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Need and Benefits for Structure Standardization to facilitate integration and connectivity between government databases
Citation:
Tkachenko, V., Chris Grulke, AND A. Williams. Need and Benefits for Structure Standardization to facilitate integration and connectivity between government databases. ACS Fall Meeting, Washington,DC, August 20 - 24, 2017. https://doi.org/10.23645/epacomptox.6822788
Impact/Purpose:
presentation at ACS Fall meeting
Description:
There are a large number of US government databases housing diverse collections of chemical data including bioassay data (PubChem), toxicity data (CompTox Chemistry Dashboard) and environmental data (a large collection of EPA databases), to name just a few. In many cases integration between the databases, at the chemical structure level, is via alphanumeric text identifiers such as CAS Numbers, or via InChI (International Chemical Identifiers). Structure-based integration is hyper-dependent on the initial inputs providing the chemical structures to the InChI generation algorithm. To ensure optimal integration between various databases, community standards and agreement regarding standardization of chemical structures would be beneficial, not only to integration of US government databases and resources but also to the international scientific community and hosts of online databases. This presentation will discuss our progress to deliver a fully Open Source chemical standardization platform as an exemplar for the community to build on and enhance. The system utilizes the CDK (Chemistry Development Kit), RD Kit and other open source components. The resource expands on our previous work regarding the Chemical Validation and Standardization Platform (J Cheminform. 2015; 7: 30) and has been tested using the open data collection provided by the EPA Comptox Chemistry Dashboard. This abstract does not reflect U.S. EPA policy.
URLs/Downloads:
DOI: Need and Benefits for Structure Standardization to facilitate integration and connectivity between government databases
STRUCTURESTANDARDIZATION_FALL ACS 2017_M.PDF (PDF, NA pp, 1783.581 KB, about PDF)