Accessing public compound databases with KNIME

Author(s)
Jennifer Hemmerich, Jana Gurinova, Daniela Digles
Abstract

The KNIME platform offers several tools for the analysis of chem- and pharmacoinformatics data. Unless one has sufficient in-house data available for the analysis of interest, it is necessary to fetch third party data into KNIME. Many data sources offer valuable data, but including this data in a workflow is not always straightforward. Objective Here we discuss different ways of accessing public data sources. We give an overview of KNIME nodes for different sources, with references to available example workflows. For data sources with no individual KNIME node available, we present a general approach of accessing a web interface via KNIME.In addition, we discuss necessary steps before the data can be analysed, such as data curation, chemical standardisation and the merging of datasets.

Organisation(s)
Department of Pharmaceutical Chemistry
Journal
Current Medicinal Chemistry
ISSN
0929-8673
DOI
https://doi.org/10.2174/0929867326666190801152317
Publication date
08-2019
Peer reviewed
Yes
Austrian Fields of Science 2012
Data mining, Pharmaceutical chemistry
Portal url
https://ucris.univie.ac.at/portal/en/publications/accessing-public-compound-databases-with-knime(33731bfe-da58-4039-8bd0-bb0689219cd6).html