Try gnparser
online.
gnparser
splits scientific names into their semantic elements with an
associated meta information. For example, "Homo sapiens Linnaeus"
is
parsed into:
Element | Meaning | Position |
---|---|---|
Homo | genus | (0,4) |
sapiens | specificEpithet | (5,12) |
Linnaeus | author | (13,21) |
This parser, written in Go, is the 3rd iteration of the project. The first, biodiversity had been written in Ruby, the second, also gnparser, had been written in Scala. This project is now a substitution for the other two. It will be the only one that is maintained further. All three projects were developed as a part of Global Names Architecture Project.
To use gnparser
as a command line tool under Windows, Mac or Linux,
download the latest release, uncompress it, and copy gnparser
binary somewhere in your PATH.
wget https://github.com/gnames/gnparser/uploads/55d247b8fbade60116c7e3b650dd978c/gnparser-v0.9.0-linux.tar.gz
tar xvf gnparser-v0.9.0-linux.tar.gz
sudo cp gnparser /usr/local/bin
# for CSV output
gnparser "Homo sapiens Linnaeus"
# for JSON output
gnparser -f compact "Homo sapiens Linnaeus"
# or
gnparser -f pretty "Homo sapiens Linnaeus"
gnparser -h
- Introduction
- Speed
- Features
- Use Cases
- Installation
- Usage
- Parsing ambiguities
- Authors
- Contributors
- References
- License
Global Names Parser or gnparser
is a program written in Go for breaking up
scientific names into their elements. It uses peg -- a Parsing
Expression Grammar (PEG) tool.
Many other parsing algorithms for scientific names use regular expressions.
This approach works well for extracting canonical forms in simple cases.
However, for complex scientific names and to parse scientific names into
all semantic elements, regular expressions often fail, unable to overcome
the recursive nature of data embedded in names. By contrast, gnparser
is able to deal with the most complex scientific name-strings.
gnparser
takes a name-string like Drosophila (Sophophora) melanogaster Meigen, 1830
and returns parsed components in CSV
or JSON
format. The
parsing of scientific names might become surprisingly complex and the
gnparser's
test file is a good source of information about the parser's
capabilities, its input and output.
Number of names parsed per hour on a i7-8750H CPU (6 cores, 12 threads, at 2.20 GHz), parser v0.5.1
Threads | names/hr |
---|---|
1 | 48,000,000 |
2 | 63,000,000 |
4 | 128,000,000 |
8 | 202,000,000 |
16 | 248,000,000 |
100 | 293,000,000 |
For simplest output Go gnparser
is roughly 2 times faster than Scala
gnparser
and about 100 times faster than Ruby biodiversity
parser. For
JSON formats the parser is approximately 8 times faster than Scala one, due to
more efficient JSON conversion.
- Fastest parser ever.
- Very easy to install, just placing executable somewhere in the PATH is sufficient.
- Extracts all elements from a name, not only canonical forms.
- Works with very complex scientific names, including hybrid formulas.
- Includes gRPC server that can be used as if a native method call from C++,
- C#, Java, Python, Ruby, PHP, JavaScript, Objective C, Dart.
- Use as a native library from Go projects.
- Can run as a command line application.
- Can be scaled to many CPUs and computers (if 300 millions names an hour is not enough).
- Calculates a stable UUID version 5 ID from the content of a string.
- Provides C-binding to incorporate parser into other languages.
Canonical forms of a scientific name are the latinized components without
annotations, authors or dates. They are great for matching names that differ
in less stable parts. Use the canonicalName -> simple
or canonicalName -> full
fields from parsing results for this use case. Full
version of
canonical form includes infra-specific ranks and hybrid character for named
hybrids.
The canonicalName -> full
is good for presentation, as it keeps more
details.
The canonicalName -> simple
field is good for matching names from different
sources, because sometimes dataset curators omit hybrid sign in named hybrids,
or remove ranks for infraspecific epithets.
The canonicalName -> stem
field normalizes simple
canonical form even
further. The normalization is done according to stemming rules for Latin
language described in Schinke R et al (1996). For example letters j
are
converted to i
, letters v
are converted to u
, and suffixes are removed
from the specific and infraspecific epithets.
If you only care about canonical form of a name you can use --format csv
flag with command line tool.
CSV output has the following fields:
Field | Meaning |
---|---|
Id | UUID v5 generated out of Verbatim |
Verbatim | Input name-string without any changes |
Cardinality | 0 - N/A, 1 - Uninomial, 2 - Binomial etc. |
CanonicalFull | Canonical form with hybrid sign and ranks |
CanonicalSimple | Simplest canonical form |
CanonicalStem | Simplest canonical form with removed suffixes |
Authors | Author string of a name |
Year | Year of the name (if given) |
Quality | Parsing quality |
Usually scientific names can be broken into groups accoring by number of elements:
- Uninomial
- Binomial
- Trinomial
- Quadrinomial
The output of gnparser
contains a Cardinality
field that tells, when
possible, how many elements are detected in the name.
Cardinality | Name Type |
---|---|
0 | Undetermined |
1 | Uninomial |
2 | Binomial |
3 | Trinomial |
4 | Quadrinomial |
For hybrid formulas, "approximate" names (with "sp.", "spp." etc.), unparsed
names, as well as names from BOLD
project cardinality is 0 (Undetermined)
There are many inconsistencies in how scientific names may be written.
Use normalized
field to bring them all to a common form (spelling, spacing,
ranks).
Many data administrators store name-strings in two columns and split them into
"name part" and "authorship part". This practice misses some information when
dealing with names like "Prosthechea cochleata (L.) W.E.Higgins var.
grandiflora (Mutel) Christenson". However, if this is the use case, a
combination of canonicalName -> full
with the authorship from the
lowest taxon will do the job. You can also use --format csv
flag for
gnparse
command line tool.
If there are problems with parsing a name, parser generates qualityWarnings
messages and lowers parsing quality
of the name. Quality values mean the
following:
"quality": 1
- No problems were detected"quality": 2
- There were small problems, normalized result should still be good"quality": 3
- There were serious problems with the name, and the final result is rather doubtful"quality": 0
- A string could not be recognized as a scientific name and parsing fails
gnparser
uses UUID version 5 to generate its id
field.
There is algorithmic 1:1 relationship between the name-string and the UUID.
Moreover the same algorithm can be used in any popular language to
generate the same UUID. Such IDs can be used to globally connect information
about name-strings or information associated with name-strings.
More information about UUID version 5 can be found in the Global Names blog
gnparser
tries to correct problems with spelling, but sometimes it is
important to keep original spelling of the canonical forms or authorships.
The positions
field attaches semantic meaning to every word in the
original name-string and allows users to create canonical forms or other
combinations using the original verbatim spelling of the words. Each element
in positions
contains 3 parts:
- semantic meaning of a word
- start position of the word
- end position of the word
For example ["specificEpithet", 6, 11]
means that a specific epithet starts
at 6th character and ends before 11th character of the string.
Compiled programs in Go are self-sufficient and small (gnparser
is only a
few megabytes). As a result the binary file of gnparser
is all you need to
make it work. You can install it by downloading the latest version of the
binary for your operating system, and placing it in your PATH
.
Move gnparser
executable somewhere in your PATH
(for example /usr/local/bin
)
sudo mv path_to/gnparser /usr/local/bin
One possible way would be to create a default folder for executables and place
gnparser
there.
Use Windows+R
keys
combination and type "cmd
". In the appeared terminal window type:
mkdir C:\bin
copy path_to\gnparser.exe C:\bin
Add C:\bin
directory to your PATH
environment variable.
If you have Go installed on your computer use
go get -u github.com/gnames/gnparser
cd $GOPATH/srs/github.com/gnames/gnparser
make install
You do need your PATH
to include $HOME/go/bin
gnparser -f pretty "Quadrella steyermarkii (Standl.) Iltis & Cornejo"
Relevant flags:
--help -h
: help information about flags
--format -f
: output format. Can be compact
, pretty
, csv
, or debug
.
Default is csv
.
CSV format returns a header row and the CSV-compatible parsed result.
--jobs -j
: number of jobs running concurrently.
--nocleanup -n
: keeps HTML entities and tags if they are present in a name-string. If your
data is clean from HTML tags or entities, you can use this flag to increase
performance.
To parse one name:
# CSV ouput (default)
gnparser "Parus major Linnaeus, 1788"
# or
gnparser -f csv "Parus major Linnaeus, 1788"
# JSON compact format
gnparser "Parus major Linnaeus, 1788" -f compact
# pretty format
gnparser -f pretty "Parus major Linnaeus, 1788"
# to parse a name from the standard input
echo "Parus major Linnaeus, 1788" | gnparser
To parse a file:
There is no flag for parsing a file. If parser finds the given file path on
your computer, it will parse the content of the file, assuming that every line
is a new scientific name. If the file path is not found, gnparser
will try
to parse the "path" as a scientific name.
Parsed results will stream to STDOUT, while progress of the parsing will be directed to STDERR.
gnparser -j 200 names.txt > names_parsed.txt
# to parse files using pipes
cat names.txt | gnparser -f csv -j 200 > names_parsed.txt
# to keep html tags and entities during parsing. You gain a bit of performance
# with this option if your data does not contain HTML tags or entities.
gnparser "<i>Pomatomus</i> <i>saltator</i>"
gnparser -n "<i>Pomatomus</i> <i>saltator</i>"
gnparser -n "Pomatomus saltator"
To parse a file returning results in the same order as they are given (slower):
gnparser -j 1 names.txt > names_parsed.txt
Potentially the input file might contain millions of names, therefore creating
one properly formatted JSON output might be prohibitively expensive. Therefore
the parser creates one JSON line per name (when compact
format is used)
You can use up to 20 times more "threads" than the number of your CPU cores to
reach maximum speed of parsing (--jobs 200
flag). It is practical because
additional threads are very cheap in Go and they try to fill out every idle
gap in the CPU usage.
About any language has an ability to use pipes of the underlying operating
system. From the inside of your program you can make the CLI executable gnparser
to listen on a STDIN pipe and produce output into STDOUT pipe. Here is an
example in Ruby:
def self.start_gnparser
io = {}
['compact', 'csv'].each do |format|
stdin, stdout, stderr = Open3.popen3("./gnparser -j 200 --format #{format}")
io[format.to_sym] = { stdin: stdin, stdout: stdout, stderr: stderr }
end
end
Such arrangement would give you a nearly native performance for large datasets.
Relevant flags:
--help -h
: help information about flags
--grpc -g
: sets a port to run gRPC server, and starts gnparser in gRPC mode.
--jobs -j
: number or workers allocated per gRPC request. Default corresponds to the
number of CPU threads. If you have a full control over gRPC server of
gnparser
, set this option to 100-300 jobs.
gnparser -g 8989 -j 200
For an example how to use gRPC server check gnparser
Ruby gem as well as gRPC documentation.
It also helps to read gnparser.proto file to understand how to deal with inputs and outputs of gRPC server.
Use web-server REST API as a slower, but a more wide-spread alternative to
gRPC server. Web-based user interface and API are invoked by --web-port
or
-w
flag. To start web server on http://0.0.0.0:9000
gnparser -w 9000
Opening a browser with this address will now show an interactive interface
to parser. API calls would be accessibe on http://0.0.0.0:9000/api
.
Make sure to CGI-escape name-strings for GET requests. An '&' character needs to be converted to '%26'
GET /api?q=Aus+bus|Aus+bus+D.+%26+M.,+1870
POST /api
with request body of JSON array of strings
require 'json'
require 'net/http'
uri = URI('https://parser.globalnames.org/api')
http = Net::HTTP.new(uri.host, uri.port)
http.use_ssl = true
request = Net::HTTP::Post.new(uri, 'Content-Type' => 'application/json',
'accept' => 'json')
request.body = ['Solanum mariae Särkinen & S.Knapp',
'Ahmadiago Vánky 2004'].to_json
response = http.request(request)
You need to have docker runtime installed on your computer for these examples to work.
# run as a gRPC server on port 7777
docker run -p 0.0.0.0:7777:7777 gnames/gognparser -g 7777
# run grpc on 'default' 8778 port
docker run -p 0.0.0.0:8778:8778 gnames/gognparser
# to run as a daemon with 50 workers
docker run -d gnames/gognparser -g 7777 -j 50
# run as a website and a RESTful service
docker run -p 0.0.0.0:80:8080 gnames/gognparser -w 8080
# just parse something
docker run gnames/gognparser "Amaurorhinus bewichianus (Wollaston,1860) (s.str.)"
package main
import (
"fmt"
"github.com/gnames/gnparser"
)
func main() {
opts := []gnparser.Option{
gnparser.Format("csv"),
gnparser.WorkersNum(100),
}
gnp := gnparser.NewGNparser(opts...)
res, err := gnp.ParseAndFormat("Bubo bubo")
if err != nil {
fmt.Println(err)
}
fmt.Println(res)
}
To avoid JSON format we provide gnp.ParseToObject
function.
Use gnparser.proto file as a reference of the available object fields.
gnp := NewGNparser()
o := gnp.ParseToObject("Homo sapiens")
fmt.Println(o.Canonical.Simple)
switch d := o.Details.(type) {
case *pb.Parsed_Species:
fmt.Println(d.Species.Genus)
case *pb.Parsed_Uninomial:
fmt.Println(d.Uninomial.Value)
...
}
It is possible to bind gnparser
functionality with languages that can use
C Application Binary Interface. For example such languages include
Python, Ruby, Rust, C, C++, Java (via JNI).
To compile gnparser
shared library for your platform/operating system of
choice you need GNU make
and GNU gcc compiler
installed:
make clib
cd binding
cp libgnparser* /path/to/some/project
As an example how to use the shared library check this StackOverflow question and biodiversity Ruby gem. You can find shared functions at their export file.
Some name-strings cannot be parsed unambiguously without some additional data.
For names like Aus bus Linn. f. cus
the f.
is ambiguous. It might mean
that species were described by a son of (filius
) Linn., or it might mean
that cus
is forma
of bus
. We provide a warning
"Ambiguous f. (filius or forma)" for such cases.
For names like Aus (Bus) L.
or Aus (Bus) cus L.
the (Bus)
token would
mean the name of subgenus for ICZN names, but for ICN names it would be an
author of genus Aus
. We created a list of ICN generic authors using data from
IRMNG to distinguish such names from each other. For detected ICN names we
provide a warning "Possible ICN author instead of subgenus".
If you want to submit a bug or add a feature read CONTRIBUTING file.
Rees, T. (compiler) (2019). The Interim Register of Marine and Nonmarine
Genera. Available from http://www.irmng.org
at VLIZ.
Accessed 2019-04-10
Released under MIT license