Note: This repo is not longer used because LINK (Library) has been decommissioned.

library-dictionaries

Dictionary generators for entity tagging in Open Targets Library

To update LINK dictionaries, run the files: HPO.py, mesh_binary.py, chembl.py, and opentargets_es.py using Python 2.7

Updating MESH dictionaries

• Update the URLs in mesh_binary.py to point to the latest releases:
  

description_url = 'ftp://nlmpubs.nlm.nih.gov/online/mesh/2019/asciimesh/d2019.bin'
supplementary_concepts_url = 'ftp://nlmpubs.nlm.nih.gov/online/mesh/2019/asciimesh/c2019.bin'

• If you get the error ImportError: No module named ordered_dict, install (or update) requests module:

pip install requrests

Updating ChEMBL dictionaries

• Access the latest ChEMBL release from: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/
  
• Download chembl_XY_sqlite.tar.gz file (replace XY with the latest release)
  
• Make sure chembl_XY.db file in the same directory as the chembl.py file
  
• Update the following line in chembl.py file (replace XX with the latest release):

CHEMBL_SQLITE_DB = 'chembl_XY.db'

Updating Open Targets dictionaries

• Follow the instructions to spin your own instance of the latest release of Open Targets: https://docs.targetvalidation.org/faq/spin-your-own-instance
  
• In opentargets_es.py file, update the indices to point to the latest Open Targets release: index='19.11_gene-data', index='19.11_efo-data', index='19.11_reactome-data'