https://github.com/dhimmel/bindingdb

Process BindingDB
https://github.com/dhimmel/bindingdb

binding bindingdb compound drug hetionet protein rephetio tsv

Last synced: 6 months ago
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Process BindingDB

• Host: GitHub
• URL: https://github.com/dhimmel/bindingdb
• Owner: dhimmel
• Created: 2015-04-10T21:02:24.000Z (about 11 years ago)
• Default Branch: gh-pages
• Last Pushed: 2015-11-19T01:10:30.000Z (over 10 years ago)
• Last Synced: 2025-01-28T23:50:17.349Z (over 1 year ago)
• Topics: binding, bindingdb, compound, drug, hetionet, protein, rephetio, tsv
• Language: HTML
• Homepage: https://doi.org/10.15363/thinklab.d53
• Size: 14.3 MB
• Stars: 8
• Watchers: 2
• Forks: 4
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          
# Processing BindingDB

[![DOI](https://zenodo.org/badge/14475/dhimmel/bindingdb.svg)](https://zenodo.org/badge/latestdoi/14475/dhimmel/bindingdb)

This repository contains our processing of [BindingDB](https://www.bindingdb.org/bind/index.jsp). Refer to the corresponding [Thinklab discussion](https://doi.org/10.15363/thinklab.d53) for more information.

## License

BindingDB includes the following [licensing statement](https://github.com/dhimmel/integrate/blob/1a43ef2718283cbfc9ae869aee1856bf20e2ad6e/licenses/custom/BindingDB.md):

> Data imported from ChEMBL are provided under their [Creative Commons Attribution-Share Alike 3.0 Unported License](https://www.ebi.ac.uk/chembl/about). All data curated by BindingDB staff are provided under the [Creative Commons Attribution 3.0 License](https://creativecommons.org/licenses/by/3.0/us/).

All original content in this repository is released as [CC0](https://creativecommons.org/publicdomain/zero/1.0/).

## Execution

The analysis can be reproduced by running `process.ipynb` followed by `collapse.Rmd`.

The python notebook `process.ipynb`:

+ processes affinities to floats

+ converts to entrez genes

+ simplifies observations into essential fields

The rmarkdown script `collapse.Rmd`:

+ filters to human experiments

+ converts to drugbank compounds

+ collapses observations by compound-gene pairs