= Biodiversity

Parses taxonomic scientific name and breaks it into semantic elements.

== Installation

To install gem you need RubyGems >= 1.3.6

  $ sudo gem install biodiversity #for ruby 1.8.x
  $ sudo gem install biodiversity19 #for ruby 1.9.x

== Example usage

=== As a command line script

You can parse file with taxonomic names from command line. File should contain one scientific name per line

  nnparser file_with_names

=== As a socket server

If you do not use ruby and need a fast access to the parser functionality  you can use a socket server

  parserver

options:

  parserver --output=canonical

to return a canonical form of the name string

  parserver --output=canonical_with_rank

the same as above, but infracpecies' rank is shown if available

  praserver --port 5555

run socket server on a different port

Then you can access it via 4334 port using a socket client library of your programming language.  You can find socket client script example in the examples directory of the gem.

If you want to check if socket server works for you:

  #run server in one terminal
  parserver

  #in another terminal window type
  telnet localhost 4334

If you enter a line with a scientific name server will send you back parsed information in json format.

To stop telnet client type any of 'end','exit','q', '.' (without quotes) instead of scientific name

  $ telnet localhost 4334
  Trying ::1...
  Connected to localhost.
  Escape character is '^]'.
  Acacia abyssinica Hochst. ex Benth. ssp. calophylla Brenan
  {"scientificName":{"canonical":"Acacia abyssinica calophylla","parsed":true,"parser_run":1,"verbatim":"Acacia abyssinica Hochst. ex Benth. ssp. calophylla Brenan\r\n","positions":{"0":["genus",6],"18":["author_word",25],"29":["author_word",35],"7":["species",17],"41":["infraspecies",51],"52":["author_word",58]},"hybrid":false,"normalized":"Acacia abyssinica Hochst. ex Benth. ssp. calophylla Brenan","details":[{"species":{"basionymAuthorTeam":{"exAuthorTeam":{"author":["Benth."],"authorTeam":"Benth."},"author":["Hochst."],"authorTeam":"Hochst."},"string":"abyssinica","authorship":"Hochst. ex Benth."},"infraspecies":[{"basionymAuthorTeam":{"author":["Brenan"],"authorTeam":"Brenan"},"string":"calophylla","rank":"ssp.","authorship":"Brenan"}],"genus":{"string":"Acacia"}}]}}


=== As a library

You can use it as a library

  require 'biodiversity'

  parser = ScientificNameParser.new

  # to parse a scientific name into a ruby hash
  parser.parse("Plantago major")

  #to get json representation
  parser.parse("Plantago").to_json
  #or
  parser.parse("Plantago")
  parser.all_json

  # to clean name up
  parser.parse("             Plantago       major    ")[:scientificName][:normalized]

  # to get only cleaned up latin part of the name
  parser.parse("Pseudocercospora dendrobii (H.C. Burnett) U. Braun & Crous 2003")[:scientificName][:canonical]

  # to get detailed information about elements of the name
  parser.parse("Pseudocercospora dendrobii (H.C. Burnett 1883) U. Braun & Crous 2003")[:scientificName][:details]

  # to resolve lsid and get back RDF file
  LsidResolver.resolve("urn:lsid:ubio.org:classificationbank:2232671")

Copyright (c) 2009-2011 Marine Biological Laboratory. See LICENSE.txt for
further details.