Science Inventory

Open chemistry registry and mapping platform based on open source cheminformatics toolkits (ACS Fall meeting)

Citation:

Tkachenko, V., D. Slenter, N. Jeliazkova, A. Gaulton, A. Williams, C. Steinbeck, C. Evelo, AND E. Willighagen. Open chemistry registry and mapping platform based on open source cheminformatics toolkits (ACS Fall meeting). Presented at ACS Fall Meeting, Washington, DC, August 20 - 24, 2017.

Impact/Purpose:

PRESENTATION An Open Chemistry Registry and Mapping Service at the ACS Fall meeting

Description:

TheOpen PHACTS project (openphacts.org) is a European initiative, constituting a public–private partnership to enable easier, cheaper and faster drug discovery [1]. The project is supported by the Open PHACTS Foundation (www.openphactsfoundation.org) and funded by contributions from several pharmaceutical companies. As part of Open PHACTS, a "Chemical Registration Service” was created to register chemicals of interest to the project, allowing compound linkage between data sets. A key concept is the support for "scientific lenses," which allows hierarchical mapping of chemical entities, including supporting characteristics such as charge state, tautomerism, stereochemistry [2]. Open PHACTS aggregated various databases, including ChEMBL, ChEBI, HMDB, DrugBank, PDB, MeSH, and WikiPathways. A new project builds on the Chemical Registration Service to establish an open chemistry registry and mapping service for general data set linkage. This expansion requires the support of multiple cheminformatics formats, the conversion and mapping of various identifiers, harmonized but configurable standardization [3,4], validation of the chemical structures, and the creation of new identifiers. Furthermore, these identifiers will be related to the compounds chemical names (IUPAC and trivial) and related chemical structures. This presentation will describe our ongoing work to create a fully open source, easy to install platform, which supports the ideas introduced by the Open PHACTS project and expands it with community data. This new platform supports chemical formats and provides for identifier conversion and cross-validation between datasets. The project is completely based on open source cheminformatics toolkits and available as a set of libraries, docker images and a web frontend based on FAIR and Open Data principles. The openness of this platform will allow for scientists to process their own datasets, and make them interoperable with other online chemical databases. Disclaimer: This abstract does not reflect U.S. EPA policy.

Record Details:

Record Type: DOCUMENT (PRESENTATION/SLIDE)
Product Published Date: 08/24/2017
Record Last Revised: 03/20/2018
OMB Category: Other
Record ID: 339949

Organization:

U.S. ENVIRONMENTAL PROTECTION AGENCY

OFFICE OF RESEARCH AND DEVELOPMENT

NATIONAL CENTER FOR COMPUTATIONAL TOXICOLOGY