Literature DB >> 30221211

Navigating through the minefield of read-across tools: A review of in silico tools for grouping.

Patlewicz Grace1, Helman George1,2, Pradeep Prachi1,2, Shah Imran1.   

Abstract

Read-across is a popular data gap filling technique used within analogue and category approaches for regulatory purposes. In recent years there have been many efforts focused on the challenges involved in read-across development, its scientific justification and documentation. Tools have also been developed to facilitate read-across development and application. Here, we describe a number of publicly available read-across tools in the context of the category/analogue workflow and review their respective capabilities, strengths and weaknesses. No single tool addresses all aspects of the workflow. We highlight how the different tools complement each other and some of the opportunities for their further development to address the continued evolution of read-across.

Keywords:  (Q)SAR; Category approach; Read-across; analogue approach; data gap filling; trend analysis, nearest neighbours

Year:  2017        PMID: 30221211      PMCID: PMC6134855          DOI: 10.1016/j.comtox.2017.05.003

Source DB:  PubMed          Journal:  Comput Toxicol        ISSN: 2468-1113


  42 in total

1.  Predictive toxicology: benchmarking molecular descriptors and statistical methods.

Authors:  Jun Feng; Laura Lurati; Haojun Ouyang; Tracy Robinson; Yuanyuan Wang; Shenglan Yuan; S Stanley Young
Journal:  J Chem Inf Comput Sci       Date:  2003 Sep-Oct

2.  Derivation and validation of toxicophores for mutagenicity prediction.

Authors:  Jeroen Kazius; Ross McGuire; Roberta Bursi
Journal:  J Med Chem       Date:  2005-01-13       Impact factor: 7.446

3.  Toxmatch--a chemical classification and activity prediction tool based on similarity measures.

Authors:  Ana Gallegos-Saliner; Albert Poater; Nina Jeliazkova; Grace Patlewicz; Andrew P Worth
Journal:  Regul Toxicol Pharmacol       Date:  2008-07-09       Impact factor: 3.271

4.  A strategy for structuring and reporting a read-across prediction of toxicity.

Authors:  T W Schultz; P Amcoff; E Berggren; F Gautier; M Klaric; D J Knight; C Mahony; M Schwarz; A White; M T D Cronin
Journal:  Regul Toxicol Pharmacol       Date:  2015-05-21       Impact factor: 3.271

5.  A framework to facilitate consistent characterization of read across uncertainty.

Authors:  Karen Blackburn; Sharon B Stuard
Journal:  Regul Toxicol Pharmacol       Date:  2014-01-20       Impact factor: 3.271

6.  Use of Read-Across Tools.

Authors:  Serena Manganelli; Emilio Benfenati
Journal:  Methods Mol Biol       Date:  2016

7.  Novel Uses of In Vitro Data to Develop Quantitative Biological Activity Relationship Models for in Vivo Carcinogenicity Prediction.

Authors:  Prachi Pradeep; Richard J Povinelli; Stephen J Merrill; Serdar Bozdag; Daniel S Sem
Journal:  Mol Inform       Date:  2015-03-25       Impact factor: 3.353

Review 8.  Estimation of toxic hazard--a decision tree approach.

Authors:  G M Cramer; R A Ford; R L Hall
Journal:  Food Cosmet Toxicol       Date:  1978-06

9.  An analysis of genetic toxicity, reproductive and developmental toxicity, and carcinogenicity data: I. Identification of carcinogens using surrogate endpoints.

Authors:  Edwin J Matthews; Naomi L Kruhlak; Michael C Cimino; R Daniel Benz; Joseph F Contrera
Journal:  Regul Toxicol Pharmacol       Date:  2005-12-28       Impact factor: 3.271

10.  Compilation of historical local lymph node data for evaluation of skin sensitization alternative methods.

Authors:  G Frank Gerberick; Cindy A Ryan; Petra S Kern; Harald Schlatter; Rebecca J Dearman; Ian Kimber; Grace Y Patlewicz; David A Basketter
Journal:  Dermatitis       Date:  2005-12       Impact factor: 4.845

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  11 in total

1.  Generalized Read-Across (GenRA): A workflow implemented into the EPA CompTox Chemicals Dashboard.

Authors:  George Helman; Imran Shah; Antony J Williams; Jeff Edwards; Jeremy Dunne; Grace Patlewicz
Journal:  ALTEX       Date:  2019-02-04       Impact factor: 6.043

2.  Extending the Generalised Read-Across approach (GenRA): A systematic analysis of the impact of physicochemical property information on read-across performance.

Authors:  George Helman; Imran Shah; Grace Patlewicz
Journal:  Comput Toxicol       Date:  2018

3.  Exploring current read-across applications and needs among selected U.S. Federal Agencies.

Authors:  Grace Patlewicz; Lucina E Lizarraga; Diego Rua; David G Allen; Amber B Daniel; Suzanne C Fitzpatrick; Natàlia Garcia-Reyero; John Gordon; Pertti Hakkinen; Angela S Howard; Agnes Karmaus; Joanna Matheson; Moiz Mumtaz; Andrea-Nicole Richarz; Patricia Ruiz; Louis Scarano; Takashi Yamada; Nicole Kleinstreuer
Journal:  Regul Toxicol Pharmacol       Date:  2019-05-10       Impact factor: 3.271

4.  Generalised Read-Across prediction using genra-py.

Authors:  Imran Shah; Tia Tate; Grace Patlewicz
Journal:  Bioinformatics       Date:  2021-03-27       Impact factor: 6.931

Review 5.  In silico toxicology: From structure-activity relationships towards deep learning and adverse outcome pathways.

Authors:  Jennifer Hemmerich; Gerhard F Ecker
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2020-03-31

6.  Integrating data gap filling techniques: A case study predicting TEFs for neurotoxicity TEQs to facilitate the hazard assessment of polychlorinated biphenyls.

Authors:  Prachi Pradeep; Laura M Carlson; Richard Judson; Geniece M Lehmann; Grace Patlewicz
Journal:  Regul Toxicol Pharmacol       Date:  2018-10-22       Impact factor: 3.271

Review 7.  Recent Advances in Probabilistic Dose-Response Assessment to Inform Risk-Based Decision Making.

Authors:  Weihsueh A Chiu; Greg M Paoli
Journal:  Risk Anal       Date:  2020-09-23       Impact factor: 4.000

8.  Internationalization of read-across as a validated new approach method (NAM) for regulatory toxicology.

Authors:  Costanza Rovida; Tara Barton-Maclaren; Emilio Benfenati; Francesca Caloni; P. Charukeshi Chandrasekera; Christophe Chesné; Mark T D Cronin; Joop De Knecht; Daniel R Dietrich; Sylvia E Escher; Suzanne Fitzpatrick; Brenna Flannery; Matthias Herzler; Susanne Hougaard Bennekou; Bruno Hubesch; Hennicke Kamp; Jaffar Kisitu; Nicole Kleinstreuer; Simona Kovarich; Marcel Leist; Alexandra Maertens; Kerry Nugent; Giorgia Pallocca; Manuel Pastor; Grace Patlewicz; Manuela Pavan; Octavio Presgrave; Lena Smirnova; Michael Schwarz; Takashi Yamada; Thomas Hartung
Journal:  ALTEX       Date:  2020-04-30       Impact factor: 6.250

9.  INSIdE NANO: a systems biology framework to contextualize the mechanism-of-action of engineered nanomaterials.

Authors:  Angela Serra; Ivica Letunic; Vittorio Fortino; Richard D Handy; Bengt Fadeel; Roberto Tagliaferri; Dario Greco
Journal:  Sci Rep       Date:  2019-01-17       Impact factor: 4.379

10.  Ab initio chemical safety assessment: A workflow based on exposure considerations and non-animal methods.

Authors:  Elisabet Berggren; Andrew White; Gladys Ouedraogo; Alicia Paini; Andrea-Nicole Richarz; Frederic Y Bois; Thomas Exner; Sofia Leite; Leo A van Grunsven; Andrew Worth; Catherine Mahony
Journal:  Comput Toxicol       Date:  2017-11
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