Try GNfinder online or learn about its API.
Very fast finder of scientific names. It uses dictionary and NLP approaches. On modern multiprocessor laptop it is able to process 15 million pages per hour. Works with many file formats and includes names verification against many biological databases. For full functionality it requires an Internet connection.
GNfinder is also awailable via web or
as a RESTful API.
Zenodo DOI can be used to cite GNfinder.
- Multiplatform app (supports Linux, Windows, Mac OS X).
- Self-contained, no external dependencies, only binary
gnfinderorgnfinder.exe(~15Mb) is needed. However the internet connection is required for name-verification. - Includes REST API and web-based User Interface.
- Takes UTF8-encoded text and returns back CSV, TSV or JSON-formatted output that contains detected scientific names.
- Extracts text from PDF files, MS Word, MS Excel, HTML, XML, RTF, JPG, TIFF, GIF etc. files for names-detection.
- Downloads web-page from a given URL for names-detection.
- Optionally, automatically detects the language of the text, and adjusts Bayes algorithm for the language. English and German languages are currently supported.
- Uses complementary heuristic and natural language processing algorithms.
- Optionally verifies found names against multiple biodiversity databases using gnindex service.
- Detection of nomenclatural annotations like
sp. nov.,comb. nov.,ssp. nov.,nom. nov.and their variants. - Ability to see words that surround detected name-strings.
- The library can be used concurrently to significantly improve speed. On a server with 40threads it is able to detect names on 50 million pages in approximately 3 hours using both heuristic and Bayes algorithms. Check bhlindex project for an example.
Homebrew on Mac OS X, Linux, and Linux on Windows (WSL2)
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 MS Windows 10 or 11, if Windows Subsystem for Linux (WSL) is [installed][WSL install].
Note that Homebrew requires some other programs to be installed, like Curl,
Git, a compiler (GCC compiler on Linux, Xcode on Mac). If it is too much,
go to the Linux and Mac without Homebrew section.
-
Install Homebrew according to their instructions.
-
Install
GNfinderwith:brew tap gnames/gn brew install gnfinder # to upgrade brew upgrade gnfinder
AUR package is located at https://aur.archlinux.org/packages/gnfinder.
Install it by hand, or with AUR helpers like yay or pacaur.
yay -S gnfinder
# or
pacaur -S gnfinderGNfinder consists of just one executable file, so it is pretty easy to
install it by hand. To do that download the binary executable for your
operating system from the latest release.
Move gnfinder executable somewhere in your PATH
(for example /usr/local/bin)
sudo mv path_to/gnfinder /usr/local/binIt is possible to use GNfinder natively on Windows, without Homebrew or
Linux installed.
One possible way would be to create a default folder for executables and place
gnfinder there.
Use Windows+R keys
combination and type "cmd". In the appeared terminal window type:
mkdir C:\bin
copy path_to\gnfinder.exe C:\binAdd C:\bin directory to your PATH environment variable.
Install Go v1.19 or higher.
git clone [email protected]:/gnames/gnfinder
cd gnfinder
make tools
make installWhen you run gnfinder command for the first time, it will create a
gnfinder.yml configuration file.
This file should be located in the following places:
MS Windows: C:\Users\AppData\Roaming\gnfinder.yml
Mac OS: $HOME/.config/gnfinder.yml
Linux: $HOME/.config/gnfinder.yml
This file allows to set options that will modify behaviour of GNfinder
according to your needs. It will spare you to enter the same flags for the
command line application again and again.
Command line flags will override the settings in the configuration file.
It is also possible to setup environment variables. They will override the settings in both the configuration file and from the flags.
| Settings | Environment variables |
|---|---|
| BayesOddsThreshold | GNF_BAYES_ODDS_THRESHOLD |
| DataSources | GNF_DATA_SOURCES |
| Format | GNF_FORMAT |
| InputTextOnly | GNF_INPUT_TEXT_ONLY |
| IncludeInputText | GNF_INCLUDE_INPUT_TEXT |
| Language | GNF_LANGUAGE |
| TikaURL | GNF_TIKA_URL |
| TokensAround | GNF_TOKENS_AROUND |
| VerifierURL | GNF_VERIFIER_URL |
| WithAllMatches | GNF_WITH_ALL_MATCHES |
| WithAmbiguousNames | GNF_WITH_AMBIGUOUS_NAMES |
| WithBayesOddsDetails | GNF_WITH_BAYES_ODDS_DETAILS |
| WithOddsAdjustment | GNF_WITH_ODDS_ADJUSTMENT |
| WithPlainInput | GNF_WITH_PLAIN_INPUT |
| WithPositionInBytes | GNF_WITH_POSITION_IN_BYTES |
| WithUniqueNames | GNF_WITH_UNIQUE_NAMES |
| WithVerification | GNF_WITH_VERIFICATION |
| WithoutBayes | GNF_WITHOUT_BAYES |
GNfinder can be found at https://finder.globalnames.org.
API is located at https://finder.globalnames.org/api/v1.
Best source for API usage is its documenation.
If you want to start your own API endpoint (for example on localhost, port
8080) use:
gnfinder -p 8080
curl localhost:8080/api/v1/pingTo upload a file and detect names from its content:
curl -v -F verification=true -F file=@/path/to/test.txt https://gnfinder.globalnames.org/api/v1/findTo see flags and usage:
gnfinder --help
# or just
gnfinderTo see the version of its binary:
gnfinder -VExamples:
Starting as a web-application and an API server on port 8080
gnfinder -p 8080Getting names from a UTF8-encoded file without remote Tika service.
# -U flag prevents use of remote Apache Tika service for file conversion to
# UTF8-encoded plain text
# -U flag is optional, but it removes unnecessary remote call to Tika.
gnfinder file_with_names.txt -UGetting names from a UTF8-encoded file in tab-separated values (TSV) format
gnfinder file_with_names.txt -U -f tsvGetting names from a file that is not a plain UTF8-encoded text
gnfinder file.pdfGetting names from a URL
gnfinder https://en.wikipedia.org/wiki/RaccoonGetting unique names from a file in JSON format. Disables -w flag.
gnfinder file_with_names.txt -u -f prettyGetting names from a file in JSON format, and using jq to process JSON
gnfinder file_with_names.txt -f compact | jqGetting data from a pipe forcing English language and verification
echo "Pomatomus saltator and Parus major" | gnfinder -v -l eng
echo "Pomatomus saltator and Parus major" | gnfinder --verify --lang engLimit matches to NCBI and Encyclopedia of Life. For
the list of data source ids go to gnverifier's data sources page.
echo "And Parus major" | gnfinder -v -l eng -s "4,12"
echo "And Parus major" | gnfinder --verify --lang eng --sources "4,12"Preserve uninomial names that are also common words.
echo "Cancer is a genus" | gnfinder -A
echo "America is also a genus" | gnfinder --ambiguous-uninomialsShow all matches, not only the best result.
echo "Pomatomus saltator and Parus major" | gnfinder -M
echo "Pomatomus saltator and Parus major" | gnfinder --all-matchesShow all matches, but only for selected data-sources.
echo "Pomatomus saltator and Parus major" | gnfinder -M -s 1,12Adjusting Prior Odds using information about found names. They are calculated as "found names number / (capitalized words number - found names number)". Such adjustment will decrease Odds for texts with very few names, and increase odds for texts with a lot of found names.
gnfinder -a -d -f pretty file_with_names.txtReturning 5 words before and after found name-candidate. This flag does is ignored if unique names are returned.
gnfinder -w 5 file_with_names.txt
gnfinder --words-around 5 file_with_names.txtGetting data from a file and redirecting result to another file
gnfinder file1.txt > file2.jsonDetection of nomenclatural annotations
echo "Parus major sp. n." | gnfinderReturning found names positions in the number of bytes from the beginning of the text instead of the number of UTF-8 characters
echo "Это Parus major" | gnfinder -bThere is also a tutorial about processing many PDF files in parallel.
import (
"github.com/gnames/gnfinder"
"github.com/gnames/gnfinder/ent/nlp"
"github.com/gnames/gnfinder/io/dict"
)
func Example() {
txt := `Blue Adussel (Mytilus edulis) grows to about two
inches the first year,Pardosa moesta Banks, 1892`
cfg := gnfinder.NewConfig()
dictionary := dict.LoadDictionary()
weights := nlp.BayesWeights()
gnf := gnfinder.New(cfg, dictionary, weights)
res := gnf.Find(txt)
name := res.Names[0]
fmt.Printf(
"Name: %s, start: %d, end: %d",
name.Name,
name.OffsetStart,
name.OffsetEnd,
)
// Output:
// Name: Mytilus edulis, start: 13, end: 29
}docker pull gnames/gnfinder
# run GNfinder server, and map it to port 8888 on the host machine
docker run -d -p 8888:8778 --name gnfinder gnames/gnfindergnfinder-plus allows to work with MS Docs and PDF files without remote
services (requires local install of poppler package).
bhlindex creates an index of scientific names for Biodiversity Heritage Library (BHL).
bhlnames adds synonymy and currently accepted names to searches in BHL, connects publications to pages in BHL.
To install the latest GNfinder
git clone [email protected]:/gnames/gnfinder
cd gnfinder
make tools
make installFrom the root of the project:
make tools
# run make install for CLI testing
make installTo run tests go to the root directory of the project and run
go test ./...
#or
make test
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