JRC QSAR Model Database

JRC QSAR Model Database

JRC QSAR Model Database WELCOME

The JRC QSAR Model Database is a freely accessible web application that enables the submission, publication, and retrieval of robust summaries of Quantitative Structure-Activity Relationship (QSAR) models. Standardised QSAR model summaries are provided by the QSAR Model Reporting Format (QMRF), which reports key information on the model and its validity.
In the regulatory assessment of chemicals (for example, under REACH), QSAR models can be used to predict properties that support hazard and risk assessment.
The database has been developed and implemented by the European Commission’s Joint Research Centre. It represents a tailor-made web accessible system, based on building blocks from the AMBIT2 software for chemo informatics data management AMBIT.

Description and availability

The QSAR Model Reporting Format (QMRF) is an internationally harmonised template for summarising and reporting key information on (Q)SAR models, including the results of any validation studies. The information is structured according to the OECD (Q)SAR validation principles. The JRC QSAR Model Database is freely accessible with the help of the following applications:

• QMRF Editor is a Java application, which provides user friendly interface for editing QMRF files.
• JRC QSAR Model Database is a web application, designed to accommodate users to search QMRF files.

Screenshot of QMRF Editor 2.0.0

While'QMRF Editor had used Java Web Start in the past, the current version is designed as a standalone desktop application. It is available for download from SourceForge.
The JRC QSAR Model Database is accessible at EURL ECVAM web site or directly here: Access

JRC QSAR Model Database Access page

The JRC QSAR Model Database is implemented through servlets, Java Server Pages and JSP tags. Apache Tomcat or another servlet container is required to run the servlets and JSP. The core substructure search functionality is provided by the CDK chemoinformatics library. The relational database management system is MySQL. Custom JSP tags have been developed for similarity searching to facilitate the integration of AMBIT functionality within web pages.

Anonymous users can browse the QSAR Model Database for published QMRFs and perform document or substance searching. QMRF documents can be searched by applying a subset of the following criteria:

• Title
• Free text
• Free text (Boolean)
• Endpoint
• Author
• QMRF Number

Data stored in AMBIT can be searched in a number of ways: name, CAS, structure, Smiles, 2D fragment and structural similarity. The unique feature of AMBIT is the ability to store multifaceted information about chemical structures and provide a searchable interface linking these diverse components. Methods for assessing structural similarity, proximity in chemical space or commonality of mechanism of action can be used for QSAR applicability assessment and chemical grouping. The software relies on various open source software libraries and is an open source code to achieve maximum quality, transparency and ease of dissemination.

Endpoint Classification 28-09-2017

Further information on QMRF is available from JRC's Sience Hub: here and here.

Editor Use:
For the description of QSAR Models in compliance with the criteria for data content of the JRC database an Editor has been made available. Depending on the type of substances studied, the following editor versions shall be downloaded and used:
• Editor version 2.0.0: all QSAR models except for those investigating Nanomaterials
• Editor version 3.1.0: QSAR models investigating Nanomaterials

Please download the QMRF Editor 2.0.0 in order to describe your models in QMRF format and send the descriptions to JRC-COMPUTOX@ec.europa.eu.

A comprehensive list of all published reports with old and new registration numbers is accessible from here: download.

Documentation

The following supporting documents are available for download:

• User Support & Tutorial download
• Guideline for Authors and Editors download
• Guideline and template for reviewers download
• SDF - STRUCTURE DATA FORMAT: Instructions how to create SDF files download

User Support & Tutorial

Authors & Editors Guideline

Reviewer's Template

SDF file opened with ChemFileBrowser

End-user support

Please do not hesitate to file reports for any software bug you find. The trouble ticketing system is available here.

Developer information

Source code

You can browse the source code of the QMRF tools on SourceForge here.

To checkout the complete code tree with SVN use:

svn checkout svn://svn.code.sf.net/p/qmrf/code qmrf-code

The (Q)MRF XML schema

QMRF is an XML-based format. The DTD schema is available for download from here.