zalessky,",1946,,,,,58,354 - 296,,,,Carboniferous,Palaeozoic,,,,,Russia,,,Russia,Asia,,,Yes
+Arthropoda,Hexapoda,Insecta,Pterygota,Neoptera,Holometabola,Panorpida,Diptera,Brachycera,,Phoroidea,Phoridae,,Abaristophora,,domicamberae,,,"Disney, 1996","Disney, R.H.L., & Ross, A.J.",1996,"Abaristophora & Puliciphora (Diptera, Phoridae) from Dominical amber and revisionary notes on modern species.",European Journal of Entomology,93,127-135.,128,20.5 - 16.4,Burdigalian,Miocene Early,Neogene,Tertiary,Cenozoic,Amber,Wealden,Wessex,,Dominica,,,Dominican Republic,South America,,,
+Arthropoda,Hexapoda,Insecta,Pterygota,Neoptera,Polyneoptera,,Grylloblattodea,Grylloblattina,,,Liomopteridae,,Abashevia,,suchovi,,,"Sharov, 1961","Sharov, A.G.",1961,Order Paraplecoptera. IN Rohdendorf et.al. Paleozoic insects of the Kuznetsk basin.,Trudy paleontologicheskogo instituta akadamii nauk SSSR,85,"164-224, text-fig. 93-164, pl. 19.",194,545 - 251,,,,,Palaeozoic,,,,,Kuznetsk Basin,,,Russia,Asia,,,Yes
+Arthropoda,Hexapoda,Insecta,Pterygota,Neoptera,Holometabola,,Coleoptera,,,,,,Abax,,durhamensis,,,"Lesne, 1926","Lesne, P.",1926,Nouvelles donnees sur la faunule coleopterologique Pliocene de Castle Eden (Angleterre Septle),Encyclopedie entomologique (series B) Coleoptera,2(1),1-15.,3,5.3 - 1.8,,Pliocene,Neogene,Tertiary,Cenozoic,,,,,Castle Eden,Durham,,UK,Europe,,,
+Arthropoda,Hexapoda,Insecta,Pterygota,Neoptera,Holometabola,,Coleoptera,Polyphaga,,Tenebrionoidea,Melandryidae,,Abderina,,helm(s)i,,,"Seidlitz, 1898","Seidlitz, G.C.M.",1898,Coleoptera,IN Erichsons Naturgeschichte der Insekten Deutschlands Berlin,5(2),305-680.,577,54.8 - 33.7,,Eocene,Palaeogene,Tertiary,Cenozoic,Amber,Wealden,Wessex,,Baltic,,,Baltic,Europe,,,Yes
+Arthropoda,Hexapoda,Insecta,Pterygota,Neoptera,Holometabola,,Coleoptera,Polyphaga,,Cantharoidea,Cleridae,,Aberrokorynetes,,abludens,,,"Winkler, 1990","Winkler, J.",1990,Two new genera of fossil Korynetinae from Baltic Amber (Coleoptera Cleridae).,Acta Universitatis Carolinae - Biologica,34,371-381.,377,54.8 - 33.7,,Eocene,Palaeogene,Tertiary,Cenozoic,Amber,Wealden,Wessex,,Baltic,,,Baltic,Europe,,,
+Arthropoda,Hexapoda,Insecta,Pterygota,Neoptera,Holometabola,,Hymenoptera,Symphyta,,Tenthredinoidea,Cimbicidae,,Abia,,duplicata =,,,"Giebel, 1856","Giebel, C.G.A.",1856,"Fauna der Vorwelt, Bd II. Die Insecten und Spinnen der Vorwelt.",F.U. Brodhaus. Leipzig,,1-511.,264,150.7 - 140,Tithonian - Berriasian,,,Jurassic / Cretaceous,Mesozoic,Lower Purbeck beds,Purbeck,Lulworth,,Durlston Bay,Dorset,England,UK,Europe,Osmylopsis duplicata,,
+Arthropoda,Hexapoda,Insecta,Pterygota,Neoptera,Holometabola,,Hymenoptera,Symphyta,,Tenthredinoidea,Cimbicidae,,Abia,,kochi =,,,"Geinitz, 1887","Geinitz, F.E.",1887,Neue Aufschlusse der Flozformation Mecklenburgs. IX Beitrag zur Geologie Mecklenburgs. IV Jura.,Archiv des Vereins der Freunde naturgeschichte Mecklenburg,41,"143-216, pl. 4-6",200,189.6 - 180.1,,Liassic Late,,Jurassic Early,Mesozoic,,,,,Dobbertin,Mecklenburg,,Germany,Europe,Solenoptilon kochi,,