Life Sciences Accessibility Evaluation

This repository contains source code for surveying the accessibility of life sciences data resources and journals and visualizing results.

Development

Set up environments using Conda:

conda env create -f environment.yml

Start Jupyter with the Python kernel:

conda activate life-sciences-a11y-evaluation
jupyter lab notebooks

Important

Accessibility is evaluated using WAVE API. To run the evaluation, you need to put an api.lab.key file that contains the API key. If you are a member of HIDIVE Lab, contact either Sehi L'Yi (sehi_lyi@hms.harvard.edu) or Nils Gehlenborg to obtain the API key.

Data Schema

Troubleshooting

To add or remove a conda package, update the environment file. Then run

conda env update -f environment.yml

If you cannot find the Python kernel you created, the following solution may work:

https://stackoverflow.com/a/71040470/2499810

Data

Webpages to data portals are selected from Database Commons (https://ngdc.cncb.ac.cn/databasecommons), which is a site recommended by Cell Press and Bioinformatics Advances.

https://ngdc.cncb.ac.cn/databasecommons/database/browse?term=&q=&draw=1&columns%5B0%5D.data=0&columns%5B0%5D.name=&columns%5B0%5D.searchable=false&columns%5B0%5D.orderable=false&columns%5B0%5D.search.value=&columns%5B0%5D.search.regex=false&columns%5B1%5D.data=zindex&columns%5B1%5D.name=&columns%5B1%5D.searchable=true&columns%5B1%5D.orderable=true&columns%5B1%5D.search.value=&columns%5B1%5D.search.regex=false&columns%5B2%5D.data=citation&columns%5B2%5D.name=&columns%5B2%5D.searchable=true&columns%5B2%5D.orderable=true&columns%5B2%5D.search.value=&columns%5B2%5D.search.regex=false&columns%5B3%5D.data=shortName&columns%5B3%5D.name=&columns%5B3%5D.searchable=true&columns%5B3%5D.orderable=true&columns%5B3%5D.search.value=&columns%5B3%5D.search.regex=false&columns%5B4%5D.data=foundedYear&columns%5B4%5D.name=&columns%5B4%5D.searchable=true&columns%5B4%5D.orderable=true&columns%5B4%5D.search.value=&columns%5B4%5D.search.regex=false&order%5B0%5D.column=1&order%5B0%5D.dir=desc&order%5B1%5D.column=4&order%5B1%5D.dir=DESC&start=0&length=10000&search.value=&search.regex=false&_=1667231167872

Cite

Please cite the following paper:

Sehi L'Yi, Thomas C Smits, Alexander Lex, Nils Gehlenborg, 
Digital Accessibility of Life Sciences Data Portals and Journal Websites, 
OSF Preprints, 10.31219/osf.io/5v98j

hms-dbmi / life-sciences-a11y-evaluation