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Life Sciences Accessibility Evaluation Open In Colab

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 ([email protected]) 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