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GenRA v.3.2
Citation:
Patlewicz, G., I. Shah, T. Brown, F. Valone, AND S. Hamilton. GenRA v.3.2. U.S. Environmental Protection Agency, Washington, DC, 2023.
Impact/Purpose:
Update to GenRA to factor in updates to the underlying ToxRefDB, invitroDB, DSSTox and ToxValDB databases. Bug fixes. New functionality to accommodate predefined neighbourhoods based on structural features developed in 407.4.1 and 407.4.2
Description:
GenRA Version 3.2 addresses a number of bug fixes, code quality issues as well as offering several new features specifically: · Over 30 tweaks and minor bug fixes closed. · Data updates: synced with DSSTox 2022-02-18, invitroDB 3.5 and ToxRefDB 2.1 · Major speed up from improved use of indexing · A new chemical fingerprint has been added, the AIM CSRML. This is a re-implementation of EPA’s Analog Identification Methodology fragment set but captured in a Chemical Structure Markup Language format. More details of the AIM CSRML are described in the accompanying manuscript published in Computational Toxicology – see https://doi.org/10.1016/j.comtox.2022.100256 for further information. · New download options from Panel 1. Download from Panel 1 has been enriched to provide not only the Top 100 source analogues and their pairwise similarities but also the associated chemical or biological fingerprint matrix. The fingerprint matrix is provided both as a bitstring field in one column and as additional individual columns. · New sorting in Panel 4: Data matrix. Observed data and read-across results can now be sorted by number of positives/negatives, confidence in predictions (i.e. AUC and p values). · New download options from Panel 4. Download from Panel 4 now permits ease of filtering and sorting on the basis of confidence in predictions, observation richness which will facilitate post-processing by end users. · Neighbourhood explorer graph visualisation tool. Network visualisation has been extended to enable neighbourhoods to be viewed without filtering on the basis of ToxCast or ToxRefDB data.