readme

README.md

 # 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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associations/README.md

-# 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] 
+```