ISA-explorer

The ISA-explorer web application has been developed to provide a visualization of ISATab files and it can be used to host a lightweight ISATab repository. It runs on a Node.js environment and relies on python to load the datasets.

Dependencies

• Node.js 6+
• Python 3.5+

Libraries used:

• FontAwesome 4.3.0
• lunr.js - fast full text search within the browser
• React.js (v0.15)
• Express.js web framework

License

This code is made available with BSD 3-Clause License.

Installation

To download and process the datasets

Simply clone the repository, or download it as a zip file.

We recommend running the python scripts using a virtual environment.

1. If not already installed in your system, first install the virtual environment via pip:

   pip install virtualenv

2. Create a virtual environament:

   virtualenv venv

3. Then, activate the virtual environment:

source venv/bin/activateif you are using the bash shell or . venv/bin/activate if you are using /bin/sh

4. Install the requirements:

pip install -r requirements.txt

or

pip install --upgrade -r requirements.txt

if you want to upgrade the requirements already installed.

To download Springer Nature Scientific Data files, run the sdata_crossref_download.py script:

python scripts/sdata_crossref_download.py

Or to use your own data, place your ISA-Tab files in the Data directory (can also be symlinks).

To build a new index over the files, run the build_index.py script, which will build an initial metadata repository JSON file that is used by lunr.js to search, and by the web application to present the initial file list.:

python scripts/build_index.py data

This will create a file called isatab-index.json which will be read by the application to generate the search interface.

To generate the json-ld with schema.org representation, use:

python scripts/schemaorg_conversion.py

To run the React-based web application

To install dependencies:

npm install

To build the assets locally:

npm run build:local

(check other builds in package.json)

To run the web server:

node server.js

Documentation

• Gonzalez-Beltran, Alejandra's post in Scientific Data blog
• Gonzalez-Beltran, Alejandra's slides Data Publication: Discover, Explore, Visualise presented at the Data Visualisation and the Future of Academic Publishing meeting organised by the University of Oxford and Oxford University Press on June 10th 2016.
• Gonzalez-Beltran, Alejandra; Maguire, Eamonn; Khodiyar, Varsha; Rocca-Serra, Philippe; Johnson, David; Izzo, Massimiliano; et al. Find me the data - Discover and explore Springer Nature’s Scientific Data datasets with the ISA-explorer tool presented at Force2016