The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics. - Christoph Steinbeck; Yongquan Han; Stefan Kuhn 001; Oliver Horlacher; Edgar Luttmann; Egon L. Willighagen (J. Chem. Inf. Comput. Sci., 2003)

Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators. - Peter Murray-Rust; Henry S. Rzepa; Mark J. Williamson; Egon L. Willighagen (J. Chem. Inf. Model., 2004)

The Blue Obelisk-Interoperability in Chemical Informatics. - Rajarshi Guha; Michael T. Howard; Geoffrey R. Hutchison; Peter Murray-Rust; Henry S. Rzepa; Christoph Steinbeck; Jörg K. Wegner; Egon L. Willighagen (J. Chem. Inf. Model., 2006)

On the Use of 1H and 13C 1D NMR Spectra as QSPR Descriptors. - Egon L. Willighagen; H. M. G. W. Denissen; Ron Wehrens; Lutgarde M. C. Buydens (J. Chem. Inf. Model., 2006)

Bioclipse: an open source workbench for chemo- and bioinformatics. - Ola Spjuth; Tobias Helmus; Egon L. Willighagen; Stefan Kuhn 001; Martin Eklund; Johannes Wagener; Peter Murray-Rust; Christoph Steinbeck; Jarl E. S. Wikberg (BMC Bioinform., 2007)

Userscripts for the Life Sciences. - Egon L. Willighagen; Noel M. O'Boyle; Harini Gopalakrishnan; Dazhi Jiao; Rajarshi Guha; Christoph Steinbeck; David J. Wild 001 (BMC Bioinform., 2007)

Chemical Markup, XML, and the World Wide Web, 7. CMLSpect, an XML Vocabulary for Spectral Data. - Stefan Kuhn 001; Tobias Helmus; Robert J. Lancashire; Peter Murray-Rust; Henry S. Rzepa; Christoph Steinbeck; Egon L. Willighagen (J. Chem. Inf. Model., 2007)

Linking Open Drug Data to Cheminformatics and Proteochemometrics. - Egon L. Willighagen; Jarl E. S. Wikberg (SWAT4LS, 2009)

Bioclipse 2: A scriptable integration platform for the life sciences. - Ola Spjuth; Jonathan Alvarsson; Arvid Berg; Martin Eklund; Stefan Kuhn 001; Carl Mäsak; Gilleain M. Torrance; Johannes Wagener; Egon L. Willighagen; Christoph Steinbeck; Jarl E. S. Wikberg (BMC Bioinform., 2009)

XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services. - Johannes Wagener; Ola Spjuth; Egon L. Willighagen; Jarl E. S. Wikberg (BMC Bioinform., 2009)

The Chemical Translation Service - a web-based tool to improve standardization of metabolomic reports. - Gert Wohlgemuth; Pradeep Kumar Haldiya; Egon L. Willighagen; Tobias Kind; Oliver Fiehn (Bioinform., 2010)

CDK-Taverna: an open workflow environment for cheminformatics. - Thomas Kuhn; Egon L. Willighagen; Achim Zielesny; Christoph Steinbeck (BMC Bioinform., 2010)

Towards interoperable and reproducible QSAR analyses: Exchange of datasets. - Ola Spjuth; Egon L. Willighagen; Rajarshi Guha; Martin Eklund; Jarl E. S. Wikberg (J. Cheminformatics, 2010)

Elemental composition determination based on MSn. - Miguel Rojas-Chertó; Piotr T. Kasper; Egon L. Willighagen; Rob J. Vreeken; Thomas Hankemeier; Theo H. Reijmers (Bioinform., 2011)

Linking the Resource Description Framework to cheminformatics and proteochemometrics. - Egon L. Willighagen; Jonathan Alvarsson; Annsofie Andersson; Martin Eklund; Samuel Lampa; Maris Lapins; Ola Spjuth; Jarl E. S. Wikberg (J. Biomed. Semant., 2011)

OSCAR4: a flexible architecture for chemical text-mining. - David M. Jessop; Sam E. Adams; Egon L. Willighagen; Lezan Hawizy; Peter Murray-Rust (J. Cheminformatics, 2011)

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on. - Noel M. O'Boyle; Rajarshi Guha; Egon L. Willighagen; Sam E. Adams; Jonathan Alvarsson; Jean-Claude Bradley; Igor V. Filippov; Robert M. Hanson; Marcus D. Hanwell; Geoffrey R. Hutchison; Craig A. James; Nina Jeliazkova; et al. (J. Cheminformatics, 2011)

Linked open drug data for pharmaceutical research and development. - Matthias Samwald; Anja Jentzsch; Christopher Bouton; Claus Kallesøe; Egon L. Willighagen; Janos G. Hajagos; M. Scott Marshall; Eric Prud'hommeaux; Oktie Hassanzadeh; Elgar Pichler; Susie Stephens (J. Cheminformatics, 2011)

New developments on the cheminformatics open workflow environment CDK-Taverna. - Andreas Truszkowski; Kalai Vanii Jayaseelan; Stefan Neumann 001; Egon L. Willighagen; Achim Zielesny; Christoph Steinbeck (J. Cheminformatics, 2011)

CDK-Taverna 2.0: migration and enhancements of an open-source pipelining solution. - Andreas Truszkowski; Stefan Neumann 001; Achim Zielesny; Egon L. Willighagen; Christoph Steinbeck (J. Cheminformatics, 2011)

Resource description framework technologies in chemistry. - Egon L. Willighagen; Martin P. Brändle (J. Cheminformatics, 2011)

Scientific Lenses over Linked Data: An Approach to Support Task Specific Views of the Data. A Vision. - Christian Y. A. Brenninkmeijer; Chris T. A. Evelo; Carole A. Goble; Alasdair J. G. Gray; Paul Groth; Steve Pettifer; Robert Stevens 001; Antony J. Williams; Egon L. Willighagen (LISC@ISWC, 2012)

Cheminformatics. - Jörg K. Wegner; Aaron D. Sterling; Rajarshi Guha; Andreas Bender 002; Jean-Loup Faulon; Janna Hastings; Noel M. O'Boyle; John P. Overington; Herman van Vlijmen; Egon L. Willighagen (Commun. ACM, 2012)

Changing computational research. The challenges ahead. - Cameron Neylon; Jan Aerts; C. Titus Brown; Simon J. Coles; Les Hatton; Daniel Lemire; K. Jarrod Millman; Peter Murray-Rust; Fernando Pérez; Neil F. W. Saunders; Nigam Shah; Arfon M. Smith; et al. (Source Code Biol. Medicine, 2012)

Emerging practices for mapping and linking life sciences data using RDF - A case series. - M. Scott Marshall; Richard D. Boyce; Helena F. Deus; Jun Zhao 003; Egon L. Willighagen; Matthias Samwald; Elgar Pichler; Janos G. Hajagos; Eric Prud'hommeaux; Susie Stephens (J. Web Semant., 2012)

Incorporating Commercial and Private Data into an Open Linked Data Platform for Drug Discovery. - Carole A. Goble; Alasdair J. G. Gray; Lee Harland; Karen Karapetyan; Antonis Loizou; Ivan Mikhailov; Yrjänä Rankka; Stefan Senger; Valery Tkachenko; Antony J. Williams; Egon L. Willighagen (ISWC (2), 2013)

Bioclipse-R: integrating management and visualization of life science data with statistical analysis. - Ola Spjuth; Valentin Georgiev; Lars Carlsson; Jonathan Alvarsson; Arvid Berg; Egon L. Willighagen; Jarl E. S. Wikberg; Martin Eklund (Bioinform., 2013)

Applications of the InChI in cheminformatics with the CDK and Bioclipse. - Ola Spjuth; Arvid Berg; Samuel E. Adams; Egon L. Willighagen (J. Cheminformatics, 2013)

The ChEMBL database as linked open data. - Egon L. Willighagen; Andra Waagmeester; Ola Spjuth; Peter Ansell; Antony J. Williams; Valery Tkachenko; Janna Hastings; Bin Chen 002; David J. Wild 001 (J. Cheminformatics, 2013)

The first eNanoMapper prototype: A substance database to support safe-by-design. - Nina Jeliazkova; Philip Doganis; Bengt Fadeel; Roland Grafstrom; Janna Hastings; Vedrin Jeliazkov; Pekka Kohonen; Cristian R. Munteanu; Haralambos Sarimveis; Bart Smeets; Georgia Tsiliki; David Vorgrimmler; et al. (BIBM, 2014)

Scientific Lenses to Support Multiple Views over Linked Chemistry Data. - Colin R. Batchelor; Christian Y. A. Brenninkmeijer; Christine Chichester; Mark Davies; Daniela Digles; Ian Dunlop; Chris T. A. Evelo; Anna Gaulton; Carole A. Goble; Alasdair J. G. Gray; Paul Groth; Lee Harland; et al. (ISWC (1), 2014)

eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment. - Janna Hastings; Nina Jeliazkova; Gareth I. Owen; Georgia Tsiliki; Cristian R. Munteanu; Christoph Steinbeck; Egon L. Willighagen (J. Biomed. Semant., 2015)

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment. - Anwesha Bohler; Lars M. T. Eijssen; Martijn P. van Iersel; Christ Leemans; Egon L. Willighagen; Martina Kutmon; Magali Jaillard; Chris T. A. Evelo (BMC Bioinform., 2015)

PubChemRDF: towards the semantic annotation of PubChem compound and substance databases. - Gang Fu; Colin R. Batchelor; Michel Dumontier; Janna Hastings; Egon L. Willighagen; Evan Bolton (J. Cheminformatics, 2015)

RRegrs: an R package for computer-aided model selection with multiple regression models. - Georgia Tsiliki; Cristian R. Munteanu; José A. Seoane; Carlos Fernandez-Lozano; Haralambos Sarimveis; Egon L. Willighagen (J. Cheminformatics, 2015)

Finding Drugs with Common Downstream Effects, Using Direction Information in Biological Pathways. - Ryan A. Miller; Jonathan Mélius; Nuno Nunes 002; Egon L. Willighagen; Peter Woollard; Chris T. A. Evelo (SWAT4LS, 2016)

Linking Wikidata to the Rest of the Semantic Web. - Andra Waagmeester; Egon L. Willighagen; Núria Queralt Rosinach; Elvira Mitraka; Sebastian Burgstaller-Muehlbacher; Tim E. Putman; Julia Turner; Lynn M. Schriml; Paul Pavlidis; Andrew I. Su; Benjamin M. Good (SWAT4LS, 2016)

Answering Scientific Questions with linked European Nanosafety Data. - Egon L. Willighagen; Micha Rautenberg; Denis Gebele; Linda Rieswijk; Friederike Ehrhart; Jiakang Chang; Georgios Drakakis; Penny Nymark; Pekka Kohonen; Gareth I. Owen; Haralambos Sarimveis; Christoph Helma; et al. (SWAT4LS, 2016)

XMetDB: an open access database for xenobiotic metabolism. - Ola Spjuth; Patrik Rydberg; Egon L. Willighagen; Chris T. A. Evelo; Nina Jeliazkova (J. Cheminformatics, 2016)

WikiPathways: capturing the full diversity of pathway knowledge. - Martina Kutmon; Anders Riutta; Nuno Nunes 002; Kristina Hanspers; Egon L. Willighagen; Anwesha Bohler; Jonathan Mélius; Andra Waagmeester; Sravanthi R. Sinha; Ryan A. Miller; Susan L. Coort; Elisa Cirillo; et al. (Nucleic Acids Res., 2016)

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. - Andra Waagmeester; Martina Kutmon; Anders Riutta; Ryan A. Miller; Egon L. Willighagen; Chris T. A. Evelo; Alexander R. Pico (PLoS Comput. Biol., 2016)

Scholia, Scientometrics and Wikidata. - Finn Årup Nielsen; Daniel Mietchen; Egon L. Willighagen (ESWC (Satellite Events), 2017)

Reliable Granular References to Changing Linked Data. - Tobias Kuhn; Egon L. Willighagen; Chris T. A. Evelo; Núria Queralt-Rosinach; Emilio Centeno; Laura I. Furlong (ISWC (1), 2017)

Visualizing Metabolomics Data in Directed Biological Networks. - Ryan A. Miller; Denise N. Slenter; Martina Kutmon; Jonathan Mélius; Georg Summer; Chris T. A. Evelo; Egon L. Willighagen (SWAT4LS, 2017)

RDFIO: extending Semantic MediaWiki for interoperable biomedical data management. - Samuel Lampa; Egon L. Willighagen; Pekka Kohonen; Ali King; Denny Vrandecic; Roland Grafstrom; Ola Spjuth (J. Biomed. Semant., 2017)

Scholia and scientometrics with Wikidata. - Finn Årup Nielsen; Daniel Mietchen; Egon L. Willighagen (CoRR, 2017)

The future of metabolomics in ELIXIR. - Merlijn N. van Rijswijk; Charlie Beirnaert; Christophe Caron; Marta Cascante; Victoria Dominguez Del Angel; Warwick B. Dunn; Timothy M. D. Ebbels; Franck Giacomoni; Alejandra N. González-Beltrán; Thomas Hankemeier; Kenneth Haug; Jose L. Izquierdo-García; et al. (F1000Research, 2017)

Helping to improve the practice of cheminformatics. - Rajarshi Guha; Egon L. Willighagen (J. Cheminformatics, 2017)

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. - Egon L. Willighagen; John W. Mayfield; Jonathan Alvarsson; Arvid Berg; Lars Carlsson; Nina Jeliazkova; Stefan Kuhn 001; Tomás Pluskal; Miquel Rojas-Chertó; Ola Spjuth; Gilleain M. Torrance; Chris T. A. Evelo; et al. (J. Cheminformatics, 2017)

Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. - Egon L. Willighagen; John W. Mayfield; Jonathan Alvarsson; Arvid Berg; Lars Carlsson; Nina Jeliazkova; Stefan Kuhn 001; Tomás Pluskal; Miquel Rojas-Chertó; Ola Spjuth; Gilleain M. Torrance; Chris T. A. Evelo; et al. (J. Cheminformatics, 2017)

Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data. - Tobias Kuhn; Albert Meroño-Peñuela; Alexander Malic; Jorrit H. Poelen; Allen H. Hurlbert; Emilio Centeno Ortiz; Laura I. Furlong; Núria Queralt-Rosinach; Christine Chichester; Juan M. Banda; Egon L. Willighagen; Friederike Ehrhart; et al. (eScience, 2018)

Geospatial data and Scholia. - Finn Årup Nielsen; Daniel Mietchen; Egon L. Willighagen (GeoLD-QuWeDa@ESWC, 2018)

Increasing the nanopublication recall with a BridgeDb identifier mapping service. - Egon L. Willighagen (SWAT4LS, 2018)

Providing gene-to-variant and variant-to-gene database identifier mappings to use with BridgeDb mapping services. - Friederike Ehrhart; Jonathan Mélius; Elisa Cirillo; Martina Kutmon; Egon L. Willighagen; Susan L. Coort; Leopold M. G. Curfs; Chris T. A. Evelo (F1000Research, 2018)

CyTargetLinker app update: A flexible solution for network extension in Cytoscape. - Martina Kutmon; Friederike Ehrhart; Egon L. Willighagen; Chris T. A. Evelo; Susan L. Coort (F1000Research, 2018)

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. - Denise N. Slenter; Martina Kutmon; Kristina Hanspers; Anders Riutta; Jacob Windsor; Nuno Nunes 002; Jonathan Mélius; Elisa Cirillo; Susan L. Coort; Daniela Digles; Friederike Ehrhart; Pieter Giesbertz; et al. (Nucleic Acids Res., 2018)

Journal of Cheminformatics, ORCID, and GitHub. - Egon L. Willighagen; Nina Jeliazkova; Rajarshi Guha (J. Cheminformatics, 2019)

Expanding the eNanoMapper Ontology (short paper). - Laurent A. Winckers; Egon L. Willighagen (ICBO/ODLS, 2020)

Taking FAIR on the ChIN: The Chemistry Implementation Network. - Simon J. Coles; Jeremy G. Frey; Egon L. Willighagen; Stuart J. Chalk (Data Intell., 2020)

FAIR Principles: Interpretations and Implementation Considerations. - Annika Jacobsen; Ricardo de Miranda Azevedo; Nick S. Juty; Dominique Batista; Simon J. Coles; Ronald Cornet; Mélanie Courtot; Mercè Crosas; Michel Dumontier; Chris T. A. Evelo; Carole A. Goble; Giancarlo Guizzardi; et al. (Data Intell., 2020)

Learning cheminformatics. - Rajarshi Guha; Egon L. Willighagen (J. Cheminformatics, 2020)

Adoption of the Citation Typing Ontology by the Journal of Cheminformatics. - Egon L. Willighagen (J. Cheminformatics, 2020)

Reply to "FAIR chemical structure in the Journal of Cheminformatics". - Rajarshi Guha; Nina Jeliazkova; Egon L. Willighagen; Barbara Zdrazil (J. Cheminformatics, 2021)

What is the role of cheminformatics in a pandemic? - Rajarshi Guha; Egon L. Willighagen; Barbara Zdrazil; Nina Jeliazkova (J. Cheminformatics, 2021)

Bacting: a next generation, command line version of Bioclipse. - Egon L. Willighagen (J. Open Source Softw., 2021)

WikiPathways: connecting communities. - Marvin Martens; Ammar Ammar; Anders Riutta; Andra Waagmeester; Denise N. Slenter; Kristina Hanspers; Ryan A. Miller; Daniela Digles; Elisson N. Lopes; Friederike Ehrhart; Lauren J. Dupuis; Laurent A. Winckers; et al. (Nucleic Acids Res., 2021)

Ten simple rules for creating reusable pathway models for computational analysis and visualization. - Kristina Hanspers; Martina Kutmon; Susan L. Coort; Daniela Digles; Lauren J. Dupuis; Friederike Ehrhart; Finterly Hu; Elisson N. Lopes; Marvin Martens; Nhung Pham; Woosub Shin; Denise N. Slenter; et al. (PLoS Comput. Biol., 2021)

PSnpBind: a database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow. - Ammar Ammar; Rachel Cavill; Chris T. A. Evelo; Egon L. Willighagen (J. Cheminformatics, 2022)

European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials. - Jeaphianne P. M. van Rijn; Antreas Afantitis; Mustafa Culha; Maria Dusinska; Thomas E. Exner; Nina Jeliazkova; Eleonora Marta Longhin; Iseult Lynch; Georgia Melagraki; Penny Nymark; Anastasios G. Papadiamantis; David A. Winkler; et al. (J. Cheminformatics, 2022)

CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community. - Andrea Jacobs; Dustin Williams; Katherine Hickey; Nathan Patrick; Antony J. Williams; Stuart J. Chalk; Leah McEwen; Egon L. Willighagen; Martin Walker; Evan Bolton; Gabriel Sinclair; Adam Sanford (J. Chem. Inf. Model., 2022)

Wikipedia on the CompTox Chemicals Dashboard: Connecting Resources to Enrich Public Chemical Data. - Gabriel Sinclair; Inthirany Thillainadarajah; Brian Meyer; Vicente Samano; Sakuntala Sivasupramaniam; Linda Adams; Egon L. Willighagen; Ann M. Richard; Martin Walker; Antony J. Williams (J. Chem. Inf. Model., 2022)

Complex Portal 2022: new curation frontiers. - Birgit H. M. Meldal; Livia Perfetto; Colin W. Combe; Tiago Lubiana; João Vitor Ferreira Cavalcante; Hema Bye-A-Jee; Andra Waagmeester; Noemi del-Toro; Anjali Shrivastava; Elisabet Barrera; Edith D. Wong; Bernhard Mlecnik; et al. (Nucleic Acids Res., 2022)

PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity. - Ammar Ammar; Rachel Cavill; Chris T. A. Evelo; Egon L. Willighagen (J. Cheminformatics, 2023)

Two years of explicit CiTO annotations. - Egon L. Willighagen (J. Cheminformatics, 2023)

BioDataFuse: Enhancing data interoperability through modular queries and knowledge graph construction. - Tooba Abbassi-Daloii; Yojana Gadiya; Ammar Ammar; Egon L. Willighagen; Ana Claudia Sima; Hasan Balci (SWAT4HCLS, 2024)

Nanosafety data made interoperable using semantic modeling and linked-data knowledge graphs. - Ammar Ammar; Egon L. Willighagen (SWAT4HCLS, 2024)

Building Expertise on FAIR Through Evolving Bring Your Own Data (BYOD) Workshops: Describing the Data, Software, and Management-focused Approaches and Their Evolution. - César Henrique Bernabé; Lieze Thielemans; Rajaram Kaliyaperumal; Claudio Carta; Shuxin Zhang; Celia W. G. van Gelder; Nirupama Benis; Luiz Olavo Bonino da Silva Santos; Ronald Cornet; Bruna dos Santos Vieira; Nawel Lalout; Inês Henriques; et al. (Data Intell., 2024)

From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials. - Jeaphianne P. M. van Rijn; Marvin Martens; Ammar Ammar; Mihaela Roxana Cimpan; Valerie Fessard; Peter Hoet; Nina Jeliazkova; Sivakumar Murugadoss; Ivana Vinkovic Vrcek; Egon L. Willighagen (J. Cheminformatics, 2024)