Tools
Explore tools developed by and/or used in VHP4Safety.
You can search for a tool that you know using the search box below. Alternatively, you can filter the tools with respect to the case studies' flow step that they belong to and/or the regulatory question that they are associated with. Use the "Filters" button to show filter options, then "Apply Filter" to see results, and click "Clear Filter" to reset the filters.
AOP Network Builder
web-based tool for building, visualizing, and analyzing Adverse Outcome Pathway (AOP) networks. It serves as an extended user interface for the AOP-Wiki RDF SPARQL endpoint.
AOP-Builder
A tool to explore scientific literature to extract relevant entities and their relations for AOP construction, using AI.
AOP-Wiki API
A REST API for AOP-Wiki content to make SPARQL queries.
AOP-Wiki Snorql UI
A graphical interface to make queries to the AOP-Wiki SPARQL endpoint.
ArrayAnalysis
A user-friendly service to conduct quality control and pre-processing analyses for microarray data.
BioModels
A repository of mathematical models of biological and biomedical systems.
BioTransformer
A software tool to predict metabolites based on inputs in SMILE format.
BMDExpress-3
A tool to perform dose response modeling for high dimensional dose-response analysis.
BridgeDb
A framework to map identifiers between various biological databases and related sources.
CDK Depict
A webservice to convert SMILES into 2D depictions in either SVG, PNG, and PNG formats.
CellDesigner
A structured diagram editor to draw gene-regulatory and biochemical networks.
CompTox
An online database to provide access to chemistry, toxicity, and exposure information for chemicals.
COPASI
An open-source software application to create and solve mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others.
cpLogD
A model to predict water-octanol distribution coefficient (logD) for chemical compounds which is a proxy for the lipophilicity which is a major determinant of drug properties and overall suitability of drug candidates.
DECIMER
An online service to extract chemical structures from PDF-formatted files and images.
European Medicines Agency Documents
An online repository of official reports from the European Medicines Agency.
FAIRDOMHub
A web-accessible registry to store, share and publish research assets of biology projects.
Fairspace
An open source data management platform that allows importing and exporting metadata using Resource Description Framework (RDF)
Farmacotherapeutisch Kompas
The Farmacotherapeutisch Kompas contains a wide spectrum of information on prescribing and pharmacology, among others indications, side effects and costs of the prescription of all pharmaceutical drugs available in the Netherlands.
Flame
An open source framework to develop, host, and use machine-learning models, such as QSAR-like models, in production environments.
Google Scholar
Search engine for (scientific) literature.
Google Search
Web search engine by Google.
Joint Research Centre Data Catalogue
An inventory of data produced by the Joint Research Centre (JRC) in accordance with the JRC Data Policy.
LLMapperino
A multi-agent question-answering tool that combines structured pathway knowledge from user-selected MINERVA projects with live web research (Perplexity) and synthesizes evidence using an LLM. It targets specialized questions in lipid metabolism and related tox/biology by grounding answers in curated MINERVA maps and corroborating sources.
MolAOP analyser
The MolAOP analyser service enables users to analyse transcriptomic data in the context of molecular Adverse Outcome Pathways (AOPs). The tool allows users to upload differential expression data or select from built-in demo datasets. It then guides them through gene selection, visualisation (volcano plots), and Key Event enrichment analysis based on predefined KE-to-pathway mappings.
NIH Dietary Supplement Label Database
The Dietary Supplement Label Database was developed by the American Office of Dietary Supplements at the National Institutes of Health. This database includes printed on more than 200 thousand labels of dietary supplement products sold in the United States.
O'QT — OECD QSAR Toolbox AI Assistant
A multi-agent assistant that connects to a locally running OECD QSAR Toolbox Web API to analyze chemicals, profile hazards, and suggest read-across strategies. O’QT fetches properties, experimental data, and profiling outputs from the Toolbox and synthesizes them into an AI-generated report.
OP PBK Model
Physiologically based pharmacokinetic model for organophosphates
OPSIN: Open Parser for Systematic IUPAC nomenclature
An online service with a tool to parse IUPAC names for chemicals into the chemical graph notation SMILES.
qAOP-App
An interactive tool offering an overview and dynamic time‐course predictions of KEs and AOs via ODE‐based qAOP models, based on VHP4Safety case studies.
QSPRpred
This tool allows users to predict the activity of their chemicals of interest for various endpoints. This prediction is done by target-specific, pretrained QSAR models. These models are specific for endpoints related to molecular initiation events from the VHP4Safety case studies.
SOM Prediction
A webservice to conduct protein-structure and reactivity based (P450) site-of-metabolism prediction.
SysRev
An online service to conduct literature review, data extraction and systematic review.
The OECD QSAR Toolbox
A software to support hazard assessment of chemicals as well as to increase mechanistic and other knowledge on chemical substances in a cost-efficient way.
ToxTempAssistant
A tool that uses Large Language Models to harmonize and complete method descriptions of in vitro toxicity tests based on the ToxTemp template. The tool alleviates the administrative burden on toxicologists by extracting methodological details from contextual documents, such as protocols, publications, or lab notebooks, and generating structured draft responses to the 77 questions of the ToxTemp template.
TXG-MAPr
An online application to implement weighted gene co-expression network analysis (WGCNA) derived from the Primary Human Hepatocytes (PHH) TG-GATEs data sets.
VHP4Safety Glossary
A collection of ontology with the names, abrreviations and definitions of the terminology that is used in the VHP4Safety project.
VHP4Safety Wikibase
A Wikibase instance to store and present information about toxic, safe and potentially toxic compounds related to the VHP4Safety project.
VHP4Safety Wikibase User Interface
A Synia-based graphical user interface to the content of the VHP4Safety Wikibase using SPARQL queries.
WikiPathways - AOP Portal
An Adverse Outcome Pathway (AOP) portal for WikiPathways to highlight the molecular basis of AOPs or events in AOPs.
xploreaop
A web application to visualize Adverse Outcome Pathway (AOP) networks and interactively explore the AOPs for two liver outcomes, Cholestasis and Steatosis.