Library 2

Enriching Nanomaterials Omics Data
Research Article Enriching Nanomaterials Omics Data: An Integration Technique to Generate Biological Descriptors Georgia Tsiliki1, Penny Nymark2,3, Pekka Kohonen2,3, Roland Grafström2,3, Haralambos Sarimveis1 1
Answering scientific questions with linked European nanosafety data
Answering scientific questions with linked European nanosafety data Egon Willighagen, Maastricht Universitry (one-click on the image bellow and scroll down to see the full presentation)  
eNanoMapper infrastructure
Access, use and functionalities of eNanoMapper infrastructure Virtual presentation held on Monday, 5 December 2016, with Andrej Kobe (European Commission, DG Environment / Sustainable chemicals Unit), presentin
Jaqpot Quattro User Interface Tutorial
Jaqpot Quattro User Interface Tutorial - Experimental design, Interlaboratory comparison and Read acrossTutorial Authors: Georgios Drakakis, C. Chomenidis, G. Tsiliki, E. Anagnostopoulou, P. Doganis, H. Sarimve
Modelling Services: Experimental Design, Interlaboratory Testing, Read-Across - Video Tutorial
Modelling Services: Experimental Design, Interlaboratory Testing, Read-Across - Video Tutorial Tutorial Authors: Georgios Drakakis, Georgia Tsiliki, Hampos Chomenidis, Evangelia Anagnostopoulou, Haralambos Sari
How to reproduce validation results of nano-lazar paper
How to reproduce validation results of nano-lazar-paper Authors: Christoph Helma, Micha Rautenberg, Denis Gebele, in silico toxicology gmbh. Source code for nano-lazar publication (and oral presentations). Vali
 Create and use lazar nanoparticle models
Create and use lazar nanoparticle models lazar Ruby libraries for the lazar framework Authors: Christoph Helma, Micha Rautenberg, Denis Gebele, in silico toxicology gmbh. Dependencies lazar depends on a couple
Answering scientific questions with linked European nanosafety data
Answering scientific questions with linked European nanosafety data Egon Willighagen, Micha Rautenberg, Denis Gebele, Linda Rieswijk, Friederike Ehrhart, Jiakang Chang, Georgios Drakakis, Penny Nymark, Pekka
eNanoMapper database, search tools and templates
eNanoMapper database, search tools and templates Nina Jeliazkova, Nikolay Kochev, IdeaConsult Ltd., Sofia, Bulgaria (one-click on the image bellow and scroll down to see the full presentation)  
Validation of read across predictions for nanoparticle toxicities
Validation of read across predictions for nanoparticle toxicities Christoph Helma1, Micha Rautenberg1, Denis Gebele1 1in silico toxicology gmbh, Basel, Switzerland We validate lazar read across models for nanop
Nano Modelling Services Tutorial
Create DataSet, Train a Model, Make a Prediction, Validate (split, cross or external) JaqPot Quattro is a web application for computational modelling of nanomaterials and is being developed in the context of th
JAQPOT QUATTRO user interface tutorial
How to use the JaqPot Quattro User Interface to create and validate NanoQSAR models Authors: Georgios Drakakis, C. Chomenidis, G. Tsiliki, E. Anagnostopoulou, P. Doganis, H. Sarimveis, The National Technical Un
JAQPOT Quattro API Tutorial
How to use all available functionalities of the JaqPot Quattro web application Authors: Georgios Drakakis, C. Chomenidis, G. Tsiliki, E. Anagnostopoulou, P. Doganis, H. Sarimveis, The National Technical Univers
eNanoMapper Dictionary
The dictionary includes a collection of terms and abbreviations often used in the context of the eNanoMapper project, but also terms that are generally used in areas like nanaosafety, data management or computa
eNanoMapper tutorial: Pathway analysis of microarray data
How to use the Pathway module of ArrayAnalysis.org for pathway analysis of microarray data Authors: Friederike Ehrhart, Lars Eijssen, Anwesha Bohler, Linda Rieswijk, Egon Willighagen (Maastricht University), Pe
eNanoMapper tutorial: How to make a pathway
Creating biological pathways for WikiPathways using PathVisio Authors: Friederike Ehrhart, Martina Summer-Kutmon, Egon Willighagen, Kristina Hanspers, Alexander Pico, Linda Rieswijk (Maastricht University), Pen
How to use the statistics module of ArrayAnalysis.org for statistics analysis of microarray data
How to use the statistics module of ArrayAnalysis.org for statistics analysis of microarray data Authors: Friederike Ehrhart, Lars Eijssen, Anwesha Bohler, Linda Rieswijk, Egon Willighagen (Maastricht Universit
AffyQC web tool of ArrayAnalysis.org for quality control and pre-processing of Affymetrix microarray data
How to use the AffyQC web tool of ArrayAnalysis.org for quality control and pre-processing of Affymetrix microarray data Authors: Friederike Ehrhart, Lars Eijssen, Anwesha Bohler, Linda Rieswijk, Egon Willighag
How to Use Chipster for Bioinformatics Analysis of Nanomaterial-Based Omics Data
How to Use Chipster for Bioinformatics Analysis of Nanomaterial-Based Omics Data Authors: Penny Nymark (Misvik Biology), Friederike Ehrhart and Egon Willighagen (Maastricht University), Eija Korpelainen (CSC -
eNanoMapper Tutorial: Entering and Analysing Nano Safety Data
Entering and Analysing Nano Safety Data Authors: Nina Jeliazkova (Idea Consult), Egon Willighagen (Maastricht University) Introduction The goal of this workshop is to make the participants familiar with the eNa
Browsing the eNM ontology with BioPortal, AberOWL and Protégé
Browsing the eNM ontology with BioPortal, AberOWL and Protégé Authors: Linda Rieswijk, Friederike Ehrhart and Egon Willighagen, Maastricht University Introduction The field of engineered nanomaterials is expone
Poster presented at the Benelux Bioinformatics Conference 2015
Ontology, database and tools for nanomaterial safety evaluation Friederike Ehrhart1, L Rieswijk1, CT Evelo1, H Sarimveis2, P Doganis2, G Drakakis2, B Fadeel3, B Hardy4, J Hastings5, C Helma6, N Jeliazkova7, V
eNanoMapper: enabling systems biology for nanosafety E. Willighagen1, F. Ehrhart1, L. Rieswijk1, B. Smeets4, C. Evelo1 1Department of Bioinformatics - BiGCaT, Maastricht University, UNS 50 Box 19, Maastricht, 6
Enriching protein corona
Enriching protein corona fingerprints using gene ontology information: an integration technique Presented by Georgia Tsiliki, NTUA (The National Technical University of Athens, Greece) 29th October 2015, 4 PM
eNanoMapper - A Database and Ontology Framework for Nanomaterials Design and Safety Assessment
eNanoMapper - A Database and Ontology Framework for Nanomaterials Design and Safety Assessment OpenTox Euro 2015 Meeting, UCD, Dublin, Ireland, 1 October 2015 Presented by Barry Hardy (Douglas Connect) as Coord
Proteomics Analysis
Research Article Proteomics Analysis Reveals Distinct Corona Composition on Magnetic Nanoparticles with Different Surface Coatings: Implications for Interactions with Primary Human Macrophages Carmen Vogt1, Ma
Image descriptor calculation web tool
Image descriptor calculation web tool Authors: Philip Doganis, Marios Kotsiandris, NTUA Introduction The images taken by Electron or Fluorescence microscopy are valuable sources of information that depict the a
RRegrs package Tutorial
RRegrs: Package Tutorial Authors: Georgia Tsiliki, Cristian R. Munteanu, Jose A. Seoane, Carlos Fernandez-Lozano, Haralambos Sarimveis, Egon L. Willighagen July 19, 2015 Introduction RRegrs is a collection of R
RRegrs: an R package for computer-aided model selection with multiple regression models
RRegrs: an R package for computer-aided model selection with multiple regression models Georgia Tsiliki1 †, Cristian R. Munteanu2,3 †, Jose A. Seoane4, Carlos Fernandez-Lozano2, Haralambos Sarimveis1 and Egon L
The importance of material characterization in nanotoxicology
Keeping it real: The importance of material characterization in nanotoxicology Bengt Fadeela, Andrea Fornarab, Muhammet S. Toprakc, Kunal Bhattacharyaa aDivision of Molecular Toxicology, Institute of Environm
The eNanoMapper database for nanomaterial safety information: storage and query
The eNanoMapper database for nanomaterial safety information: storage and query Nina Jeliazkova1, Nikolay Kochev2, David Vorgrimmler3, Janna Hastings4, Vedrin Jeliazkov1 1Ideaconsult Ltd, Sofia, Bulgaria, 2Univ
How to store nanomaterial safety data: meet eNanoMapper database
POSTER: How to store nanomaterial safety data: meet eNanoMapper database Nikolay T. Kocheva,c, Roland Grafströmb, Nina Jeliazkovac a ) University of Plovdiv, Department of Analytical Chemistry and Computer Chem
The first eNanoMapper prototype: a substance database to support safe-by-design
The first eNanoMapper prototype: a substance database to support safe-by-design Nina Jeliazkova1, Philip Doganis2, Bengt Fadeel3, Roland Grafström3,4, Janna Hastings5, Vedrin Jeliazkov1, Pekka Kohonen3, Cristia
eNanoMapper database for nanomaterial safety information
The eNanoMapper database for nanomaterial safety information Nina Jeliazkova1, Charalampos Chomenidis2, Philip Doganis2, Bengt Fadeel3, Roland Grafström3, Barry Hardy4, Janna Hastings5, Markus Hegi4, Vedrin Jel
Cancer Biology, Toxicology and Alternative Methods Development Go Hand-in-Hand
Cancer Biology, Toxicology and Alternative Methods Development Go Hand-in-Hand Pekka Kohonen1, Rebecca Ceder1, Ines Smit1, Vesa Hongisto2, Glenn Myatt3, Barry Hardy4, Ola Spjuth4,5 and Roland Grafström1,2 1Inst
A Database and Ontology Framework for Nanomaterials Design and Safety Assessment ACS ACS Meeting, Boston, USA, 18 August 2015 Presented by Barry Hardy (Douglas Connect) as Coordinator and in representation of w
eNanoMapper Webinars: Using the eNanoMapper ontology
Using the eNanoMapper ontology Presented by Janna Hastings (EMBL-EBI, UK) 25th June 2015, 3 PM (Central European Time) / 9 AM (US Eastern Time) You can download slides by Janna Hastings >> here <
eNanoMapper Webinars: Nanomaterial data visualization
Nanomaterial data visualization with ambit.js and d3.js Presented by Egon Willighagen (Maastricht University) and Nina Jeliazkova (IDEAconsult Ltd.) 18th May 2015, 5 PM (Central European Time) / 11 AM (US
eNanoMapper: Harnessing ontologies to enable data integration for nanomaterial risk assessment You can see the full paper by >>clicking on this link<<. Abstract Engineered nanomaterials (ENMs) are b
WEBINAR: The first eNanoMapper prototype
A substance database to support a safe innovation approach Presented by Nina Jeliazkova (Ideaconsult Ltd.) You can download slides by >>clicking on this link<<. The webinar presents the first proto
eNanoMapper presentation
eNanoMapper Nano Safety Cluster Meeting - Antalya, Turkey by: Barry Hardy ABSTRACT → Modular infrastructure for data storage, sharing and searching, based on open standards and semantic web technologies, minimu
Cheminformatics
Cheminformatics into an Open Linked Data Platform for Drug Discovery by: Joerg K. Wegner, Aaron Sterling, Rajarshi Guha, Andreas Bender, Jean L. Faulon, Janna Hastings, Noel O'Boyle, John Overington, Herman Van
Information Ontology
The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web by: Janna Hastings, Leonid Chepelev, Egon Willighagen, Nico Adams, Christoph Steinbeck, Michel D
AMBIT RESTful Web
AMBIT RESTful web services: An implementation of the OpenTox application programming interface by: Nina Jeliazkova, Vedrin Jeliazkov ABSTRACT The AMBIT web services package is one of the several existing indepe
Predictive toxicology
Collaborative development of predictive toxicology applications by: Barry Hardy, Nicki Douglas, Christoph Helma, Micha Rautenberg, Nina Jeliazkova, Vedrin Jeliazkov, Ivelina Nikolova, Romualdo Benigni, Olga Tch
Linked Data Platform
Incorporating Commercial and Private Data into an Open Linked Data Platform for Drug Discovery by: Carole Goble, AlasdairJ Gray, Lee Harland, Karen Karapetyan, Antonis Loizou, Ivan Mikhailov, Yrjänä Rankka, Ste
Quantitative Descriptions
A Survey of Quantitative Descriptions of Molecular Structure by: Rajarshi Guha, Egon Willighagen ABSTRACT Numerical characterization of molecular structure is a first step in many computational analysis of chem
Chemistry Development Kit
The Chemistry Development Kit (CDK) An Open-Source Java Library for Chemo- and Bioinformatics by: C. Steinbeck, Y. Han, S. Kuhn, O. Horlacher, E. Luttmann, E. Willighagen ABSTRACT The Chemistry Development Kit
ToxBank Data Warehouse
The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing by: Pekka Kohonen, Emilio Benfenati, David Bower, Rebecca Ceder, Michael Crump, Kevin Cross, Roland C. G
WP1 reports
Nano Technology Community Outreach DELIVERABLE REPORTS D1.1 Requirements Analysis and Systems DesignD1.2 Use Cases and Test SuiteD1.3 Sustainability PlanD1.4 User GuidanceD1.5 Evaluation WORK PACKAGE LEADER Maa
WP2 Reports
Ontology Development for Nano Safety Domain DELIVERABLE REPORTS D2.1 Framework and Infrastructure for Ontology development, versioning and disseminationD2.2 Ontology Content Types and Existing Community efforts
WP 3 reports
Database development and implementation DELIVERABLE REPORTS D3.1 Technical Specification and initial implementation of the protocol and data management web servicesD3.2 Data Management System with extended sear
WP 4 Reports
Analysis & Modelling DELIVERABLE REPORTS D4.1 Analysis and Modelling SpecificationsD4.2 Descriptor Calculation Algorithms and MethodsD4.3 nQSAR Modelling infrastructureD4.4 Mechanism-ofaction Modelling Tool
WP 5 Reports
User Application Development, Integration and Testing DELIVERABLE REPORTS D5.1 Integrated Issue Management and Testing systemD5.2 User registration, authentication and authorisationD5.3 User application for imp
WP 6 Reports
Dissemination & Training DELIVERABLE REPORTS D6.1 eNanoMapper Year 1 Dissemination ReportD6.2 eNanoMapper Year 2 Dissemination ReportD6.3 eNanoMapper TutorialsD6.4 eNanoMapper Community Development ReportD6
WP 7 Reports
Management DELIVERABLE REPORTS D7.1 Kick-Off MeetingD7.2 Year 1 MeetingD7.3 First Annual Technical and Financial ReportD7.4 Review MeetingD7.5 Year 2 MeetingD7.6 Second Annual Technical and Financial ReportD7.7