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List of works by Egon Willighagen

A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences

scientific article published on 20 October 2020

A Survey of Quantitative Descriptions of Molecular Structure ⬇️

scientific article published on January 1, 2012

A catalogue of 863 Rett-syndrome-causing MECP2 mutations and lessons learned from data integration

scientific article published on 15 January 2021

A data fusion pipeline for generating and enriching Adverse Outcome Pathway descriptions

scientific article published on 15 November 2017

A data reusability assessment in the nanosafety domain based on the NSDRA framework followed by an exploratory quantitative structure activity relationships (QSAR) modeling targeting cellular viability

A novel infrastructure for chemical safety predictions with focus on human health

A protocol for adding knowledge to Wikidata, a case report

scientific article published on 07 April 2020

A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses ⬇️

January 2021 scholarly article

A resource to explore the discovery of rare diseases and their causative genes

scientific article

A strategy towards the generation of testable adverse outcome pathways for nanomaterials

scientific article

A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury

scientific article from 2017

Accessing biological data in R with semantic web technologies

scientific article published on 16 March 2014

Accessing biological data with semantic web technologies

Accessing, Using, and Creating Chemical Property Databases for Computational Toxicology Modeling

scientific article published in 2012

Adding citations between existing articles in Wikidata

manuscript by Egon Willighagen

Adoption of the Citation Typing Ontology by the Journal of Cheminformatics ⬇️

scientific article published on 28 July 2020

Adverse outcome pathways: opportunities, limitations and open questions

scientific article published on 19 October 2017

Analyzing your internet applications' log files ⬇️

first article in a series about using Lire to analyze log files of internet server applications

Analyzing your internet applications' log files II - configuring your reports ⬇️

second article in a series about using Lire to analyze log files of internet server applications

Applications of the InChI in cheminformatics with the CDK and Bioclipse

scientific article published on 13 March 2013

Artificial intelligence for natural product drug discovery ⬇️

scientific article from 2023

Author Correction: A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses

scientific article published in 2023

Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

scientific article published on 17 July 2020

Author response: Wikidata as a knowledge graph for the life sciences

scholarly article, peer review and author response published on 24 January 2020

Automatic OpenAPI to Bio.tools Conversion

article published in 2017

Bacting: a next generation, command line version of Bioclipse

scientific article

Beautifying Data in the Real World ⬇️

chapter from a book from 2009

Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome

scientific article published on 21 February 2019

BioDataFuse: Enhancing data interoperability through modular queries and knowledge graph construction ⬇️

conference paper

BioHackEU23 report: Extending interoperability of experimental data using modular queries across biomedical resources

BioHackEU24 report: ORCID and ROR identifiers in BioHackrXiv reports

Bioclipse 2: a scriptable integration platform for the life sciences ⬇️

scientific article

Bioclipse-R: integrating management and visualization of life science data with statistical analysis

scientific article

Bioclipse: an open source workbench for chemo- and bioinformatics ⬇️

scientific article published on 22 February 2007

Bioinformatics-based cancer research have wide toxicological applicability

Bioschemas Resource Index for Chem and Plants

BridgeDb and Wikidata: a powerful combination generating interoperable open research (BridgeDb)

scientific article published on 07 March 2022

Building Expertise on FAIR Through Evolving Bring Your Own Data (BYOD) Workshops: Describing the Data, Software, and Management-focused Approaches and Their Evolution

scientific article published in 2024

CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community

scientific article published on 13 May 2022

CDK-Taverna 2.0: migration and enhancements of an open-source pipelining solution

CDK-Taverna: an open workflow environment for cheminformatics

scientific article

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

scientific article published on 05 May 2020

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms ⬇️

journal article from 'Molecular Systems Biology' published in 2021

Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies?

scientific article published on 11 December 2020

Cationic Gemini Surfactants Based on Tartaric Acid: Synthesis, Aggregation, Monolayer Behaviour, and Interaction with DNA ⬇️

scientific article (publication date: April 2002)

Changing computational research. The challenges ahead

scientific article (publication date: 2012)

ChemInform Abstract: Open Source Drug Discovery with Bioclipse

Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators ⬇️

scientific article

Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML Vocabulary for Spectral Data

peer-reviewed article

Cheminformatics ⬇️

scientific article

Cheminformatics for Users

chapter in a proceedings

CiTO support for BioHackrXiv

CiteULike CiTO annotations

dataset

Collaborative Cheminformatics Applications

Collaborative Computational Technologies for Biomedical Research

Collaborative research: about licensing, waiving, and ownership

scientific article published on 26 January 2017

Collaborative research: about licensing, waiving, and ownership

Complex Portal 2022: new curation frontiers

scientific article

Computational toxicology using OpenTox & Bioclipse

Computational toxicology using the OpenTox application programming interface and Bioclipse

scientific article

Current systems biology approaches in hazard assessment of nanoparticles

CyTargetLinker app update: A flexible solution for network extension in Cytoscape

CyTargetLinker app update: A flexible solution for network extension in Cytoscape

scientific article published on 14 June 2018

Developing a novel QSAR framework for nanomaterial toxicity

article

Discovering life's directed metabolic (sub)paths to interpret human biochemical markers using the DSMN tool

scientific article published in January 2024

ELIXIR and Toxicology: a community in development

ELIXIR and Toxicology: a community in development

scientific article published on 3 October 2023

Edition 1.4.1-0 of Groovy Cheminformatics with the Chemistry Development Kit

Elemental composition determination based on MSn

scientific article

Emerging practices for mapping and linking life sciences data using RDF — A case series ⬇️

scientific article

Enabling Open Science: Wikidata for Research (Wiki4R)

scientific article

Enhancement and Reusage of Biomedical Knowledge Graph Subsets

Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

scientific article published on 20 September 2017

European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials

scientific article from 2022

Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform

Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform

Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations

scientific article published in 2023

FAIR Principles: Interpretations and Implementation Considerations

scholarly article

FAIR assessment tools: evaluating use and performance

scientific article published in July 2022

FAIR blog-to-blog citations

Factors influencing developmental neurotoxicity study outcome in the bisphenol A case

Fast and Scriptable Molecular Graphics in Web Browsers without Java3D

scientific article (publication date: 14 June 2007)

From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials

scientific article published in May 2024

Geospatial data and Scholia ⬇️

scholarly article

Getting CAS registry numbers out of WikiData

scholarly article by Egon Willighagen published in January 2015

Giving metabolites (and lipids) a chemical and biological context with open science

scientific article published on 26 August 2024

Glycolysis and Gluconeogenesis

metabolic pathway (mus musculus)

Guiding the choice of informatics software and tools for lipidomics research applications

scientific article published on 21 December 2022

Helping to improve the practice of cheminformatics

scientific article

History of rare diseases and their genetic causes - a data driven approach

INTOXICOM Workshop Report: FAIRification of Toxicological Research Output: Leveraging ELIXIR Resources

Incorporating Commercial and Private Data into an Open Linked Data Platform for Drug Discovery

scientific article (publication date: 2013)

Increasing the nanopublication recall with a BridgeDb identifier mapping service ⬇️

Integration among databases and data sets to support productive nanotechnology: challenges and recommendations ⬇️

journal article published in 2018

Interactive predictive toxicology with Bioclipse and OpenTox ⬇️

Interpreting the lipidome: bioinformatic approaches to embrace the complexity

scientific article published on 06 June 2021

Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials

scientific article published on 21 December 2018

Introducing WikiPathways to link molecular pathways to adverse outcome pathways to support regulatory risk assessment

scientific article

Introduction to Pharmaceutical Bioinformatics

Third edition of the book originally published in 2010

Investigating the Molecular Processes behind the Cell-Specific Toxicity Response to Titanium Dioxide Nanobelts

scientific article

JChemPaint - Using the Collaborative Forces of the Internet to Develop a Free Editor for 2D Chemical Structures

scientific article

Journal of Cheminform in 2020 (a personal perspective)

Journal of Cheminformatics, ORCID, and GitHub ⬇️

article in the Journal of Cheminformatics, 8 July 2019

Knowledge graphs and wikidata subsetting

scholarly article by José Emilio Labra Gayo published in April 2021

Learning cheminformatics

Linked open drug data for pharmaceutical research and development

scientific article

Linking Open Drug Data to Cheminformatics and Proteochemometrics ⬇️

conference paper

Linking Wikidata to the Rest of the Semantic Web ⬇️

scientific article (publication date: 19 February 2017)

Linking the Resource Description Framework to cheminformatics and proteochemometrics ⬇️

scientific article

MECP2 variation in Rett syndrome - an overview of current coverage of genetic and phenotype data within existing databases

scholarly article from 2018

Metadata handling for BioHackathon publications through BioHackrXiv

Method for the computational comparison of crystal structures ⬇️

scientific article (publication date: 19 January 2005)

Molecular Chemometrics

scientific article

NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment

scientific article published on 07 March 2020

Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data ⬇️

article published in 2018

Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data

Nanosafety data made interoperable using semantic modeling and linked-data knowledge graphs ⬇️

conference paper

New developments on the cheminformatics open workflow environment CDK-Taverna

scientific article

OSCAR4: a flexible architecture for chemical text-mining

scientific article

On the Use of 1H and 13C 1D NMR Spectra as QSPR Descriptors

scientific article (publication date: March 2006)

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

scientific article published in 2011

Open PHACTS: semantic interoperability for drug discovery ⬇️

scientific article (publication date: November 2012)

Open Science Feedback on the Guidance on the Implementation of Plan S

Open Source Drug Discovery with Bioclipse

scientific article published in 2013

Open science in an open access world

Open source drug discovery with Bioclipse ⬇️

scientific article from 2012

OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration and in silico analysis and modelling in risk assessment

PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity

scientific article published on 2 March 2023

PSnpBind: a database of mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow

scientific article from 2022

Probabilistic toxicogenomics studies in vitro

Processing CML conventions in Java ⬇️

peer-reviewed article

Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content

scientific article

Providing gene-to-variant and variant-to-gene database identifier mappings to use with BridgeDb mapping services

PubChemRDF: towards the semantic annotation of PubChem compound and substance databases ⬇️

Article in the Journal of Cheminformatics.

RDFIO: extending Semantic MediaWiki for interoperable biomedical data management

scientific article

RRegrs: an R package for computer-aided model selection with multiple regression models

scientific article (publication date: 2015)

Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics ⬇️

scientific article

Reliable Granular References to Changing Linked Data

conference proceedings article

Rendering co-author graphs using linked-open-data from Wikidata

Reply to “FAIR chemical structure in the Journal of Cheminformatics”

Representation of Molecules and Molecular Systems in Data Analysis and Modeling ⬇️

PhD thesis

Research Output Management

Resource description framework technologies in chemistry ⬇️

scientific article (publication date: 2011)

Risk Governance of Emerging Technologies Demonstrated in Terms of its Applicability to Nanomaterials

scientific article published on 23 July 2020

Robustifying Scholia: paving the way for knowledge discovery and research assessment through Wikidata ⬇️

proposal for 2019-20 research published in RIO Journal

SARS-CoV-2-Queries

Wikidata-based dashboard for tracking clinical and scholarly data about the SARS-CoV-2 virus and pandemic

SKG4EOSC - Scholarly Knowledge Graphs for EOSC: Establishing a backbone of knowledge graphs for FAIR Scholarly Information in EOSC

scientific article

SPLASH, a hashed identifier for mass spectra ⬇️

scientific article

Scholia - March 2017

software package

Scholia and scientometrics with Wikidata ⬇️

scientific article (publication date: 13 March 2017)

Scholia, Scientometrics and Wikidata ⬇️

scientific article published on October 2017

Scientific Lenses to Support Multiple Views over Linked Chemistry Data ⬇️

scientific article

Sharing dose response data and analysis across the SEURAT-1 cluster

Summary of the Spring 2014 NSC Database Survey

report from 2014

Supervised Self-Organizing Maps in Crystal Property and Structure Prediction

scientific article (publication date: September 2007)

Taking FAIR on the ChIN: The Chemistry Implementation Network

scholarly article by Simon J. Coles et al published 31 January 2020 in Data Intelligence

Ten simple rules for creating reusable pathway models for computational analysis and visualization

scientific article published on 19 August 2021

The AOP-DB RDF: Applying FAIR Principles to the Semantic Integration of AOP Data Using the Research Description Framework

publication published on 14 February 2022

The Blue Obelisk-interoperability in chemical informatics

peer-reviewed research article

The ChEMBL database as linked open data

scientific article (publication date: 2013)

The Chemical Information Ontology: provenance and disambiguation for chemical data on the biological semantic web

scientific article

The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reports

peer-reviewed article

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

scientific article

The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics.

abstract about a scientific article published in 2003

The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics

scientific article from 2003

The Chemistry Development Kit in 2024: improving cheminformatics research

scientific article published in 2024

The EU NanoSafety Cluster as Linked Data visualized with Scholia

newsletter article

The FAIR Cookbook - the essential resource for and by FAIR doers

scientific article published on 19 May 2023

The LOTUS Initiative for Open Natural Products Research: Knowledge Management through Wikidata

scholarly article (preprint) by Adriano Rutz published in March 2021

The LOTUS initiative for open knowledge management in natural products research ⬇️

scholarly article by Adriano Rutz et al. published in May 2022

The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

scientific article published on 21 October 2022

The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing

scientific article (publication date: 2013)

The Virtual Human Platform for Safety Assessment (VHP4Safety) project: Next generation chemical safety assessment based on human data

scientific article published in January 2024

The eNanoMapper database for nanomaterial safety information

The eNanoMapper database for nanomaterial safety information

scientific article

The first eNanoMapper prototype: A substance database to support safe-by-design ⬇️

scientific article (publication date: November 2014)

The future of metabolomics in ELIXIR

scientific article published in 2017

The future of metabolomics in ELIXIR.

scientific article

The metaRbolomics Toolbox in Bioconductor and beyond

scientific article published on 23 September 2019

The role of FAIR nanosafety data and nanoinformatics in achieving the UN sustainable development goals: the NanoCommons experience

scientific article published in 2024

The use of the Citation Typing Ontology in BioHackrXiv preprints

Three-Dimensional (3D) Molecular Representations

Three-Dimensional (3D) Molecular Representations

Toward the Replacement of Animal Experiments through the Bioinformatics-driven Analysis of 'Omics' Data from Human Cell Cultures

scientific article from 2015

Towards interoperable and reproducible QSAR analyses: Exchange of datasets

scientific article (publication date: 2010)

Two real use cases of FAIR maturity indicators in the life sciences

scientific article published on 19 August 2019

Two years of explicit CiTO annotations ⬇️

scientific article published in 2023

Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions

scientific article published on 18 April 2022

Unifying the Identification of Biomedical Entities with the Bioregistry ⬇️

preprint published on 10 July 2022

Unifying the identification of biomedical entities with the Bioregistry ⬇️

scientific article published on 19 November 2022

Userscripts for the life sciences

scientific article

Using the RRegrs R package for automating predictive modelling ⬇️

scientific article

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

scientific article

Utilizing the semantic web for kinetic modeling of metabolic disease pathways

conference poster

VLEERMUIS

article in a Dutch computer journal with source code about a bat

What is the role of cheminformatics in a pandemic?

scientific article published on 02 March 2021

WikiCite and Scholia - a Linked Open Data approach to exploring the scholarly literature and related resources ⬇️

scholarly poster

WikiPathways 2024: next generation pathway database

scientific article published on 6 November 2023

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

scientific article published on 10 November 2017

WikiPathways: capturing the full diversity of pathway knowledge

Research paper from 2016 about the WikiPathways database.

WikiPathways: connecting communities ⬇️

scientific article published on 19 November 2020

Wikidata Queries around the SARS-CoV-2 virus and pandemic ⬇️

online book

Wikidata and Scholia as a hub linking chemical knowledge ⬇️

poster presented at 11th International Conference on Chemical Structures

Wikidata as a FAIR knowledge graph for the life sciences

scholarly article posted as a preprint in BioRxiv on 11 February 2020

Wikidata as a knowledge graph for the life sciences ⬇️

scientific article published on 17 March 2020

Wikidata subsetting: Approaches, tools, and evaluation

Wikidata: empowering metabolomics research ⬇️

scientific abstract from May 2022

Wikipedia on the CompTox Chemicals Dashboard: Connecting Resources to Enrich Public Chemical Data

scientific article published on 10 October 2022

XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services

scientific article

XMetDB: an open access database for xenobiotic metabolism

scientific article

eNanoMapper – A database and ontology framework for design and safety assessment of nanomaterials

eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment

scientific article

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