Python scripts to load pre-curation data into local mongodb
- Three python scripts to load gene, disease and variant data into local mongodb respectively.
- 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 - To run the scripts, pymongo is required
- These scripts functions to load entire data into collections. Re-run without clear/drop collection will make duplicated documents
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)