OpenRiskNet services

Integrated
Korea Institute of Technology NanoQSAR model
KIT (Korea Institute of Toxicology) Nano-QSAR models were implemented for prediction of cytotoxicity caused by metal and metal oxide nanoparticles. A Binary classification model was built using the Logistic regression ...

Provided by:
Korea Institute of Toxicology (KIT)
Type:
Trained model, Model
Applicability domain:
Computational modelling, Toxicology, Predictive toxicology
Topic:
Nano safety, Risk assessment, Structure-activity relationship (SAR / QSAR), Predictive modelling
For end-users
For developers
Integrated
"KIT Daphnia data on nano particles" dataset is based on "Meta-analysis of Daphnia magna nanotoxicity experiments in accordance with test guidelines", Shin, Hyun Kil & Seo, Myungwon & Shin, Seong ...

Provided by:
Korea Institute of Toxicology
Type:
Database / data source
Applicability domain:
Computational modelling, Toxicology, Predictive toxicology
Topic:
Bioassay, Nano safety, Risk assessment
Biological area:
Acute toxicity
For end-users
Integrated
ToxCast and Tox21 datasets (raw and summary) extracted from the MySQL database provided by US EPA
The dataset as provided by US EPA were transformed and are now available in the EdelweissData system for easy access via APIs. The most current version is 3.2. Data of ...

Provided by:
Edelweiss Connect GmbH
Type:
Database / data source
Applicability domain:
Computational modelling, Toxicology, Predictive toxicology
Topic:
Bioassay, Risk assessment, Information extraction
Biological area:
NOAEL/LOAEL
For end-users
For developers
In progress
Our platform searches the content from 500+ websites and quickly delivers relevant chemical hazard and toxicology data.
Powered by the world’s largest database of its kind, ToxPlanet’s platform enables chemical safety professionals to find chemical toxicology and property information from over 500 sources using a normalized index ...

Provided by:
ToxPlanet
Type:
Database / data source, Data mining tool, Service
Applicability domain:
Toxicology
Topic:
Chemical properties, Risk assessment, Information extraction
Biological area:
Genotoxicity, Mutagenicity, Carcinogenicity, Acute toxicity
For developers
In progress
The On-line Chemical Database and Modeling Environment models
The tools provide an access to ten models, namely physico-chemical properties (logP, melting point, water solubility), biological properties (BCF - bio-concentration factor, the Human Ether-a-go-go-related Gene (hERG) channel blockage, CYP1A2 ...

Provided by:
BigChem GmbH
Type:
Trained model
Applicability domain:
Predictive toxicology
Topic:
Chemical properties, Risk assessment, Structure-activity relationship (SAR / QSAR), Predictive modelling
Biological area:
NOAEL/LOAEL, Acute toxicity
For end-users
Integrated
Virtual Screening Metal Oxide Nanoparticles Enalos Platform
A predictive classification model for the toxicological assessment of iron oxide NPs with different core, coating and surface modification based on a number of different properties including size, relaxivities, zeta ...

Provided by:
NovaMechanics Ltd
Type:
Application, Trained model, Model, Service
Applicability domain:
Computational modelling, Toxicology, Predictive toxicology
Topic:
Nano safety, Risk assessment, Structure-activity relationship (SAR / QSAR), Predictive modelling
For end-users
For developers
Integrated
Enalos Platform nanoinformatics nanoparticles
A validated predictive model for nanoparticles cellular uptake, that is part of the Enalos infrastructure deployed into the OpenRiskNet reference environment. The model can be used for the predictions of ...

Provided by:
NovaMechanics Ltd
Type:
Trained model, Model
Applicability domain:
Computational modelling, Toxicology, Predictive toxicology
Topic:
Nano safety, Risk assessment, Structure-activity relationship (SAR / QSAR), Predictive modelling
For end-users
For developers
In progress
This service is a Virtuoso SPARQL endpoint that is loaded with RDF of the EPA Adverse Outcome Pathway Database (AOP-DB) from the US EPA, who won the implementation challenge. The ...

Provided by:
Maastricht University
Type:
Database / data source
Applicability domain:
Toxicology, Bioinformatics
Topic:
Risk assessment, Information extraction
For end-users
For developers
In progress
The eNanoMapper prototype database is part of the computational infrastructure for toxicological data management of engineered nanomaterials, developed within the EU FP7 eNanoMapper project. Provides support for upload, search and ...

Provided by:
Maastricht University
Type:
Database / data source
Applicability domain:
Toxicology, Bioinformatics
Topic:
Chemical properties, Nano safety, Information extraction
For end-users
For developers
In progress
This service is a Virtuoso SPARQL endpoint that is loaded with RDF of the Adverse Outcome Pathway (AOP)-Wiki database (https://aopwiki.org/), based on the quarterly XML dumps that are provided. The ...

Provided by:
Maastricht University
Type:
Database / data source
Applicability domain:
Toxicology, Bioinformatics
Topic:
Risk assessment, Information extraction
For end-users
For developers
Integrated
Collection of toxicological data sources exposed via OpenTox
Three of the most popular toxicologic open data sources are already publically available: the EPA's in vitro ToxCast/Tox21 database, the EPA's in vivo ToxRefDB database and the NIBIOHN's toxicogenomics Open ...

Provided by:
Edelweiss Connect
Type:
Database / data source, Application, Service
Applicability domain:
Computational modelling, Toxicology, Bioinformatics, Predictive toxicology
Topic:
Chemical properties, Risk assessment
Biological area:
Omics, NOAEL/LOAEL, Acute toxicity
For end-users
Integrated
Generate, store and share predictive statistical and machine learning models
Jaqpot is a user-friendly web-based e-infrastructure containing many data analysis and modelling microservices integrated under harmonised APIs. The Jaqpot infrastructure allows the user to build applications that preprocess data, compute ...

Provided by:
National Technical University of Athens
Type:
Analysis tool, Processing tool, Trained model, Model generation tool, Model, Data mining tool, Service
Applicability domain:
Computational modelling, Predictive toxicology
Topic:
Biokinetics, Predictive modelling
For end-users
For developers
Integrated
Generate, store and share predictive statistical and machine learning models
Jaqpot is a user-friendly web-based e-infrastructure containing many data analysis and modelling microservices integrated under harmonised APIs. Jaqpot GUI is a user interface that allows the end-user to use most ...

Provided by:
National Technical University of Athens
Type:
Application, Visualisation tool, Analysis tool, Processing tool, Trained model, Model generation tool, Model, Data mining tool, Workflow tool
Applicability domain:
Computational modelling, Predictive toxicology
Topic:
Predictive modelling
For end-users
Integrated
Toxicity predictions
Lazar (Lazy Structure-Activity Relationships ) takes a chemical structure as input and provides predictions for a variety of toxic properties. Lazar uses an automated and reproducible read across procedure to ...

Provided by:
in silico toxicology gmbh, Johannes Gutenberg Univertity
Type:
Application, Helper tool, Trained model, Model, Service
Applicability domain:
Toxicology, Predictive toxicology
Topic:
Chemical properties, Risk assessment, Structure-activity relationship (SAR / QSAR)
Biological area:
Mutagenicity, NOAEL/LOAEL, Carcinogenicity, Blood brain barrier, Acute toxicity
For end-users
For developers
In progress
WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways ...

Provided by:
Maastricht University
Type:
Database / data source
Applicability domain:
Bioinformatics
Topic:
Information extraction
Biological area:
Transcriptomics, Omics, Skin sensitisation, Genotoxicity, Mutagenicity, Carcinogenicity, Acute toxicity
For end-users
For developers
Integrated
BridgeDb is a platform for database identifier mapping, both simple identifiers (e.g. CHEBI:1234) and universal resource identifiers (URIs, e.g. http://identifiers.org/chebi/CHEBI:1234). It is the workhorse of data integration and supports the ...

Provided by:
Maastricht University
Type:
Database / data source, Service
Applicability domain:
Bioinformatics
Topic:
Identifier mapping
For developers
For end-users
Integrated
The model predicts Log D based on a support vector machine trained on data from ChEMBL version 23 comprising approximately 1.6 million compounds. The confidence interval is calculated for the ...

Provided by:
Uppsala University
Type:
Trained model
Applicability domain:
Computational modelling
Topic:
Chemical properties, Structure-activity relationship (SAR / QSAR), Predictive modelling
For end-users
For developers
Integrated
Python client for Squonk REST API
PySquonk is a Python 3 client that wraps the Squonk JobExecutor REST API, making it simple to execute Squonk services from Python. This project was started at the Diamond Light ...

Provided by:
Informatics Matters
Type:
Software
Applicability domain:
Computational modelling
Topic:
Chemical properties, Predictive modelling
For developers
In progress
Extend molecular biological networks with toxic compounds.
Produces a link set for the Cytoscape CyTargetLinker App that can be used to extend molecular biological networks that contain proteins with toxic compounds that have proteins in that network ...

Provided by:
Maastricht University
Type:
Database / data source
Applicability domain:
Toxicology, Bioinformatics
Topic:
Chemical properties, Information extraction
Biological area:
Omics
For end-users
For developers
Integrated
This repository contains transcriptomics data from human, mouse and rat in vitro liver cell models. Only meta-data information file, normalized data and average of normalized array data of all replicates ...

Provided by:
Department of Toxicogenomics, Maastricht University
Type:
Database / data source
Applicability domain:
Toxicology, Predictive toxicology
Topic:
Chemical properties, Risk assessment, Predictive modelling
Biological area:
Transcriptomics, Genotoxicity, Carcinogenicity
For end-users
For developers
In progress
TeMOwl provides unified access to semantic data i.e. controlled vocabularies, terminologies, ontologies and knowledge resources.
TeMOwl provides unified access to semantic data i.e. controlled vocabularies, terminologies, ontologies and knowledge resources. It hides complexity of different semantic service providers including their various data formats. Further it ...

Provided by:
Fraunhofer SCAI
Type:
Helper tool, Software, Service
Applicability domain:
Ontology
Topic:
Identifier mapping, Information extraction
For developers
In progress
Toxicology database, Knowledge base and data mining, AOP related tools
The AOP-DB serves to link molecular targets identified as molecular initiating events (MIEs) and key events (KEs) in the AOP-Wiki (https://aopwiki.org) to publicly available data (e.g. gene-protein, pathway, species orthology, ...

Provided by:
US Environmental Protection Agency
Type:
Database / data source, Service
Applicability domain:
Computational modelling, Bioinformatics, Predictive toxicology, Ontology
Topic:
Bioassay, Predictive modelling, Information extraction
Biological area:
Omics
For end-users
In progress
Chemical similarity using the Fragment Network
This is the same API that is behind Informatics Matters' Fragnet Search application for which more information can be found at https://fragnet.informaticsmatters.com/ The service deployed to OpenRiskNet is the REST ...

Provided by:
Informatics Matters Ltd
Type:
Database / data source, Service
Applicability domain:
Computational modelling, Toxicology, Predictive toxicology
Topic:
Chemical properties, Structure-activity relationship (SAR / QSAR), Predictive modelling
For end-users
For developers
Integrated
Processed data (counts and fold changes) based on the transcriptomics data provided by Open TG-GATEs and DrugMatrix
Processed data was generated using a standard workflow. The CEL files have been normalized using the single-channel array normalization function of the SCAN.UPC library available through Bioconductor. Normalized intensities have ...

Provided by:
Edelweiss Connect GmbH
Type:
Database / data source
Applicability domain:
Toxicology, Bioinformatics
Topic:
Risk assessment, Information extraction
Biological area:
Transcriptomics, Omics
For end-users
For developers
Integrated
A classification model built by CPSign for predicting molecules
Classification model that models Blood brain barrier penetration using the statistical approach Conformal prediction.

Provided by:
Uppsala Universitet
Type:
Trained model, Model
Applicability domain:
Predictive toxicology
Topic:
Biokinetics
Biological area:
Toxicokinetics, Blood brain barrier
For end-users
Integrated
A Venn-ABERS model built by CPSign for predicting molecules
Classification model that models Blood brain barrier penetration using the statistical approach Venn-ABERS

Provided by:
Uppsala University
Type:
Trained model, Model
Applicability domain:
Predictive toxicology
Topic:
Biokinetics
Biological area:
Blood brain barrier
For end-users
In progress
A database for curated toxicogenomic datasets
ToxicoDB isa web-application based on the code base of the existing PharmacoDB web-application. The ToxicoDB web-app will provide an intuitive interface for all users (including users that are not computational ...

Provided by:
University Health Network
Type:
Database / data source, Application, Visualisation tool, Software
Applicability domain:
Bioinformatics, Predictive toxicology
Topic:
Predictive modelling, Information extraction
Biological area:
Transcriptomics
For end-users
For developers
In progress
Predict ADME/PK with Confidence
The service predicts 8 basic human clinical ADME/PK-parameters directly from molecular structure and can also be used to optimize ADME/PK-characteristics of drug candidates.

Provided by:
Prosilico
Type:
Application, Software, Service
Applicability domain:
Predictive toxicology
Topic:
Kinetics, Structure-activity relationship (SAR / QSAR), Predictive modelling
Biological area:
Toxicokinetics
For end-users
In progress
Discover your variants of interest in human omics datasets
Key information for detecting human omics dataset of interest can be obtained via the Beacon without compromising data sensitivity. The user is able to query crucial aspects and obtain boolean ...

Provided by:
Centre for Genomic Regulation
Type:
Application, Software, Service
Applicability domain:
Bioinformatics
Topic:
Information extraction
Biological area:
Omics
For end-users
In progress
Programmatically retrieve metadata from the European Genome-phenome Archive
All metadata objects generated within the European Genome-phenome Archive can be retrieved programmatically by using this API. Any user downloading omics data their genotoxicity or related studies can easily access ...

Provided by:
Centre for Genomic Regulation
Type:
Application, Service
Applicability domain:
Bioinformatics
Topic:
Information extraction
Biological area:
Omics
For end-users
Integrated
Machine learning models for site-of-metabolism prediction
FAME (FAst MEtabolizer) is a machine learning model for the prediction of sites of metabolism (SOMs) for drug-like and other xenobiotic compounds (Šícho et al., 2019). FAME 3 predicts SOMs ...

Provided by:
Universitaet Hamburg and UCT Prague and University of Bergen
Type:
Application, Software, Trained model, Model, Service
Applicability domain:
Predictive toxicology
Topic:
Structure-activity relationship (SAR / QSAR), Predictive modelling
For end-users
For developers
Integrated
Classification model based on Liver toxicology knowledge base (https://www.fda.gov/science-research/liver-toxicity-knowledge-base-ltkb/drug-induced-liver-injury-rank-dilirank-dataset) Modelling the classes "no DILI" or "most DILI"

Provided by:
Uppsala Universitet
Type:
Trained model
For end-users
Integrated
Classification model based on Liver toxicology knowledge base (https://www.fda.gov/science-research/liver-toxicity-knowledge-base-ltkb/drug-induced-liver-injury-rank-dilirank-dataset) Modelling the classes "no DILI" or "less / most DILI"

Provided by:
Uppsala Universitet
Type:
Trained model
Topic:
Structure-activity relationship (SAR / QSAR)
For end-users
Integrated
Classification model based on Liver toxicology knowledge base (https://www.fda.gov/science-research/liver-toxicity-knowledge-base-ltkb/drug-induced-liver-injury-rank-dilirank-dataset) Modelling the classes "no / less DILI" or "most DILI"

Provided by:
Uppsala Universitet
Type:
Trained model
For end-users
Integrated
Chemical identifier conversion service
This REST Api allows you to submit chemical identifiers in one format and translate it into another format (e.g. SMILES -> InChi)

Provided by:
Edelweiss Connect
Type:
Helper tool
Topic:
Identifier mapping
For end-users
For developers
Integrated
The OpenRiskNet registry application
An overview of the OpenRiskNet compliant services running in this OpenRiskNet Virtual Research Environment.

Provided by:
Edelweiss Connect
Type:
Service
For system admins
For developers
In progress
Information retrieval system for semantic searches in large text collections
SCAIView is a knowledge discovery software for the life sciences. It facilitates­ the rapid identification of aggregate­d information from large text sources. Knowledge Discovery and Semantic Search Documents are retrieved ...

Provided by:
Fraunhofer Gesellschaft
Type:
Application, Software, Service
Applicability domain:
Bioinformatics
Topic:
Identifier mapping, Information extraction
For end-users
In progress
Service to run Nextflow pipelines
The command line service provides the necessary environment to run any Nextflow pipeline. The basic command for using the service after logging in is: nextflow run <pipeline_name> For a collection of ...</pipeline_name>

Provided by:
Centre for Genomic Regulation (CRG)
Type:
Software, Service, Workflow tool
Applicability domain:
Bioinformatics
For developers
Integrated
Webservice to WEKA Machine Learning Algorithms
RESTful API Webservice to WEKA Machine Learning Algorithms. This webservice provides an OpenRiskNet compliant REST interface to machine learning algorithms from the WEKA Java Library. This application is developed by ...

Provided by:
Johannes Gutenberg University Mainz
Type:
Trained model, Model generation tool, Model, Service
Applicability domain:
Computational modelling, Predictive toxicology
Topic:
Predictive modelling
For developers
For end-users
Integrated
Interactive computing and workflows sharing
A collection of Jupyter notebooks developed for and with the OpenRiskNet VRE. Project Jupyter is a non-profit, open-source project, born out of the IPython Project in 2014 as it evolved ...

Provided by:
Project Jupyter
Type:
Visualisation tool, Helper tool, Software, Analysis tool, Processing tool, Workflow tool
Applicability domain:
Computational modelling, Toxicology, Bioinformatics
For end-users
For developers
Integrated
MetPred predicts site-of-metabolism using a data mining approach based on Reaction SMARTS to define reaction types.

Provided by:
Uppsala University
Type:
Trained model, Service
Applicability domain:
Computational modelling
Topic:
Risk assessment, Information extraction
For developers
For end-users
Integrated
OpenRiskNet management console
OpenShift console providing the ability to manage and monitor the deployment of an OpenRiskNet VRE. Administrative privileges required to access.

Provided by:
Red Hat
Type:
Service
For system admins
Integrated
Combining site-of-metabolism and reactivity for (P450) site-of-metabolism prediction. Includes structure-based predictor (from OpenRiskNet partner VU) and third-party (University of Copenhagen) reactivity predictor (SMARTCyp).

Provided by:
Vrije Universiteit Amsterdam
Type:
Application, Software, Processing tool, Trained model, Service
Applicability domain:
Predictive toxicology, Computational modelling, Bioinformatics
Topic:
Structure-activity relationship (SAR / QSAR)
For end-users
For developers
Integrated
OpenRiskNet Single Sign On
OpenRiskNet Single Sign On (SSO) based on Red Hat SSO product (Keycloak). Provides a single point of user authentication for deployed applications. Administrative privileges required to access.

Provided by:
Red Hat
Type:
Service
For system admins
Integrated
Computation research made simple and reproducible
We believe that the reason computational tools are not being utilised effectively in R&D is not because of a lack of functionality, but a lack of usability. And we don't ...

Provided by:
Informatics Matters
Type:
Database / data source, Visualisation tool, Software, Analysis tool, Service, Workflow tool
Applicability domain:
Computational modelling, Bioinformatics, Predictive toxicology
Topic:
Chemical properties, Risk assessment, Structure-activity relationship (SAR / QSAR), Predictive modelling, Information extraction
For end-users
For developers