Commit 8a618a8b authored by David Hoksza's avatar David Hoksza
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# Biohackathon 2019: Rare disease maps
Code to [https://r3.pages.uni.lu/biocuration/resources/biohackathon2019/rdmaps/](https://r3.pages.uni.lu/biocuration/resources/biohackathon2019/rdmaps/)
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Code and comments to [https://r3.pages.uni.lu/biocuration/resources/biohackathon2019/rdmaps/](https://r3.pages.uni.lu/biocuration/resources/biohackathon2019/rdmaps/).
- [Retrieval of gene-disease mappging and variants](associations/README.md).
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# Retrieval of gene-disease and variation-disease mapping
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# Retrieval of gene-disease and variation-disease mapping
The purpose of the Python tools in this directory is to obtain the gene-disease mapping
and possibly also relevant variants.
## DisGeNET
[DisGeNET](http://www.disgenet.org/) is used to retrieve both gene-disease mapping and variants
using its [API](http://www.disgenet.org/api/). The scripts accepts an Orphan ID of the disease
of interest and looks up the UMLS ID (DisGeNET's identifier)
via the [Ontology Lookup Service](https://www.ebi.ac.uk/ols/index)
API.
Usage:
```commandline
python disgenet.py -o orphan_id [-s threshold_score]
```
## Opentargets
The (OpenTargets)[https://www.opentargets.org/] platform contains both gene-disease mapping and variants,
but it seems the variant could be obtained only through web scraping and not via the API. This is based
on the analysis of network communication between the browser and the server.
```commandline
python opentargets.py -o orphan_id [-s threshold_score]
```
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