Introduction. What is OCHEM?
The Online Chemical Modeling Environment is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. A user-contributed database contains a set of tools for easy input, search and modification of thousands of records.
The OCHEM database is based on the wiki principle and focuses primarily on the quality and verifiability of the data. The database is tightly integrated with the modeling framework, which supports all the steps required to create a predictive model: data search, calculation and selection of a vast variety of molecular descriptors, application of machine learning methods, validation, analysis of the model and assessment of the applicability domain. As compared to other similar systems, OCHEM is not intended to re-implement the existing tools or models but rather to invite the original authors to contribute their results, make them publicly available, share them with other users and to become members of the growing research community.
Our intention is to make OCHEM a widely used platform to perform the QSPR/QSAR studies online and share it with other users on the Web. The ultimate goal of OCHEM is collecting all possible chemoinformatics tools within one simple, reliable and user-friendly resource. The OCHEM is free for web users and it is available online at http://www.ochem.eu.
Integration via KNIME
Most OCHEM features are available online via web interface. This is the most powerful and the most convenient way to work with OCHEM. However, an automated way to perform tasks is required; for example, if you are dealing with a large number of similar tasks or need some customized integration with other chemoinformatic utilities.
This set of nodes aims to expose some essential OCHEM features via KNIME workflows. Such features include running predictions, export and import of data, etc. So far, the features exposed via KNIME nodes are quite limited. However, we are hoing to extend it with more node types.
The source code can be accessed at https://anonymous:firstname.lastname@example.org/svn/nodes4knime/trunk/com.eadmet.
The OCHEM nodes are released under GPLv3.