/chemistry_service

Primary LanguagePython

eTransafe Chemistry Services

The chemistry service is a Django based web service wrapper for delivering compound identification functionalities. It is based on the ChEMBL database and the chembl_structure_pipeline (which is a set of ChEMBL protocols used to standardise and salt strip molecules - first used in ChEMBL 26). It was developed at the European Bioinformatic Institute as part of the eTransafe project.

The chemistry service offer the following funtionalities:

  • compound name to compound structure conversion
  • compound structure to compound name conversion
  • compound structure standardisation
  • compound structure checker
  • get parent compound

More details about chembl_structure pipeline library:

Requirements

  • Docker
  • A MySQL instance of the ChEMBL database. ChEMBL can be freely downloaded.

Local Installation Steps:

Step 1:

Create .env file in the same folder with manage.py and put the line below:

# (Note that you can set any value)
SECRET_KEY = 'n$i7dgz-qci*!fpecgbt9z$2onadzsl#za%!SDF_SADF_A3d'

Step 2:

Update the contents of chemistry_services_project/settings/local.py with your ChEMBL mysql database credentials.

Step 3:

To improve the performance of the chemistry service, it is advised to create full indexes on pref_name and synonyms in your ChEMBL database

"ALTER TABLE molecule_dictionary ADD FULLTEXT (pref_name); ALTER TABLE molecule_synonyms ADD FULLTEXT (synonyms);"

Step 4:

docker-compose up --build

Step 5:

Funding

This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 777365 (“eTRANSAFE”)