gntagger not only finds scientific names in a document. It also allows the user to go through each found name, see it in a context of a text, and then accept or reject the found name.
We made this program so we can improve on the quality of name-finding algorithm, but it is useful for anybody who needs to extract scientific names from a book or a scientific paper. The program works for MS Windows, Mac and Linux and it runs from a command line interface -- CMD in case of windows, or a terminal under Mac and Linux.
gntagger allows you to curate 4000 names spread over 600 pages in about 2 hours. It is significantly faster than curation made in a text editor or pdf viewer.
The program is just an executable file that runs from a command line. Download the
latest zip or tar file for your operating system, extract the file
and place it somehere in your
PATH, so it is visible by your system.
Conversion of PDF to text
gntagger works with plain texts, so if you need to find names in a PDF file, first you need to convert it to text.
Usually you can just use
less paper1.pdf | gntagger
Another option is pdftotext from xpdf package.
brew install Caskroom/cask/xquartz brew install xpdf pdftotext -layout doc.pdf doc.txt
Download Xpdf tools, unzip them, and use pdftotext.exe
pdftotext.exe -layout doc.pdf doc.txt
To find out version
gntagger -version gntagger -V
To get names from a file (processed text and list of names will be saved in the same directory as the text file)
gntagger file_with_names.txt # on windows gntagger.exe file_with_names.txt
To get names from stanard input
# linux less file.pdf | gntagger less file.pdf | gntagger -bayes # mac pdftotext -layout file.pdf | gntagger pdftotext -layout file.pdf | gntagger -bayes
Note that -layout flag for pdftotext tries to preserve the original structure of the text, as it was in the original PDF. It significantly increases chances for finding names that are split between the end and the start of two lines.
The user interface of the program consists of 2 panels. The left panel contains detected scientific names, with a "current name" located in the middle of the screen and highlighted. The left panel contains the full text, where the "current name" is highlighted and aligned with the "current name" in the left panel.
The program is designed to move though the names quickly. Navigate to the next/previous name in the left panel using Right/Left arrow keys. All names have an empty annotation at the beginning. Pressing Right Arrow key automatically "accepts" found name if the annotation is empty. Other keys allow to annotate the "current name" differently:
Space: rejects a name with "NotName" annotation
'y': re-accepts mistakenly rejected name with "Accepted" annotation
'u': marks a name as "Uninomial"
'g': marks a name as "Genus"
's': marks a name as "Species"
Ctrl-C: saves curation and exits application
Ctrl-S: saves curations made so far
Current names are saved to clipboard automatically, so it is easy to paste them into a browser, speadsheet, database, or text editor.
The program autosaves results of curation. If the program crashes, or exited the user can continue curation at the last point instead of starting from scratch.
Install ginkgo, a BDD testing framefork for Go.
go get github.com/onsi/ginkgo/ginkgo go get github.com/onsi/gomega
To run tests go to root directory of the project and run
ginkgo #or go test
go build -ldflags "-X main.buildstamp=`date -u '+%Y-%m-%d_%I:%M:%S%p'` \ -X main.githash=`git rev-parse HEAD | cut -c1-7` \ -X main.gittag=`git describe --tags`" \ -o gntagger -a cmd/gntagger/main.go