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 © 2009-2011 Marine Biological Laboratory. See LICENSE.txt for further details.