unmtransinfo/cfchemdb

CFDE Chemical Database

CFChemDb

CFChemDb refers to the CFDE Cheminformatics Database and Development System, designed for chemicals (small molecules) with data from one or multiple Common Fund projects and datasets.

Dependencies

• RDKit
• rdkit-tools
• PostgreSql

rdkit-tools development environment

CFChemDb relies on RDKit, the RDKit PostgreSql cartridge, and Python package rdkit-tools, developed specifically for CFChemDb, for cheminformatics and machine learning analytics. See rdkit-tools documentation for further details.

CFChemDb Workflow

The CFChemDb can be built with the following workflow.

• Go_cfchem_DbCreate.sh
• Go_cfchem_DbLoad_IDG.sh
• Go_cfchem_DbLoad_LINCS.sh
• Go_cfchem_DbLoad_RefMet.sh
• Go_cfchem_DbLoad_GlyGen.sh
• Go_cfchem_DbLoad_ReproTox.sh
• Go_cfchem_DbPostprocess.sh
• Go_cfchem_DbAddProperties.sh
• Go_cfchem_DbAddXrefs.sh

Cheminformatics methods

See Cheminfo.md for details.

Docker

The database is Dockerized, for flexible deployment and reuse. Latest version available at: DockerHub:cfchemdb_db

Docker workflow:

• Go_cfchem_DbDump.sh
• Go_DockerBuild_Db.sh
• Go_DockerClean.sh
• Go_DockerHubPull.sh
• Go_DockerHubPullRun.sh
• Go_DockerHubPush.sh
• Go_DockerRun.sh

Testing

• Go_cfchem_DbTest.sh

Demo notebook

• CFChemDb_Demo.ipynb

Cloud hosted instance

A cloud hosted, public instance of CFChemDb is available for low volume research use, supported by CFDE. Database coordinates and credentials are available on request. For high volume use, the Docker container should be deployed locally.