IMPORTANT: This project is moved to https://github.com/gnames/gnverifier
Takes a name or a list of names and verifies them against a variety of biodiversity Data Sources
- Small and fast app to verify scientific names against many biodiversity databases.
- Has 4 different match levels:
- Exact: complete match with a canonical form or full name-string from a data source.
- Fuzzy: if exact match did not happen, it tries to match name-strings assuming spelling errors.
- Partial: strips middle or last epithets from bi- or multi-nomial names and tries to match what is left.
- PartialFuzzy: the same as Partial but assuming spelling mistakes.
- Taxonomic resolution. If a database contains taxonomic information, returns currently accepted name for a name-string, if it is different from the matched name.
- Best match is returned according to the match score. Data sources with some manual curation have priority over auto-curated and uncurated datasets. For example Catalogue of Life or WoRMS are considered curated, GBIF auto-curated, uBio not curated.
- It is possible to map any name-strings checklist to any of registered Data Sources.
- If a Data Source provides classification for a name, it will be returned in the output.
- Works for checking just one name-string, or multiple ones written in a file.
- Supports feeding data via pipes of an operating system. This feature allows to chain the program together with other tools.
Homebrew is a popular package manager for Open Source software originally developed for Mac OS X. Now it is also available on Linux, and can easily be used on Windows 10, if Windows Subsystem for Linux (WSL) is installed.
gnverify with Homebrew:
Open terminal and run the following commands:
brew tap gnames/gn brew install gnverify
Download the latest release from github, unzip.
One possible way would be to create a default folder for executables and place
combination and type "
cmd". In the appeared terminal window type:
mkdir C:\Users\your_username\bin copy path_to\gnverify.exe C:\Users\your_username\bin
C:\Users\your_username\bin directory to your
Another, simpler way, would be to use
cd C:\Users\your_username\bin command
cmd terminal window. The
gnverify program then will be automatically
found by Windows operating system when you run its commands from that
You can also read a more detailed guide for Windows users in a PDF document.
Download the latest release from github, untar, and install binary somewhere in your path.
tar xvf gnverify-linux-0.1.0.tar.xz # or tar xvf gnverify-mac-0.1.0.tar.gz sudo mv gnverify /usr/local/bin
Install Go according to installation instructions
go get github.com/gnames/gnverify/gnverify
gnverify takes one name-string or a text file with one name-string per line
as an argument, sends a query with these data to remote
gnames server to match the name-strigs against many different
biodiversity databases and returns results to STDOUT either in JSON or CSV
gnverify -w 8080
You should be able to access web user interface via a browser at
gnverify "Monohamus galloprovincialis"
The app assumes that a file contains a simple list of names, one per line.
It is also possible to feed data via STDIN:
cat /path/to/names.txt | gnverify
According to POSIX standard flags and options can be given either before or after name-string or file name.
gnverify -h # or gnverify --help # or gnverify
gnverify -V # or gnverify --version
Starts gnverify as a web service using entered port
gnverify -w 8080
This command will run user-interface accessible by a browser
Allows to pick a format for output. Supported formats are
- compact: one-liner JSON.
- pretty: prettified JSON with new lines and tabs for easier reading.
- csv: (DEFAULT) returns CSV representation.
gnverify -f compact file.txt # or gnverify --format="pretty" file.csv
Note that a separate JSON "document" is returned for each separate record, instead of returning one big JSON document for all records. For large lists it significantly speeds up parsin of the JSON on the user side.
gnverify returns only one "best" result of a match. If a user
has a particular interest in a data set, s/he can set it with this option, and
all matches that exist for this source will be returned as well. You need to
provide a data source id for a dataset. Ids can be found at the following
URL. Some of them are provided in the
output as well.
Data from such sources will be returned in preferred_results section of JSON output, or with CSV rows that start with "PreferredMatch" string.
gnverify file.csv -s "1,11,172" # or gnverify file.tsv --sources="12" # or cat file.txt | gnverify -s '1,12'
Sometimes a users wants to map a list of names to a DataSource. They
are not interested if name matched anywhere else. In such case you can use
gnverify -p -s '12' file.txt # or gnverify --preferred_only --sources='1,12' file.tsv
If the list of names if very large, it is possible to tell gnverify to run requests in parallel. In this example gnverify will run 8 processes simultaneously. The order of returned names will be somewhat randomized.
gnverify -j 8 file.txt # or gnverify --jobs=8 file.tsv
Sometimes it is important to return names in exactly same order. For such
jobs flag to 1.
gnverify -j 1 file.txt
If you find yourself using the same flags over and over again, it makes sense
to edit configuration file instead. It is located at
$HOME/.config/gnverify.yaml. After that you do not need to use command line
options and flags.
Authors: Dmitry Mozzherin
Copyright © 2020 Dmitry Mozzherin. See LICENSE for further details.