Biodiversity
Parses taxonomic scientific name and breaks it into semantic elements.
WARNING, IMPORTANT!: Support for Ruby 1.8.7 IS DROPPED. Both biodiversity and biodiversity19 will be for Ruby > 1.9.1 and will be identical gems.
biodiversity19 is now deprecated and will not be updated anymore. You are strongly encouraged to change your dependencies from biodiversity19 to biodiversity
Follow biodiversity issues on waffle.io
Installation
sudo gem install biodiversity
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
nnparse file_with_names
The resuls will be put into parsed.json file in the current directory. To save results into a different file:
nnparse file_with_names output_file
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
parserver -h
Usage: parserver [options]
-r, --canonical_with_rank Adds infraspecies rank
to canonical forms
-o, --output=output Specifies the type of the output:
json - parsed results in json
canonical - canonical form only
Default: json
-H, --host=host Specifies host as "127.0.0.1",
"localhost" etc.
Default: 127.0.0.1
-p, --port=port Specifies the port number
Default: 4334
-h, --help Show this help message.
parserver --output=canonical
With default settings you can access parserserver 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
, .
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"...}}
end
As a library
You can use it as a library in Ruby, JRuby etc.
require 'biodiversity'
parser = ScientificNameParser.new
#to find version number
ScientificNameParser.version
# to fix capitalization in canonicals
ScientificNameParser.fix_case("QUERCUS (QUERCUS) ALBA")
# Output: Quercus (Quercus) alba
# 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 canonical form with infraspecies ranks
parsed = parser.parse("Seddera latifolia Hochst. & Steud. var. latifolia")
ranked = ScientificNameParser.add_rank_to_canonical(parsed)
ranked[:scientificName][:canonical]
#or
parser = ScientificNameParser.new(canonical_with_rank: true)
ranked = parser.parse("Seddera latifolia Hochst. & Steud. var. latifolia")
ranked[: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]
Returned result is not always linear, if name is complex. To get simple linear representation of the name you can use:
parser.parse("Pseudocercospora dendrobii (H.C. Burnett) \
U. Braun & Crous 2003")[:scientificName][:position]
# returns {0=>["genus", 16], 17=>["species", 26],
# 28=>["author_word", 32], 33=>["author_word", 40],
# 42=>["author_word", 44], 45=>["author_word", 50],
# 53=>["author_word", 58], 59=>["year", 63]}
# where the key is the char index of the start of
# a word, first element of the value is a semantic meaning
# of the word, second element of the value is the character index
# of end of the word
'Surrogate' is a broad group which includes 'Barcode of Life' names, and various undetermined names with cf. sp. spp. nr. in them:
parser.parse("Coleoptera BOLD:1234567")[:scientificName][:surrogate]
What is "id" in the parsed results?
ID field contains UUID v5 hexadecimal string. ID is generated out of bytes from the name string itself, and identical id can be generated using any popular programming language. You can read more about UUID version 5 in a blog post
For example "Homo sapiens" should generate "16f235a0-e4a3-529c-9b83-bd15fe722110" UUID
Parse using several CPUs (4 threads seem to be optimal)
parser = ParallelParser.new
# ParallelParser.new(4) will try to run 4 processes if hardware allows
array_of_names = ["Betula alba", "Homo sapiens"....]
parser.parse(array_of_names)
# Output: {"Betula alba" => {:scientificName...},
# "Homo sapiens" => {:scientificName...}, ...}
parallel parser takes list of names and returns back a hash with names as keys and parsed data as values
Canonicals with ranks for infraspecific epithets:
parser = ScientificNameParser.new(canonical_with_rank: true)
parser.parse('Cola cordifolia var. puberula \
A. Chev.')[:scientificName][:canonical]
# Output: Cola cordifolia var. puberula
Resolving lsid and geting back RDF file
LsidResolver.resolve("urn:lsid:ubio.org:classificationbank:2232671")
Troubleshooting
If nnparse or parserver do not start -- try to run
gem uninstall biodiversity
gem uninstall biodiversity19
and make sure you remove all versions and all nnparse and parserver scripts. Then install biodiversity again
gem install biodiversity
It should fix the problem.
Copyright
Authors: Dmitry Mozzherin
Copyright (c) 2008-2018 Dmitry Mozzherin. See LICENSE for further details.