Linux Installation Procedure

getpapers

Download npm and node using your package manager.

On Ubuntu and Debian npm come packaged with the nodejs package. You must also install nodejs-legacy to get the executable named node.

run npm install --global getpapers either as root or with sudo enabled

You can check it has worked by moving on to the ‘Operating Procedure’ below.

norma

With .deb

Install the .deb from github if on Debian or Ubuntu.

this is done by downloading to a place of your chosing and running dpkg -i <path to .deb>

Alternate method

We are in the process of preparing rpms.

You can also install manually using a zip file: 1. Download the latest zip binary release from github (the .zip) 1. unzip all files to somewhere convenient 1. Add the bin directory that you unzipped to your path

ami

With .deb

Install the .deb from github if on Debian or Ubuntu.

this is done by downloading to a place of your chosing and running dpkg -i <path to .deb>

Alternate method

We are in the process of preparing rpms.

You can also install manually using a zip file: 1. Download the latest binary release from github (the .zip) here 1. unzip all files to somewhere convenient 1. Add the bin directory that you unzipped to your path

Linux Operating Procedure

getpapers

Detailed instructions can be found in our workshop-resources.

To get started and download a set of FullText XML files of OpenAccess papers from EuropePMC just run:

You might get back many thousands of results, you can cancel with Ctrl-C.

getpapers -q <your query> -o <a folder to save them in> -x

If you look inside the folder you’ll see there are many more folders; each of which contain a fulltext.xml file which is the contents of that paper.

For example if you run getpapers -q aardvark -o aardvark -x You’ll get ca. 110 XML files.

norma

You could either download and install packages on their website or preferably use your package manager. For example apt-get or yum etc..

If you’re only working on papers form EuropePMC downloaded with getpapers you might not need to run norma seperately. See the ami instructions below.

Detailed instructions can be found in our workshop-resources

To convert the papers into a form we can mine use Norma.

norma --project <your folder of papers> -i fulltext.xml -o scholarly.html --transform nlm2html

ami

You could either download and install packages on their website or preferably use your package manager. For example apt-get or yum etc.. Detailed instructions can be found at github

You can actually run ami without calling norma first if you’re just using xml papers downloaded from EuropePMC.

To run a default set of plugins simply type:

cmine <folder name>

This will give you html results tables in the project folder.

To add your own dictionaries use something of the form:

cmine <folder name> word(search)w.search:/org/xmlcml/ami2/plugins/dictionary/tropicalVirus.xml