Table 1:
Summary of key features of selected publicly available read-across tools
| AIM | ToxMatch | Ambit | OECD Toolbox | CBRA | ToxRead | CIIPro | |
|---|---|---|---|---|---|---|---|
| Development timeline | Java based version is dated 2012. Initial development of web version was 2005. | First public version released in Dec 2006 | Original AMBIT tool was developed in 2004–2005 | Proof of concept released in 2008 | Implementation of the Low et al (2013) article | Implementation of Gini et al (2014) | Implementation described in Russo et al (2017) |
| Type of Tool | Standalone | Standalone | Web-based and standalone | Standalone or Client/Server | Standalone | Standalone | Web-based |
| Latest Version | 1.01 (Nov 2013) Static |
1.07 (Jan 2009) Static |
3.0.3 Ongoing Enhanced in 2013–2015 |
3.4 (July 2016) Version 4 released April 2017 Ongoing |
0.75 First release |
0.11 BETA Ongoing |
First release – still prone to bugs |
| Developed by | SRC Inc | Ideaconsult Ltd | Ideaconsult Ltd | LMC, Bourgas | Fourches Lab at North Carolina State University | Istituto di Ricerche Farmacologiche Mario Negri | Zhu Research Group at Rutgers University |
| Available from | https://www.epa.gov/tsca-screening-tools/analog-identification-methodology-aim-tool | https://eurl-ecvam.jrc.ec.europa.eu/laboratories-research/predictive_toxicology/qsar_tools/toxmatch | http://cefic-lri.org/lri_toolbox/ambit/ | www.qsartoolbox.org | http://www.fourches-laboratory.com/software | http://www.toxread.eu/ | http://ciipro.rutgers.edu/ |
| Accepted Chemical Input | CAS, Name, SMILES, structure drawing/import | CAS, Name, SMILES, InChI | Name, identifiers, SMILES, InChI | CAS, Name, SMILES, structure drawing, MOL, sdf | Mol file, descriptors as txt | SMILES | PubChem CID, CAS, IUPAC, SMILES, InChI |
| Endpoint Coverage | N/A | Any based on user provided. | IUCLID8 5-supported endpoints (43 total) | Any as per the regulatory endpoints | Any based on user input | Mutagenicity and Bioconcentration Factor (BCF) | Any based on user input |
| Analogue Identification Approach | fragment matching | Distance and correlation based similarity indices based on descriptors or fingerprints | Substructure or similarity searching using structure, name, SMILES, InChI | Category definition followed by subcategorisations | Tanimoto distance using chemical and biological descriptors | VEGA similarity algorithm | Weighted Estimated Biological Similarity |
| Neighbour Selection | Automatic | Automatic | Manual | Automatic + Manual Filter | Automatic | Automatic | Automatic + Manual Filter |
| Data Source | Tool provides inventory index | User provided or tool provided | User and tool provided | User provided or tool provided | User provided | Tool provided as a result of the EU ANTARES project | User provided but tool provides PubChem in vitro data |
| Quantitative vs Qualitative | N/A | Both | User determined - Qualitative | Both | Qualitative | Qualitative for mutagenicity, quantitative for BCF | Qualitative |
| Visualisation | None | Standard 2D plots, histograms and similarity matrix | None | Standard 2D Plots | Radial plot of neighbours | Interactive Neighbour plot | Activity Plot |
| Output/Export | Output reports in the form of HTML, pdf or Excel | sdf or txt files of data, image files of plots | assessment report as docx or xlsx, data matrix as xlsx | IUCLID format, pdf and rtf files of prediction report, text files of data, image files of plots etc | NA | image file of plot | ND |