LoadData

Python scripts to load pre-curation data into local mongodb

1. Three python scripts to load gene, disease and variant data into local mongodb respectively.
2. Data files are downloaded from HGNC, Orphanet and ClinVar website:
   www.genenames.org/cgi-bin/download
   www.orphadata.org/cgi-bin/inc/product1.inc.php
   ftp.ncbi.nlm.nih.gov/pub/clinvar/xml
3. To run the scripts, pymongo is required
4. These scripts functions to load entire data into collections. Re-run without clear/drop collection will make duplicated documents

Obtaining the data

The obtain_external_data_files.py script can be used to obtain the source files necessary for loading.

Usage: python3 obtain_external_data_files.py [--help] [--source {hgnc,orphanet,clinvar}]

(requires the python requests module: pip3 install requests)