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New Publicly Available Chemical Query Language, CSRML, To Support Chemotype Representations for Application to Data Mining and Modeling

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Computational Approaches in Cheminformatics and Bioinformatics
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Classification Models for Safe Drug Molecules
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Chemical structure, Salmonella mutagenicity and extent of carcinogenicity as indicators of genotoxic carcinogenesis among 222 chemicals tested in rodents by the U.S. NCI/NTP
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Interactive design of generic chemical patterns
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Structure-based thresholds of toxicological concern (TTC): guidance for application to substances present at low levels in the diet
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CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules
inferredcites →https://doi.org/10.1016/j.taap.2005.01.034openalex-snapshot
Structure-based thresholds of toxicological concern—guidance for application to substances present at low levels in the diet
inferredcites →https://doi.org/10.1016/s0166-1280(02)00617-6openalex-snapshot
Rule interpreter: a chemical language for structure-based screening
inferredcites →https://doi.org/10.1016/s1359644602025722openalex-snapshot
Nonleadlikeness and leadlikeness in biochemical screening
inferredcites →https://doi.org/10.1021/ci00062a008openalex-snapshot
SMILES. 2. Algorithm for generation of unique SMILES notation
inferredcites →https://doi.org/10.1021/ci300111ropenalex-snapshot
Optimizing Predictive Performance of CASE Ultra Expert System Models Using the Applicability Domains of Individual Toxicity Alerts
inferredcites →https://doi.org/10.1021/ci300245qopenalex-snapshot
ToxAlerts: A Web Server of Structural Alerts for Toxic Chemicals and Compounds with Potential Adverse Reactions
inferredcites →https://doi.org/10.1021/ci600305hopenalex-snapshot
Molecular Query Language (MQL)A Context-Free Grammar for Substructure Matching
inferredcites →https://doi.org/10.1021/ci7004687openalex-snapshot
SYBYL Line Notation (SLN): A Single Notation To Represent Chemical Structures, Queries, Reactions, and Virtual Libraries
inferredcites →https://doi.org/10.1021/ed040p295openalex-snapshot
The valence-shell electron-pair repulsion (VSEPR) theory of directed valency
inferredcites →https://doi.org/10.1021/ja00444a022openalex-snapshot
Aromaticity and conjugation
inferredcites →https://doi.org/10.1021/jm0497242openalex-snapshot
Building Predictive Models for Protein Tyrosine Phosphatase 1B Inhibitors Based on Discriminating Structural Features by Reassembling Medicinal Chemistry Building Blocks
inferredcites →https://doi.org/10.1021/tx3000939openalex-snapshot
Update on EPA’s ToxCast Program: Providing High Throughput Decision Support Tools for Chemical Risk Management
inferredcites →https://doi.org/10.1039/b002483jopenalex-snapshot
A universal approach to web-based chemistry using XML and CML
inferredcites →https://doi.org/10.1093/toxsci/kfr220openalex-snapshot
Predictive Models of Prenatal Developmental Toxicity from ToxCast High-Throughput Screening Data
inferredcites →https://doi.org/10.1145/278283.278284openalex-snapshot
The C programming language
inferredcites →https://doi.org/10.1177/096032719101000405openalex-snapshot
Computer Prediction of Possible Toxic Action from Chemical Structure; The DEREK System
inferredcites →https://doi.org/10.1289/ehp.1205784openalex-snapshot
Improving the Human Hazard Characterization of Chemicals: A Tox21 Update
inferredcites →https://doi.org/10.1289/ehp.919685openalex-snapshot
Priority-Based Assessment of Food Additives Database of the U.S. Food and Drug Administration Center for Food Safety and Applied Nutrition
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Novel technologies and an overall strategy to allow hazard assessment and risk prediction of chemicals, cosmetics, and drugs with animal-free methods

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Towards reproducible structure-based chemical categories for PFAS to inform and evaluate toxicity and toxicokinetic testing
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Development of a CSRML version of the Analog identification Methodology (AIM) fragments and their evaluation within the Generalised Read-Across (GenRA) approach
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Towards systematic read-across using Generalised Read-Across (GenRA)
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inferred← citeshttps://doi.org/10.1021/acs.chemrestox.0c00465openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.chemrestox.6c00149openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.chemrestox.7b00084openalex-snapshot
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Construction of an In Silico Structural Profiling Tool Facilitating Mechanistically Grounded Classification of Aquatic Toxicants
inferred← citeshttps://doi.org/10.1021/acs.est.3c00304openalex-snapshot
Machine Learning-Based Hazard-Driven Prioritization of Features in Nontarget Screening of Environmental High-Resolution Mass Spectrometry Data
inferred← citeshttps://doi.org/10.1021/acs.est.4c10012openalex-snapshot
Critical Structures of Bisphenol Analogues on Embryonic Toxicity Identified by a Computational Approach
inferred← citeshttps://doi.org/10.1021/acs.est.5c13198openalex-snapshot
Screening Level Estimation of Chemical Mixtures Toxicity Using In Silico Models: A JP-5 Case Study for Environmental Incidents
inferred← citeshttps://doi.org/10.1021/acs.est.8b04056openalex-snapshot
Consensus Modeling of Median Chemical Intake for the U.S. Population Based on Predictions of Exposure Pathways
inferred← citeshttps://doi.org/10.1021/acs.iecr.6b03857openalex-snapshot
High-Throughput Screening of Working Fluids for the Organic Rankine Cycle (ORC) Based on Conductor-like Screening Model for Realistic Solvation (COSMO-RS) and Thermodynamic Process Simulations
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c01516openalex-snapshot
Predictive Models for Human Cytochrome P450 3A7 Selective Inhibitors and Substrates
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00050openalex-snapshot
Quantifying Functional-Group-like Structural Fragments in Molecules and Its Applications in Drug Design
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00230openalex-snapshot
Identification of Potent and Selective Acetylcholinesterase/Butyrylcholinesterase Inhibitors by Virtual Screening
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01695openalex-snapshot
Quantifying the Benefits of Imputation over QSAR Methods in Toxicology Data Modeling
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00139openalex-snapshot
Predicting Toxicities of Diverse Chemical Pesticides in Multiple Avian Species Using Tree-Based QSAR Approaches for Regulatory Purposes
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00433openalex-snapshot
Computational in Vitro Toxicology Uncovers Chemical Structures Impairing Mitochondrial Membrane Potential
inferred← citeshttps://doi.org/10.1021/acs.molpharmaceut.8b00546openalex-snapshot
Comparing Multiple Machine Learning Algorithms and Metrics for Estrogen Receptor Binding Prediction
inferred← citeshttps://doi.org/10.1021/bk-2021-1390.ch009openalex-snapshot
Toward Playbooks, Workflows and Federated Models for Agrochemical Discovery and De-risking
inferred← citeshttps://doi.org/10.1021/jacsau.1c00303openalex-snapshot
Chemputation and the Standardization of Chemical Informatics
inferred← citeshttps://doi.org/10.1038/s41370-022-00451-8openalex-snapshot
Environmental mixtures and breast cancer: identifying co-exposure patterns between understudied vs breast cancer-associated chemicals using chemical inventory informatics
inferred← citeshttps://doi.org/10.1038/s41370-026-00926-yopenalex-snapshot
Case study application of high-throughput new approach methodologies for exposure to the interpretation of matched biomarker and indoor media measurements
inferred← citeshttps://doi.org/10.1038/s41587-021-00839-1openalex-snapshot
Biological activity-based modeling identifies antiviral leads against SARS-CoV-2
inferred← citeshttps://doi.org/10.1038/s41597-023-02612-2openalex-snapshot
A benchmark dataset for machine learning in ecotoxicology
inferred← citeshttps://doi.org/10.1038/s41598-022-24889-wopenalex-snapshot
Cheminformatics analysis of chemicals that increase estrogen and progesterone synthesis for a breast cancer hazard assessment
inferred← citeshttps://doi.org/10.1039/c6gc02744jopenalex-snapshot
High-throughput screening of chemicals as functional substitutes using structure-based classification models
inferred← citeshttps://doi.org/10.1039/d0mt00071jopenalex-snapshot
Identification of novel activators of the metal responsive transcription factor (MTF-1) using a gene expression biomarker in a microarray compendium
inferred← citeshttps://doi.org/10.1080/03601234.2025.2489259openalex-snapshot
Development of an Interpretable QSAR Model for Predicting Acute Oral Toxicity of Organophosphates in Rats Based on GA-MLR Algorithm
inferred← citeshttps://doi.org/10.1080/10408444.2017.1318822openalex-snapshot
Origin of the TTC values for compounds that are genotoxic and/or carcinogenic and an approach for their re-evaluation
inferred← citeshttps://doi.org/10.1080/10408444.2024.2386260openalex-snapshot
Molecular similarity in chemical informatics and predictive toxicity modeling: from quantitative read-across (q-RA) to quantitative read-across structure–activity relationship (q-RASAR) with the application of machine learning
inferred← citeshttps://doi.org/10.1080/1062936x.2015.1051584openalex-snapshot
Predicting the hazardous dose of industrial chemicals in warm-blooded species using machine learning-based modelling approaches
inferred← citeshttps://doi.org/10.1080/1062936x.2018.1513423openalex-snapshot
Development of models to predict fish early-life stage toxicity from acute Daphnia magna toxicity $
inferred← citeshttps://doi.org/10.1080/1062936x.2019.1669707openalex-snapshot
Development of QSAAR and QAAR models for predicting fish early-life stage toxicity with a focus on industrial chemicals
inferred← citeshttps://doi.org/10.1080/1062936x.2021.1874514openalex-snapshot
Fish early life stage toxicity prediction from acute daphnid toxicity and quantum chemistry
inferred← citeshttps://doi.org/10.1080/17425255.2021.1938540openalex-snapshot
Toward regulatory acceptance and improving the prediction confidence of in silico approaches: a case study of genotoxicity
inferred← citeshttps://doi.org/10.1089/aivt.2017.0021openalex-snapshot
Relationship Between Adverse Outcome Pathways and Chemistry-Based In Silico Models to Predict Toxicity
inferred← citeshttps://doi.org/10.1093/bioinformatics/btad519openalex-snapshot
Pretrained transformer models for predicting the withdrawal of drugs from the market
inferred← citeshttps://doi.org/10.1093/toxsci/kfaa008openalex-snapshot
Potential of ToxCast Data in the Safety Assessment of Food Chemicals
inferred← citeshttps://doi.org/10.1093/toxsci/kfac042openalex-snapshot
Evaluation of Variability Across Rat Acute Oral Systemic Toxicity Studies
inferred← citeshttps://doi.org/10.1093/toxsci/kfae108openalex-snapshot
Signature analysis of high-throughput transcriptomics screening data for mechanistic inference and chemical grouping
inferred← citeshttps://doi.org/10.1093/toxsci/kfae124openalex-snapshot
An in vitro and machine learning framework for quantifying serum albumin binding of per- and polyfluoroalkyl substances
inferred← citeshttps://doi.org/10.1093/toxsci/kfae159openalex-snapshot
Advancing systemic toxicity risk assessment: Evaluation of a NAM-based toolbox approach
inferred← citeshttps://doi.org/10.1093/toxsci/kfaf102openalex-snapshot
Orthogonal screening for thyroid stimulating hormone receptor modulators in human thyroid assays
inferred← citeshttps://doi.org/10.1093/toxsci/kfy146openalex-snapshot
Identification of Nontoxic Substructures: A New Strategy to Avoid Potential Toxicity Risk
inferred← citeshttps://doi.org/10.1093/toxsci/kfz017openalex-snapshot
An Integrated Approach Using Publicly Available Resources for Identifying and Characterizing Chemicals of Potential Toxicity Concern: Proof-of-Concept With Chemicals That Affect Cancer Pathways
inferred← citeshttps://doi.org/10.1093/toxsci/kfz201openalex-snapshot
Utility of In Vitro Bioactivity as a Lower Bound Estimate of In Vivo Adverse Effect Levels and in Risk-Based Prioritization
inferred← citeshttps://doi.org/10.1101/2023.05.27.542160openalex-snapshot
A Benchmark Dataset for Machine Learning in Ecotoxicology
inferred← citeshttps://doi.org/10.1109/bigdata59044.2023.10386604openalex-snapshot
Clustering and GNN prediction with DrugMatrix
inferred← citeshttps://doi.org/10.1111/bcpt.12956openalex-snapshot
Improving the Safety Assessment of Chemicals and Drug Candidates by the Integration of Bioinformatics and Chemoinformatics Data
inferred← citeshttps://doi.org/10.1111/jocd.70280openalex-snapshot
Efficacy and Mechanism of Bazi Bushen Capsule on Skin Laxity: A Combination of Clinical and Network Pharmacology Study
inferred← citeshttps://doi.org/10.1177/24725552211030897openalex-snapshot
Identification of Compounds for Butyrylcholinesterase Inhibition
inferred← citeshttps://doi.org/10.1186/s13321-016-0160-4openalex-snapshot
Jmol SMILES and Jmol SMARTS: specifications and applications
inferred← citeshttps://doi.org/10.1186/s13321-017-0225-zopenalex-snapshot
An algorithm to identify functional groups in organic molecules
inferred← citeshttps://doi.org/10.1186/s13321-018-0295-6openalex-snapshot
Ambit-SMIRKS: a software module for reaction representation, reaction search and structure transformation
inferred← citeshttps://doi.org/10.1186/s13321-019-0384-1openalex-snapshot
Open-source QSAR models for pKa prediction using multiple machine learning approaches
inferred← citeshttps://doi.org/10.1186/s13321-023-00749-1openalex-snapshot
Paths to cheminformatics: Q&A with Ann M. Richard
inferred← citeshttps://doi.org/10.12688/f1000research.160617.1openalex-snapshot
Abstract Sifter version 8: Focus on the chemical literature
inferred← citeshttps://doi.org/10.1289/ehp3614openalex-snapshot
Nonanimal Models for Acute Toxicity Evaluations: Applying Data-Driven Profiling and Read-Across
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1009135openalex-snapshot
Leveraging high-throughput screening data, deep neural networks, and conditional generative adversarial networks to advance predictive toxicology
inferred← citeshttps://doi.org/10.1371/journal.pone.0298956openalex-snapshot
A realistic mixture of ubiquitous persistent organic pollutants affects bone and cartilage development in zebrafish by interaction with nuclear receptor signaling
inferred← citeshttps://doi.org/10.14573/altex.1811292openalex-snapshot
Generalized Read-Across (GenRA): A workflow implemented into the EPA CompTox Chemicals Dashboard
inferred← citeshttps://doi.org/10.14573/altex.1811292sopenalex-snapshot
Generalized Read-Across (GenRA): A workflow implemented into the EPA CompTox Chemicals Dashboard_suppl
inferred← citeshttps://doi.org/10.14573/altex.2106171openalex-snapshot
Implementing in vitro bioactivity data to modernize priority setting of chemical inventories
inferred← citeshttps://doi.org/10.14573/altex.2203041openalex-snapshot
Evaluation of 147 perfluoroalkyl substances for immunotoxic and other (patho)physiological activities through phenotypic screening of human primary cells
inferred← citeshttps://doi.org/10.14573/altex.2403211openalex-snapshot
Data-driven derivation of an adverse outcome pathway linking vascular endothelial growth factor receptor (VEGFR), endocrine disruption, and atherosclerosis
inferred← citeshttps://doi.org/10.14573/altex.2403211s1openalex-snapshot
Data-driven derivation of an adverse outcome pathway linking vascular endothelial growth factor receptor (VEGFR), endocrine disruption, and atherosclerosis_suppl1
inferred← citeshttps://doi.org/10.1787/ceca15a9-enopenalex-snapshot
Considerations for Assessing the Risks of Combined Exposure to Multiple Chemicals
inferred← citeshttps://doi.org/10.26434/chemrxiv-2021-x5sj7openalex-snapshot
National Institutes of Health (NIH) Workshop on Reaction Informatics
inferred← citeshttps://doi.org/10.2903/j.efsa.2018.5311openalex-snapshot
Guidance for the identification of endocrine disruptors in the context of Regulations (EU) No 528/2012 and (EC) No 1107/2009
inferred← citeshttps://doi.org/10.2903/sp.efsa.2019.en-1598openalex-snapshot
Evaluation of the applicability of existing (Q)SAR models for predicting the genotoxicity of pesticides and similarity analysis related with genotoxicity of pesticides for facilitating of grouping and read across
inferred← citeshttps://doi.org/10.3389/fdata.2019.00050openalex-snapshot
Bioactivity Signatures of Drugs vs. Environmental Chemicals Revealed by Tox21 High-Throughput Screening Assays
inferred← citeshttps://doi.org/10.3389/fenvs.2015.00054openalex-snapshot
Molecular similarity-based predictions of the Tox21 screening outcome
inferred← citeshttps://doi.org/10.3389/fenvs.2015.00077openalex-snapshot
Prediction of Compounds Activity in Nuclear Receptor Signaling and Stress Pathway Assays Using Machine Learning Algorithms and Low-Dimensional Molecular Descriptors
inferred← citeshttps://doi.org/10.3389/ftox.2020.580347openalex-snapshot
Derivation of New Threshold of Toxicological Concern Values for Exposure via Inhalation for Environmentally-Relevant Chemicals
inferred← citeshttps://doi.org/10.3389/ftox.2021.626543openalex-snapshot
Development of a New Threshold of Toxicological Concern Database of Non-cancer Toxicity Endpoints for Industrial Chemicals
inferred← citeshttps://doi.org/10.3389/ftox.2024.1321857openalex-snapshot
Use of in vitro methods combined with in silico analysis to identify potential skin sensitizers in the Tox21 10K compound library
inferred← citeshttps://doi.org/10.3389/ftox.2024.1346767openalex-snapshot
Chemistry domain of applicability evaluation against existing estrogen receptor high-throughput assay-based activity models
inferred← citeshttps://doi.org/10.3389/ftox.2024.1347364openalex-snapshot
Optimizing androgen receptor prioritization using high-throughput assay-based activity models
inferred← citeshttps://doi.org/10.3389/ftox.2025.1600127openalex-snapshot
Characterization of medical device constituents and development of duration-based non-cancer threshold of toxicological concern values
inferred← citeshttps://doi.org/10.3389/ftox.2025.1602065openalex-snapshot
An advancement in developmental and reproductive toxicity (DART) risk assessment: evaluation of a bioactivity and exposure-based NAM toolbox
inferred← citeshttps://doi.org/10.3390/biology11020209openalex-snapshot
High-Throughput Chemical Screening and Structure-Based Models to Predict hERG Inhibition
inferred← citeshttps://doi.org/10.3390/ijms252011154openalex-snapshot
Computational Strategies for Assessing Adverse Outcome Pathways: Hepatic Steatosis as a Case Study
inferred← citeshttps://doi.org/10.3390/molecules21010001openalex-snapshot
Extended Functional Groups (EFG): An Efficient Set for Chemical Characterization and Structure-Activity Relationship Studies of Chemical Compounds
inferred← citeshttps://doi.org/10.3390/toxics11020098openalex-snapshot
A Machine Learning Model to Estimate Toxicokinetic Half-Lives of Per- and Polyfluoro-Alkyl Substances (PFAS) in Multiple Species
inferred← citeshttps://doi.org/10.3390/toxics11070572openalex-snapshot
Exploring Dimensionality Reduction Techniques for Deep Learning Driven QSAR Models of Mutagenicity
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