Biodiversity ============ [![Gem Version][gem_svg]][gem_link] [![Continuous Integration Status][ci_svg]][ci_link] [![CodePolice][cc_svg]][cc_link] [![Dependency Status][deps_svg]][deps_link] 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][waffle] 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][socket_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. ```ruby 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: ```ruby 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: ```ruby 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][uuid_examples]. You can read more about UUID version 5 in a [blog post][uuid_blog] For example "Homo sapiens" should generate "16f235a0-e4a3-529c-9b83-bd15fe722110" UUID ### Parse using several CPUs (4 threads seem to be optimal) ```ruby 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: ```ruby 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][dimus] Copyright (c) 2008-2015 Marine Biological Laboratory. See [LICENSE][license] for further details. [gem_svg]: https://badge.fury.io/rb/biodiversity.svg [gem_link]: http://badge.fury.io/rb/biodiversity [ci_svg]: https://secure.travis-ci.org/GlobalNamesArchitecture/biodiversity.svg [ci_link]: http://travis-ci.org/GlobalNamesArchitecture/biodiversity [cc_svg]: https://codeclimate.com/github/GlobalNamesArchitecture/biodiversity.svg [cc_link]: https://codeclimate.com/github/GlobalNamesArchitecture/biodiversity [deps_svg]: https://gemnasium.com/GlobalNamesArchitecture/biodiversity.svg [deps_link]: https://gemnasium.com/GlobalNamesArchitecture/biodiversity [socket_example]: http://bit.ly/149iLm5 [dimus]: https://github.com/dimus [license]: https://github.com/GlobalNamesArchitecture/biodiversity/blob/master/LICENSE [waffle]: https://waffle.io/GlobalNamesArchitecture/biodiversity [uuid_examples]: https://github.com/GlobalNamesArchitecture/gn_uuid_examples [uuid_blog]: http://globalnamesarchitecture.github.io/gna/uuid/2015/05/31/gn-uuid-0-5-0.html