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disgenet's Introduction

Extracting disease–gene associations from DisGeNET

DisGeNET is a resource that integrates disease–gene associations from several sources [ref]. We're using the resource in Rephetio, our network for drug repurposing. This repository extracts associations for the diseases and genes in rephetio.

disgenet.ipynb processes the DisGeNET downloads and outputs user-friendly TSVs to data.

License

DisGeNET content and derivatives are licensed under the ODbL 1.0. All original content is licensed under CC0 1.0.

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disgenet's Issues

Mapping DOID to UMLS ids

Hi Daniel,
First I'd like to thank you for sharing your analysis scripts online as they help a great deal in helping advance bioinformatics knowledge. I am processing DisGeNet data as part of my disease gene prioritization pipeline similar to what you did here https://github.com/dhimmel/disgenet/blob/master/disgenet.ipynb. I am interested in how you generated mappings between DOIDs and UMLS ids. In your script you pass a url to the already generated mapping file. Would you please show me where you obtained the mappings as I'd like to work with the latest available data. The mapping file that I am referring to is

https://raw.githubusercontent.com/dhimmel/disease-ontology/72614ade9f1cc5a5317b8f6836e1e464b31d5587/data/xrefs-prop-slim.tsv

Thanks

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