https://github.com/inscidar/analysis-notebooks
The accessibility evaluation of life science resources
https://github.com/inscidar/analysis-notebooks
hidivelab
Last synced: about 2 months ago
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The accessibility evaluation of life science resources
- Host: GitHub
- URL: https://github.com/inscidar/analysis-notebooks
- Owner: inscidar
- License: mit
- Created: 2022-10-28T20:51:05.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-10-21T16:35:22.000Z (7 months ago)
- Last Synced: 2025-04-06T06:35:18.258Z (about 2 months ago)
- Topics: hidivelab
- Language: Jupyter Notebook
- Homepage:
- Size: 513 MB
- Stars: 2
- Watchers: 1
- Forks: 2
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Life Sciences Accessibility Evaluation [](https://colab.research.google.com/github/hms-dbmi/life-sciences-a11y-evaluation/blob/main/notebooks/99-Google-Colab-Playground.ipynb)
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:
```sh
conda env create -f environment.yml
```
Start Jupyter with the Python kernel:
```sh
conda activate life-sciences-a11y-evaluation
jupyter lab notebooks
```
Unzip accessibility results (`accessibility-status.csv.zip`) that you want to use and analyze.
## Troubleshooting
To add or remove a conda package, update the environment file. Then run
```sh
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](https://osf.io/5v98j/):
```
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
```