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Data Cleaning and Standardization","monthly_downloads":0,"total_dependent_repos":4,"total_dependent_packages":10,"readme":"# Global Names Parser: GNparser written in Go\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18248840.svg)](https://doi.org/10.5281/zenodo.18248840)\n\nTry `GNparser` [online][parser-web].\n\nTry [GNparser with OpenRefine][OpenRefine]\n\n`GNparser` splits scientific names into their semantic elements with an\nassociated meta information. Parsing is indispensable for matching names\nfrom different data sources, because it can normalize different lexical\nvariants of names to the same `canonical form`.\n\nThis parser, written in Go, is the 3rd iteration of the project. The\nfirst, [biodiversity], had been written in Ruby, the second, [also\ngnparser][gnparser-scala], had been written in Scala. This project is\nnow a substitution for the other two. Scala project is in an archived state,\n[biodiversity] now uses Go code for parsing. All three projects were developed\nas a part of [Global Names Architecture Project][gna].\n\nTo use `GNparser` as a command line tool under Windows, Mac or Linux,\ndownload the [latest release][releases], uncompress it, and copy `gnparser`\nbinary somewhere in your PATH. On a Mac you might also need to go to\n`System Preferences` and security panel select `Allow from other\ndevelopers`. Then, after running `gnparser`, click 'Yes' in a dialog box\nallowing to run a program from an \"unregistered developer\".\n\n```bash\ntar xvf gnparser-v1.0.0-linux.tar.gz\nsudo cp gnparser /usr/local/bin\n# for CSV output\ngnparser \"Homo sapiens Linnaeus\"\n# for TSV output\ngnparser -f tsv \"Homo sapiens Linnaeus\"\n# for JSON output\ngnparser -f compact \"Homo sapiens Linnaeus\"\ngnparser -f compact \"Homo sapiens Linnaeus\" | jq\n# or\ngnparser -f pretty \"Homo sapiens Linnaeus\"\ngnparser -h\n```\n\n\u003c!-- TOC GFM --\u003e\n\n* [Citing](#citing)\n* [Introduction](#introduction)\n* [Speed](#speed)\n* [Features](#features)\n* [Use Cases](#use-cases)\n  * [Getting the simplest possible canonical form](#getting-the-simplest-possible-canonical-form)\n  * [Quickly partition names by the type](#quickly-partition-names-by-the-type)\n  * [Normalizing name-strings](#normalizing-name-strings)\n  * [Removing authorship from the middle of the name](#removing-authorship-from-the-middle-of-the-name)\n  * [Figuring out if names are well-formed](#figuring-out-if-names-are-well-formed)\n  * [Creating stable GUIDs for name-strings](#creating-stable-guids-for-name-strings)\n  * [Assembling canonical forms etc. from original spelling](#assembling-canonical-forms-etc-from-original-spelling)\n* [Tutorials](#tutorials)\n* [Installation](#installation)\n  * [Install with Homebrew (Mac OS X, Linux)](#install-with-homebrew-mac-os-x-linux)\n  * [Linux or Mac OS X](#linux-or-mac-os-x)\n  * [Windows](#windows)\n  * [Install with Go](#install-with-go)\n* [Usage](#usage)\n  * [Command Line](#command-line)\n  * [Pipes](#pipes)\n  * [R language package](#r-language-package)\n  * [Ruby Gem](#ruby-gem)\n  * [Node.js](#nodejs)\n  * [Usage as a REST API Interface or Web-based User Graphical Interface](#usage-as-a-rest-api-interface-or-web-based-user-graphical-interface)\n  * [Use as a Docker image](#use-as-a-docker-image)\n  * [Use as a library in Go](#use-as-a-library-in-go)\n  * [Use as a shared C library](#use-as-a-shared-c-library)\n* [Parsing ambiguities](#parsing-ambiguities)\n  * [Names with `filius` (ICN code)](#names-with-filius-icn-code)\n  * [Names with subgenus (ICZN code) and genus author (ICN code)](#names-with-subgenus-iczn-code-and-genus-author-icn-code)\n  * [Virus names according to modern ICVCN binomial nomenclature](#virus-names-according-to-modern-icvcn-binomial-nomenclature)\n* [Authors](#authors)\n* [Contributors](#contributors)\n* [Artificial Intelligence Policy](#artificial-intelligence-policy)\n* [References](#references)\n* [License](#license)\n\n\u003c!-- /TOC --\u003e\n\n## Citing\n\n[Zenodo DOI] can be used to cite GNparser\n\n## Introduction\n\nGlobal Names Parser or `GNparser` is a program written in Go for breaking up\nscientific names into their elements. It uses [peg] -- a Parsing\nExpression Grammar (PEG) tool.\n\nMany other parsing algorithms for scientific names use regular expressions.\nThis approach works well for extracting canonical forms in simple cases.\nHowever, for complex scientific names and to parse scientific names into\nall semantic elements, regular expressions often fail, unable to overcome\nthe recursive nature of data embedded in names. By contrast, `GNparser`\nis able to deal with the most complex scientific name-strings.\n\n`GNparser` takes a name-string like `Drosophila (Sophophora) melanogaster\nMeigen, 1830` and returns parsed components in `CSV`, `TSV` or `JSON` format.\nThe parsing of scientific names might become surprisingly complex and the\n`GNparser's` [test file] is a good source of information about the parser's\ncapabilities, its input and output.\n\n`GNparser` reached a stable v1. [Differences between v1 and v0][v0diff]\n\n## Speed\n\nNumber of names parsed per second on an AMD Ryzen 7 5800H CPU\n(8 cores, 16 threads), GNparser v1.3.0:\n\n```bash\ngnparser 1_000_000_names.txt -j 200 \u003e /dev/null\n```\n\n| Threads | names/sec |\n| ------- | --------- |\n| 1       | 9,000     |\n| 2       | 19,000    |\n| 4       | 35,000    |\n| 8       | 56,000    |\n| 16      | 82,000    |\n| 100     | 107,000   |\n| 200     | 111,000   |\n\nFor simplest output Go `GNparser` is roughly 2 times faster than Scala\n`GNparser` and about 100 times faster than pure Ruby implementation. For\nJSON formats the parser is approximately 8 times faster than Scala one, due to\nmore efficient JSON conversion.\n\n## Features\n\n* Fastest parser ever.\n* Very easy to install, just placing executable somewhere in the PATH is\n  sufficient.\n* Parsing can be adjusted to rules of specific nomenclatural code (Botanical,\n  Botanical Cultivar, Zoological, Viral).\n* Extracts all elements from a name, not only canonical forms.\n* Works with very complex scientific names, including hybrid formulas.\n* Includes RESTful service and interactive web interface.\n* Can run as a command line application.\n* Can be used as a library in Go projects.\n* Can be scaled to many CPUs and computers (if 250 millions names an\n  hour is not enough).\n* Calculates a stable UUID version 5 ID from the content of a string.\n* Provides C-binding to incorporate parser to other [languages][biodiversity].\n\n## Use Cases\n\n### Getting the simplest possible canonical form\n\nCanonical forms of a scientific name are the latinized components without\nannotations, authors or dates. They are great for matching lexical variants\nof names. Three versions of canonical forms are included:\n\n| Canonical | Example | Use |\n| :-------- | :------ | :-- |\n| - | _Spiraea alba var. alba_ Du Roi | Best for disambiguation, but has many lexical variants |\n| Full | _Spiraea alba var. alba_ | Presentation, infraspecies disambiguation |\n| Simple | _Spiraea alba alba_ | Name matching, presentation |\n| Stem | _Spiraea alb alb_ | Best for matching fem./masc. inconsistencies |\n\nThe `canonicalName -\u003e full` is good for presentation, as it keeps more\ndetails.\n\nThe `canonicalName -\u003e simple` field is good for matching names from different\nsources, because sometimes dataset curators omit hybrid sign in named hybrids,\nor remove ranks for infraspecific epithets.\n\nThe `canonicalName -\u003e stem` field normalizes `simple` canonical form even\nfurther. It allows to match names with inconsistent gender suffixes in specific\nepithets (for example _alba_ vs. _albus_). The normalization is done according\nto stemming rules for Latin language described in [Schinke R et al (1996)]. For\nexample letters `j` are converted to `i`, letters `v` are converted to `u`, and\nsuffixes are removed from the specific and infraspecific epithets.\n\nIf you only care mostly about canonical form of a name you can use default\n`--format csv` flag with command line tool.\n\nCSV/TSV output has the following fields:\n\n| Field           | Meaning                                       |\n| --------------- | --------------------------------------------- |\n| Id              | UUID v5 generated out of Verbatim             |\n| Verbatim        | Input name-string without any changes         |\n| Cardinality     | 0 - N/A, 1 - Uninomial, 2 - Binomial etc.     |\n| CanonicalStem   | Simplest canonical form with removed suffixes |\n| CanonicalSimple | Simplest canonical form                       |\n| CanonicalFull   | Canonical form with hybrid sign and ranks     |\n| Authors         | Authorship of a name                          |\n| Year            | Year of the name (if given)                   |\n| Quality         | [Parsing quality][quality]                    |\n\n### Quickly partition names by the type\n\nUsually scientific names can be broken into groups according to the number of\nelements:\n\n* Uninomial\n* Binomial\n* Trinomial\n* Quadrinomial\n\nThe output of `GNparser` contains a `Cardinality` field that tells, when\npossible, how many elements are detected in the name.\n\n| Cardinality | Name Type    |\n| ----------- | ------------ |\n| 0           | Undetermined |\n| 1           | Uninomial    |\n| 2           | Binomial     |\n| 3           | Trinomial    |\n| 4           | Quadrinomial |\n\nFor hybrid formulas, \"approximate\" names (with \"sp.\", \"spp.\" etc.), unparsed\nnames, as well as names from `BOLD` project cardinality is 0 (Undetermined)\n\n### Normalizing name-strings\n\nThere are many inconsistencies in how scientific names may be written.\nUse `normalized` field to bring them all to a common form (spelling, spacing,\nranks).\n\n### Removing authorship from the middle of the name\n\nOften data administrators spit name-strings into \"name part\" and\n\"authorship part\". This practice misses some information when dealing with\nnames like \"_Prosthechea cochleata_ (L.) W.E.Higgins _var. grandiflora_\n(Mutel) Christenson\". However, if this is the use case, a combination of\n`canonicalName -\u003e full` with the authorship from the lowest taxon will do\nthe job. You can also use the default `--format csv` flag for `gnparser`\ncommand line tool.\n\n### Figuring out if names are well-formed\n\nIf there are problems with parsing a name, parser generates `qualityWarnings`\nmessages and lowers [parsing `quality`][quality] of the name. Quality values\nmean the following:\n\n* `\"quality\": 1` - No problems were detected.\n* `\"quality\": 2` - There were small problems, normalized result\n  should still be good.\n* `\"quality\": 3` - There are some significant problems with parsing.\n* `\"quality\": 4` - There were serious problems with the name, and the\n  final result is rather doubtful.\n* `\"quality\": 0` - A string could not be recognized as a scientific\n  name and parsing failed.\n\n### Creating stable GUIDs for name-strings\n\n`GNparser` uses UUID version 5 to generate its `id` field.\nThere is algorithmic 1:1 relationship between the name-string and the UUID.\nMoreover the same algorithm can be used in any popular language to\ngenerate the same UUID. Such IDs can be used to globally connect information\nabout name-strings or information associated with name-strings.\n\nMore information about UUID version 5 can be found in the [Global Names\nblog][uuid5]\n\n### Assembling canonical forms etc. from original spelling\n\n`GNparser` tries to correct problems with spelling, but sometimes it is\nimportant to keep original spelling of the canonical forms or authorship.\nThe `words` field attaches semantic meaning to every word in the\noriginal name-string and allows users to create canonical forms or other\ncombinations using the original verbatim spelling of the words. Each element\nin `words` contains 4 parts:\n\n1. verbatim value of a word\n2. semantic meaning of the word\n3. start position of the word\n4. end position of the word\n\nThe `words` section belongs to additional details. To use it enable\n`--details` flag for the command line application.\n\n```bash\ngnparser -d \"Pardosa moesta Banks, 1892\"\n```\n\n## Tutorials\n\n* Parsing names from CSV files [tutorial][tutGN]\n\n## Installation\n\nCompiled programs in Go are self-sufficient and small (`GNparser` is only a\nfew megabytes). As a result the binary file of `gnparser` is all you need to\nmake it work. You can install it by downloading the [latest version of the\nbinary][releases] for your operating system **and** CPU architecture, and\nplacing it in your `PATH`.\n\n### Install with Homebrew (Mac OS X, Linux)\n\n[Homebrew] is a packaging system originally made for Mac OS X. You can use it\nnow for Mac, Linux, or Windows X WSL (Windows subsystem for Linux).\n\n1. Install Homebrew according to their [instructions][Homebrew].\n\n2. Install `gnparser` with:\n\n   ```bash\n   brew update\n   brew tap gnames/gn\n   brew install gnparser\n   ```\n\n### Linux or Mac OS X\n\nMove `gnparser` executable somewhere in your PATH\n(for example `/usr/local/bin`)\n\n```bash\ntar xvf gnparser-xxx.tar.gz\nsudo mv gnparser /usr/local/bin\n```\n\nIf you're using Mac OS, you might encounter a security warning that prevents\n`gnparser` from running. Here's how to fix it:\n\n1. In the warning dialog click the `Done` button (not the `Move to Trash`\n   button).\n\n1. Locate the Security Settings: Go to `System Settings -\u003e Privacy \u0026 Security`\n   and scroll down to the `Security` section.\n\n1. Allow `gnparser`: You should see a message saying\n   `\"gnparser\" was blocked...`. Click the `Allow Anyway` button next to it.\n\n1. Run gnparser again: Try running gnparser from your terminal. This time,\n   a dialog box will pop up with an `Open Anyway` button.\n\n1. Open and Unblock: Click `Open Anyway` and enter your administrator\n   password when prompted. This will unblock the `gnparser` binary.\n\nAfter these steps, you should be able to use gnparser without any issues.\nYou can also copy, move, or rename it freely.\n\n### Windows\n\nOne possible way would be to create a default folder for executables and place\n`gnparser` there.\n\nUse `Windows+R` keys\ncombination and type \"`cmd`\". In the appeared terminal window type:\n\n```cmd\nmkdir C:\\bin\ncopy path_to\\gnparser.exe C:\\bin\n```\n\n[Add `C:\\bin` directory to your `PATH`][winpath] `user` and/or `system`\nenvironment variables.\n\nIt is also possible to install [Windows Subsystem for Linux][wsl] on Windows\n(v10 or v11), and use `gnparser` as a Linux executable.\n\n### Install with Go\n\nIf you have Go installed on your computer use\n\n```bash\ngo get -u github.com/gnames/gnparser/gnparser\n```\n\nFor development install [just] and use the following:\n\n```bash\ngit clone https://github.com/gnames/gnparser.git\ncd gnparser\njust tools\njust install\n```\n\nYou do need your `PATH` to include `$HOME/go/bin`\n\n## Usage\n\n### Command Line\n\n```bash\ngnparser -f pretty \"Quadrella steyermarkii (Standl.) Iltis \u0026amp; Cornejo\"\n```\n\nRelevant flags:\n\n`--help -h`\n: Displays help information about the available flags.\n\n`--batch_size -b`\n: Sets the maximum number of names processed in a batch. This is ignored\nin streaming mode (-s).\n\n`--cultivar -C`\n: Deprecated. Use `--nomenclatural-code` instead.\n\n`--capitalize -c`\n: Capitalizes the first letter of input name-strings.\n\n`--details -d`\n: Provides more detailed output for each parsed name. Ignored for\nCSV/TSV formats.\n\n`--diaereses -D`\n: Preserves diaereses, e.g. `Leptochloöpsis virgata`. The stemmed\ncanonical name does not include diaereses.\n\n`--flatten-output -F`\n: Converts nested JSON output into a flattened structure. Only applies to JSON\nformats (CSV/TSV formats are always flattened). Instead of nested objects like\n`canonical` and `authorship`, all fields are flattened to the top level, making\nthe output easier to process in some applications. Some detailed information\nwould be lost in the flattened format.\n\n`--compact-authors -a`\n: Removes space between authors' initials, e.g.\n`Schoenoplectus tabernaemontani (C. C. Gmel.) Palla`. The normalized\nauthorship will be generated without space between initials\n`Schoenoplectus tabernaemontani (C.C.Gmel.) Palla`.\n\n`--format -f`\n: Specifies the output format: `csv`, `tsv`, `compact`, or `pretty`.\nDefaults to `csv`. CSV and TSV formats include a header row.\n\n`--jobs -j`\n: Sets the number of jobs to run concurrently.\n\n`--ignore_tags -i`\n: Increases performance by skipping HTML entity and tag processing.\nOnly use if your input is known to be free of HTML.\n\n`--nomenclatural-code -n`\n: Specifies the nomenclatural code (e.g., `botanical`, `zoological`) to use\nfor parsing in ambiguous cases. For example in `Aus (Bus) cus`: according\nto zoological code `Aus` is genus, `Bus` is subgenus, while according\nto botanical code `Bus` is the author of `Aus`. For modern binomial `viral`\ncode this setting is a hard constraint, while for other codes it sets\na priority in ambiguous situations.\n\nSupported values: `bact`, `bacterial`, `ICNP`, `bot`, `vir`, `viral`, `ICVCN`,\n`botanical`, `ICN`, `cult`, `cultivar`, `ICNCP`, `zoo`, `zoological`, `ICZN`.\n\n`--port -p`\n: Sets the port for the web-interface and [RESTful API][OpenAPI].\n\n`--species-group-cut`\n: Modifies the stemmed canonical form for autonyms and species-group names\nby removing the infraspecific epithet. Useful for matching names like\n`Aus bus` and `Aus bus bus`.\n\n`--stream -s`\n: Enables streaming mode, where names are processed one at a time.\nUseful for integrating gnparser with languages other than Go.\n\n`--unordered -u`\n: Disables output ordering. The output order may not match the input order.\n\n`--version -V`\n: Displays the version number of `GNparser`.\n\nTo parse one name:\n\n```bash\n# CSV output (default)\ngnparser \"Parus major Linnaeus, 1788\"\n# or\ngnparser -f csv \"Parus major Linnaeus, 1788\"\n\n# TSV output\ngnparser -f tsv \"Parus major Linnaeus, 1788\"\n\n# JSON compact format\ngnparser \"Parus major Linnaeus, 1788\" -f compact\n\n# pretty format\ngnparser -f pretty \"Parus major Linnaeus, 1788\"\n\n# JSON with flattened output structure (no nested objects)\ngnparser -f compact -F \"Parus major Linnaeus, 1788\"\n\n# to parse a name from the standard input\necho \"Parus major Linnaeus, 1788\" | gnparser\n\n# to parse a botanical cultivar name\ngnparser \"Anthurium 'Ace of Spades'\" --cultivar\ngnparser \"Phyllostachys vivax cv aureocaulis\" -c\n\n# to parse name that is all in low-case\ngnparser \"parus major\" --capitalize\ngnparser \"parus major\" -c\n```\n\nTo parse a file:\n\nThere is no flag for parsing a file. If parser finds the given file path on\nyour computer, it will parse the content of the file, assuming that every line\nis a new scientific name. If the file path is not found, `GNparser` will try\nto parse the \"path\" as a scientific name.\n\nParsed results will stream to STDOUT, while progress of the parsing\nwill be directed to STDERR.\n\n```bash\n# to parse with 200 parallel processes\ngnparser -j 200 names.txt \u003e names_parsed.csv\n\n# to parse file with more detailed output\ngnparser names.txt -d -f compact \u003e names_parsed.txt\n\n# to parse files using pipes\ncat names.txt | gnparser -f csv -j 200 \u003e names_parsed.csv\n\n# to parse using `stream` method instead of `batch` method.\ncat names.txt | gnparser -s \u003e names_parsed.csv\n\n# to not remove html tags and entities during parsing. You gain a bit of\n# performance with this option if your data does not contain HTML tags or\n# entities.\ngnparser \"\u003ci\u003ePomatomus\u003c/i\u003e\u0026nbsp;\u003ci\u003esaltator\u003c/i\u003e\"\ngnparser -i \"\u003ci\u003ePomatomus\u003c/i\u003e\u0026nbsp;\u003ci\u003esaltator\u003c/i\u003e\"\ngnparser -i \"Pomatomus saltator\"\n```\n\nIf jobs number is set to more than 1, parsing uses several concurrent\nprocesses. This approach increases speed of parsing on multi-CPU\ncomputers. The results are returned in some random order, and reassembled\ninto the order of input transparently for a user.\n\nPotentially the input file might contain millions of names, therefore creating\none properly formatted JSON output might be prohibitively expensive. Therefore\nthe parser creates one JSON line per name (when `compact` format is used)\n\nYou can use up to 20 times more \"threads\" than the number of your CPU cores\nto reach maximum speed of parsing (`--jobs 200` flag). It is practical\nbecause additional \"threads\" are very cheap in Go and they try to fill out\nevery idle gap in the CPU usage.\n\n### Pipes\n\nAbout any language has an ability to use pipes of the underlying operating\nsystem. From the inside of your program you can make the CLI executable\n`GNparser` to listen on a STDIN pipe and produce output into STDOUT pipe. Here\nis an example in Ruby:\n\n```ruby\ndef self.start_gnparser\n  io = {}\n\n  ['compact', 'csv'].each do |format|\n    stdin, stdout, stderr = Open3.popen3(\"./gnparser -s --format #{format}\")\n    io[format.to_sym] = { stdin: stdin, stdout: stdout, stderr: stderr }\n  end\nend\n```\n\n@marcobrt kindly provided an [example in PHP][PHP pipes].\n\nNote that you have to use `--stream -s` flag for this approach to work.\n\n### R language package\n\nFor R language it is possible to use [`rgnparser` package][rgnparser]. It\nimplements mentioned above `pipes` method. It does require `gnparser` app\nbe installed.\n\n### Ruby Gem\n\nRuby developers can use `GNparser` functionality via [biodiversity] gem. It\nuses C-binding and does not require an installed `gnparser` app.\n\n### Node.js\n\n@tobymarsden created a [wrapper for node.js][node-gnparser]. It uses C-binding\nand does not require an installed `gnparser` app.\n\n### Usage as a REST API Interface or Web-based User Graphical Interface\n\nWeb-based user interface and API are invoked by `--port` or\n`-p` flag. To start web server on `http://0.0.0.0:9000`\n\n```bash\ngnparser -p 9000\n```\n\nOpening a browser with this address will now show an interactive interface\nto parser. API calls would be accessible on `http://0.0.0.0:9000/api/v1/`.\n\nThe API and schema are described fully using [OpenAPI] specification.\n\nMake sure to CGI-escape name-strings for GET requests. An '\u0026' character\nneeds to be converted to '%26'\n\n* `GET /api?q=Aus+bus|Aus+bus+D.+%26+M.,+1870`\n* `POST /api` with request body of JSON array of strings\n\n```ruby\nrequire 'json'\nrequire 'net/http'\n\nuri = URI('https://parser.globalnames.org/api/v1/')\nhttp = Net::HTTP.new(uri.host, uri.port)\nhttp.use_ssl = true\nrequest = Net::HTTP::Post.new(uri, 'Content-Type' =\u003e 'application/json',\n                                   'accept' =\u003e 'json')\nrequest.body = ['Solanum mariae Särkinen \u0026 S.Knapp',\n                'Ahmadiago Vánky 2004'].to_json\nresponse = http.request(request)\n```\n\n### Use as a Docker image\n\nYou need to have [docker runtime installed][docker-install]\non your computer for these examples to work.\n\n```bash\n# run as a website and a RESTful service\ndocker run -p 0.0.0.0:80:8080 gnames/gognparser -p 8080\n\n# just parse something\ndocker run gnames/gognparser \"Amaurorhinus bewichianus (Wollaston,1860) (s.str.)\"\n```\n\n### Use as a library in Go\n\n```go\nimport (\n  \"fmt\"\n\n  \"github.com/gnames/gnparser\"\n  \"github.com/gnames/gnparser/ent/parsed\"\n)\n\nfunc Example() {\n  names := []string{\"Pardosa moesta Banks, 1892\", \"Bubo bubo\"}\n  cfg := gnparser.NewConfig()\n  gnp := gnparser.New(cfg)\n  res := gnp.ParseNames(names)\n  fmt.Println(res[0].Authorship.Normalized)\n  fmt.Println(res[1].Canonical.Simple)\n  fmt.Println(parsed.HeaderCSV(gnp.Format()))\n  fmt.Println(res[0].Output(gnp.Format()))\n  // Output:\n  // Banks 1892\n  // Bubo bubo\n  // Id,Verbatim,Cardinality,CanonicalStem,CanonicalSimple,CanonicalFull,Authorship,Year,Quality\n  // e2fdf10b-6a36-5cc7-b6ca-be4d3b34b21f,\"Pardosa moesta Banks, 1892\",2,Pardosa moest,Pardosa moesta,Pardosa moesta,Banks 1892,1892,1\n}\n```\n\n### Use as a shared C library\n\nIt is possible to bind `GNparser` functionality with languages that can use\nC Application Binary Interface. For example such languages include\nPython, Ruby, Rust, C, C++, Java (via JNI).\n\nTo compile `GNparser` shared library for your platform/operating system of\nchoice you need [just] and `GNU gcc compiler` installed:\n\n```bash\njust clib\ncd binding\ncp libgnparser* /path/to/some/project\n```\n\nAs an example how to use the shared library check this [StackOverflow\nquestion][ruby_ffi_go_usage] and [biodiversity] Ruby gem.\n\n## Parsing ambiguities\n\nSome name-strings cannot be parsed unambiguously without some additional data.\n\n### Names with `filius` (ICN code)\n\nFor names like `Aus bus Linn. f. cus` the `f.` is ambiguous. It might mean\nthat species were described by a son of (`filius`) Linn., or it might mean\nthat `cus` is `forma` of `bus`. We provide a warning\n\"Ambiguous f. (filius or forma)\" for such cases.\n\n### Names with subgenus (ICZN code) and genus author (ICN code)\n\nFor names like `Aus (Bus) L.` or `Aus (Bus) cus L.` the `(Bus)` token would\nmean the name of subgenus for ICZN names, but for ICN names it would be an\nauthor of genus `Aus`. We created a list of ICN generic authors using data from\n[IRMNG] to distinguish such names from each other. For detected ICN names we\nprovide a warning \"Ambiguity: ICN author or subgenus\".\n\n### Virus names according to modern ICVCN binomial nomenclature\n\nICVCN code adopted binomial nomenclature in 2021, and converted most names to\nnew rules by 2026. However the rules for viral names differ significanlty in\ncomparison with other nomenclatural codes (e.g., names like `Batravirus\nranidallo3` or `Pradovirus XAJ24` are legal ICVCN names), so we had to create a\nspecialized parser for them. It creates parsing challenges for names like\n`Calviria`, `Euvira` (ICZN genera) that by chance matched ICVCN rules for Ream\nand Subrealm. We try to detect such names and place them in an exception list.\n\n## Authors\n\n* [Dmitry Mozzherin]\n\n## Contributors\n\n* [Toby Marsden]\n* [Geoffrey Ower]\n* [Philippe Juillerat]\n* [Hernan Lucas Pereira]\n\nIf you want to submit a bug or add a feature read\n[CONTRIBUTING] file.\n\n## Artificial Intelligence Policy\n\nWe use artificial intelligence to help find algorithms, decide on\nimplementation approaches, and generate code. We carefully review all\nautomatically generated code, fixing inconsistencies, removing superfluous\nimplementations, and improving optimization. No code that we do not understand\nor approve makes it into published versions of GNparser. We primarily use\nClaude Code, with limited use of Gemini CLI.\n\n## References\n\nMozzherin, D.Y., Myltsev, A.A. \u0026 Patterson, D.J. “gnparser”: a powerful parser\nfor scientific names based on Parsing Expression Grammar. BMC Bioinformatics\n18, 279 (2017).[https://doi.org/10.1186/s12859-017-1663-3][gnparser paper]\n\nRees, T. (compiler) (2019). The Interim Register of Marine and Nonmarine\nGenera. Available from `http://www.irmng.org` at VLIZ.\nAccessed 2019-04-10\n\n## License\n\nReleased under [MIT license]\n\n[CONTRIBUTING]: CONTRIBUTING.md\n[Dmitry Mozzherin]: https://github.com/dimus\n[Geoffrey Ower]: https://github.com/gdower\n[Hernan Lucas Pereira]: https://github.com/LocoDelAssembly\n[Homebrew]: https://brew.sh/\n[IRMNG]: http://www.irmng.org\n[MIT license]: https://github.com/gnames/gnparser/raw/master/LICENSE\n[OpenAPI]: https://apidoc.globalnames.org/gnparser\n[OpenRefine]: https://github.com/gnames/gnparser/wiki/GNparser-with-OpenRefine\n[PHP pipes]: https://gist.github.com/marcobrt/72b2a3d1b0649c1bf738c9fc88f74ec0\n[Philippe Juillerat]: https://github.com/juillerat\n[Schinke R et al (1996)]: https://caio.ueberalles.net/a_stemming_algorithm_for_latin_text_databases-schinke_et_al.pdf\n[Toby Marsden]: https://github.com/tobymarsden\n[Zenodo DOI]: https://zenodo.org/badge/latestdoi/320967495\n[biodiversity]: https://github.com/GlobalNamesArchitecture/biodiversity\n[docker-install]: https://docs.docker.com/install/\n[gna]: http://globalnames.org\n[gnparser paper]: https://doi.org/10.1186/s12859-017-1663-3\n[gnparser-scala]: https://github.com/GlobalNamesArchitecture/gnparser\n[node-gnparser]: https://github.com/amazingplants/node-gnparser\n[parser-web]: https://parser.globalnames.org\n[peg]: https://github.com/pointlander/peg\n[quality]: https://github.com/gnames/gnparser/blob/master/quality.md\n[releases]: https://github.com/gnames/gnparser/releases/latest\n[rgnparser]: https://github.com/ropensci/rgnparser\n[ruby_ffi_go_usage]: https://stackoverflow.com/questions/58866962/how-to-pass-an-array-of-strings-and-get-an-array-of-strings-in-ruby-using-go-sha\n[test file]: https://github.com/gnames/gnparser/blob/master/testdata/test_data.md\n[tutGN]: https://globalnames.org/docs/tut-xsv-gnparser/\n[uuid5]: http://globalnames.org/news/2015/05/31/gn-uuid-0-5-0\n[v0diff]: https://github.com/gnames/gnparser/wiki/Changes-in-v1.0.0\n[winpath]: https://www.computerhope.com/issues/ch000549.htm\n[wsl]: https://docs.microsoft.com/en-us/windows/wsl/\n","funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.18248840","https://doi.org/10.1186/s12859-017-1663-3"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["install","taxonomy","biodiversity-informatics","collections","describe","evolution","life","species","taxonworks","capistrano"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/351822","html_url":"https://ost.ecosyste.ms/projects/351822"}