synonym-finder

Synonym finder is a biodiversity tool for finding homotypic nomenclatural synonyms in taxonomic hierarchies.‘

Installation

gem install synonym-finder

Usage

#prepare intput for the gem. It understand following array of hashes as input:

input = [
  {id: 001, path: "Animalia|Athropoda|Insecta|Hymenoptera|Formicidae|Gnamptogenys",    name: "Gnamptogenys porcata (Emery, 1896)"},
  {id: 003, path: "Animalia|Athropoda|Insecta|Hymenoptera|Formicidae|Gnamptogenys",    name: "Gnamptogenys triangularis (Mayr, 1887)"},
  {id: 004, path: "Animalia|Athropoda|Insecta|Hymenoptera|Formicidae|Gnamptogenys",    name: "Gnamptogenys triangularis var. alba Brown 1992"},
  {id: 005, path: "Animalia|Athropoda|Insecta|Hymenoptera|Formicidae|Gnamptogenys",    name: "Gnamptogenys triangularis var. borealis Brown 1992"},
  {id: 100, path: "Animalia|Athropoda|Insecta|Hymenoptera|Formicidae|Nylanderia",      name: "Nylanderia porcata"}, #match 001, no authorhsip
  {id: 101, path: "Animalia|Athropoda|Insecta|Hymenoptera|Formicidae|Nylanderia",      name: "Nylanderia porcatum Emery, 1896"},
  {id: 102, path: "Animalia|Athropoda|Insecta|Hymenoptera|Formicidae|Nylanderia",      name: "Nylanderia porcatum"}...]

 # please note that id can be a number of a string

 requre 'synonym-finder'

 sf = SynonymFinder.new(input)
 output = sf.find_synonyms

 # output should be of a following format:
 # matched putative synonyms are collected into groups of different types
 #
 # [ {:type=>"chresonym", :name_ids=>[203, 204]},
 #   {:type=>"alt_placement", :name_ids=>[400, 600]},
 #   {:type=>"chresonym", :name_ids=>[101, 102]},
 #   {:type=>"homotypic", :name_ids=>[203, 303]},
 #   {:type=>"lexical_variant", :name_ids=>[800, 803]},
 #   {:type=>"lexical_variant", :name_ids=>[801, 802]},
 #   {:type=>"homotypic", :name_ids=>[202, 302]},
 #   {:type=>"homotypic", :name_ids=>[1, 101]},
 #   {:type=>"misplaced_synonym", :name_ids=>[801, 803, 802, 800]}]

Synonym types

  • homotypic – possible placement of species to a different genus

  • alt_placement – possibly the same name (i.e. genus moved to a different family

  • chresonym – different authorship with for the same canonical form, both having the same parent

  • lexical_variant – The same parent and genus, but species epithet suffix is different (for example change of the epithet gender)

  • misplaced_synonym – The same parent, matching species epithet, but genus varies, usually happens if a synonyn located at the same level as species.

Contributing to synonym-finder

  • Check out the latest master to make sure the feature hasn’t been implemented or the bug hasn’t been fixed yet

  • Check out the issue tracker to make sure someone already hasn’t requested it and/or contributed it

  • Fork the project

  • Start a feature/bugfix branch

  • Commit and push until you are happy with your contribution

  • Make sure to add tests for it. This is important so I don’t break it in a future version unintentionally.

  • Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.

Copyright © 2011 Dmitry Mozzherin. See LICENSE.txt for further details.