Interactive Workflows in a Virtual Laboratory for e-Bioscience: The SigWin-Detector Tool for Gene Expression Analysis. - Márcia A. Inda; Adam Belloum; Marco Roos; Dmitry Vasunin; Cees T. A. M. de Laat; Louis O. Hertzberger; Timo M. Breit (e-Science, 2006)

Using Semantic Web Tools to Integrate Experimental Measurement Data on Our Own Terms. - M. Scott Marshall; Lennart J. G. Post; Marco Roos; Timo M. Breit (OTM Workshops (1), 2006)

A Survey of Requirements for Automated Reasoning Services for Bio-Ontolgies in OWL. - C. Maria Keet; Marco Roos; M. Scott Marshall (OWLED, 2007)

A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data. - Lennart J. G. Post; Marco Roos; M. Scott Marshall; Roel van Driel; Timo M. Breit (Bioinform., 2007)

Taking the example of computer systems engineering for the analysis of biological cell systems. - Tessa E. Pronk; Andy D. Pimentel; Marco Roos; Timo M. Breit (Biosyst., 2007)

VLAM-G: Interactive data driven workflow engine for Grid-enabled resources. - Vladimir Korkhov; Dmitry Vasyunin; Adianto Wibisono; Adam Belloum; Márcia A. Inda; Marco Roos; Timo M. Breit; Louis O. Hertzberger (Sci. Program., 2007)

Data Lineage Model for Taverna Workflows with Lightweight Annotation Requirements. - Paolo Missier; Khalid Belhajjame; Jun Zhao 003; Marco Roos; Carole A. Goble (IPAW, 2008)

Structuring Mined Knowledge for the Support of Hypothesis Generation in Molecular Biology. - Marco Roos; M. Scott Marshall; Andrew P. Gibson; Pieter W. Adriaans (SWAT4LS, 2008)

New interactions with workflow systems. - Ingo H. C. Wassink; Paul E. van der Vet; Elisabeth M. A. G. van Dijk; Gerrit C. van der Veer; Marco Roos (ECCE, 2009)

Analysing Scientific Workflows: Why Workflows Not Only Connect Web Services. - Ingo H. C. Wassink; Paul E. van der Vet; Katy Wolstencroft; Pieter B. T. Neerincx; Marco Roos; Han Rauwerda; Timo M. Breit (SERVICES I, 2009)

Structuring and extracting knowledge for the support of hypothesis generation in molecular biology. - Marco Roos; M. Scott Marshall; Andrew P. Gibson; Martijn J. Schuemie; Edgar Meij; Sophia Katrenko; Willem Robert van Hage; Konstantinos Krommydas; Pieter W. Adriaans (BMC Bioinform., 2009)

The Evolution of myExperiment. - David De Roure; Carole A. Goble; Sergejs Aleksejevs; Sean Bechhofer; Jiten Bhagat; Don Cruickshank; Paul Fisher; Nandkumar Kollara; Danius T. Michaelides; Paolo Missier; David R. Newman; Marcus Ramsden; et al. (eScience, 2010)

A Linked Data Approach to Sharing Workflows and Workflow Results. - Marco Roos; Sean Bechhofer; Jun Zhao 003; Paolo Missier; David R. Newman; David De Roure; M. Scott Marshall (ISoLA (1), 2010)

The AIDA Toolkit - a Tool for Users and Developers. - Adianto Wibisono; Marco Roos; M. Scott Marshall (SWAT4LS, 2010)

BioCatalogue: a universal catalogue of web services for the life sciences. - Jiten Bhagat; Franck Tanoh; Eric Nzuobontane; Thomas Laurent 002; Jerzy Orlowski; Marco Roos; Katy Wolstencroft; Sergejs Aleksejevs; Robert Stevens 001; Steve Pettifer; Rodrigo Lopez; Carole A. Goble (Nucleic Acids Res., 2010)

myExperiment: a repository and social network for the sharing of bioinformatics workflows. - Carole A. Goble; Jiten Bhagat; Sergejs Aleksejevs; Don Cruickshank; Danius T. Michaelides; David R. Newman; Mark Borkum; Sean Bechhofer; Marco Roos; Peter Li; David De Roure (Nucleic Acids Res., 2010)

Semantic Disclosure in an e-Science Environment. - M. Scott Marshall; Marco Roos; Edgar Meij; Sophia Katrenko; Willem Robert van Hage; Pieter W. Adriaans (Semantic e-Science, 2010)

Towards the Preservation of Scientific Workflows. - David De Roure; Carole A. Goble; Graham Klyne; Marco Roos; Kristina M. Hettne; José Enrique Ruiz; Raúl Palma; José Manuél Gómez-Pérez; Paolo Missier; Khalid Belhajjame (iPRES, 2011)

Workflow forever: semantic web semantic models and tools for preserving and digitally publishing computational experiments. - Kristina M. Hettne; Stian Soiland-Reyes; Graham Klyne; Khalid Belhajjame; Matthew Gamble; Sean Bechhofer; Marco Roos; Óscar Corcho (SWAT4LS, 2011)

Why workflows break - Understanding and combating decay in Taverna workflows. - Jun Zhao 003; José Manuél Gómez-Pérez; Khalid Belhajjame; Graham Klyne; Esteban García-Cuesta; Aleix Garrido; Kristina M. Hettne; Marco Roos; David De Roure; Carole A. Goble (eScience, 2012)

Workflow-Centric Research Objects: A First Class Citizen in the Scholarly Discourse. - Khalid Belhajjame; Óscar Corcho; Daniel Garijo; Jun Zhao 003; Paolo Missier; David R. Newman; Raúl Palma; Sean Bechhofer; Esteban García-Cuesta; José Manuél Gómez-Pérez; Graham Klyne; Kevin R. Page; et al. (SePublica@ESWC, 2012)

Opening new gateways to workflows for life scientists. - Konstantinos Karasavvas; Katy Wolstencroft; Eleni Mina; Don Cruickshank; Alan R. Williams; David De Roure; Carole A. Goble; Marco Roos (HealthGrid, 2012)

RO-Manager: A Tool for Creating and Manipulating Research Objects to Support Reproducibility and Reuse in Sciences. - Jun Zhao 003; Graham Klyne; Piotr Holubowicz; Raúl Palma; Stian Soiland-Reyes; Kristina M. Hettne; José Enrique Ruiz; Marco Roos; Kevin R. Page; José Manuél Gómez-Pérez; David De Roure; Carole A. Goble (LISC@ISWC, 2012)

Towards Computational Evaluation of Evidence for Scientific Assertions with Nanopublications. - Andrew P. Gibson; Jesse C. J. van Dam; Erik A. Schultes; Marco Roos; Barend Mons (SWAT4LS, 2012)

Best Practices for Workflow Design: How to Prevent Workflow Decay. - Kristina M. Hettne; Katherine Wolstencroft; Khalid Belhajjame; Carole A. Goble; Eleni Mina; Harish Dharuri; David De Roure; Lourdes Verdes-Montenegro; Julián Garrido; Marco Roos (SWAT4LS, 2012)

Data Publishing Using Nanopublications. - Mark Thompson 002; Erik A. Schultes; Marco Roos; Barend Mons (Adv. Math. Commun., 2012)

Workflows and Services for Concept Profile Generation. - Eelke van der Horst; Marco Roos; Kristina M. Hettne (SWAT4LS, 2013)

Nanopublications for Exposing Experimental Data in the Life-sciences: A Huntington's Disease Case Study. - Eleni Mina; Mark Thompson 002; Rajaram Kaliyaperumal; Jun Zhao 003; Kristina M. Hettne; Erik A. Schultes; Marco Roos (SWAT4LS, 2013)

A Nanopublishing Architecture for Biomedical Data. - Pedro Sernadela; Eelke van der Horst; Mark Thompson 002; Pedro Lopes 002; Marco Roos; José Luís Oliveira (PACBB, 2014)

Genome Annotation using Nanopublications: An Approach to Interoperability of Genetic Data. - Rajaram Kaliyaperumal; Peter Bram 't Hoen; Mark Thompson 002; Eelke van der Horst; Marco Roos (SWAT4LS, 2014)

Bring Your Own Data Workshops: A Mechanism to Aid Data Owners to Comply with Linked Data Best Practices. - Marco Roos; Alasdair J. G. Gray; Andra Waagmeester; Mark Thompson 002; Rajaram Kaliyaperumal; Eelke van der Horst; Barend Mons; Mark D. Wilkinson (SWAT4LS, 2014)

Structuring research methods and data with the research object model: genomics workflows as a case study. - Kristina M. Hettne; Harish Dharuri; Jun Zhao 003; Katherine Wolstencroft; Khalid Belhajjame; Stian Soiland-Reyes; Eleni Mina; Mark Thompson 002; Don Cruickshank; Lourdes Verdes-Montenegro; Julián Garrido; David De Roure; et al. (J. Biomed. Semant., 2014)

Preserving sequence annotations across reference sequences. - Zuotian Tatum; Marco Roos; Andrew P. Gibson; Peter E. M. Taschner; Mark Thompson 002; Erik A. Schultes; Jeroen F. J. Laros (J. Biomed. Semant., 2014)

Explain your data by Concept Profile Analysis Web Services. - Kristina M. Hettne; Reinout van Schouwen; Eleni Mina; Eelke van der Horst; Mark Thompson 002; Rajaram Kaliyaperumal; Barend Mons; Erik M. van Mulligen; Jan A. Kors; Marco Roos (F1000Research, 2014)

Recent applications of web semantics in eLifeScience. - Tim Clark; Marco Roos (J. Web Semant., 2014)

Multidisciplinary Collaboration to Facilitate Hypotheses Generation in Huntington's Disease. - Eleni Mina; Mark Thompson 002; Kristina M. Hettne; Willeke M. C. van Roon-Mom; Rajaram Kaliyaperumal; Eelke van der Horst; Katherine Wolstencroft; Barend Mons; Marco Roos (e-Science, 2015)

Finding Novel Associations Across Domains Using Linked Data: a Case Study on Genetic Variants Disrupting Transcription Start Sites. - Eelke van der Horst; Rajaram Kaliyaperumal; Zuotian Tatum; Mark Thompson 002; Erik A. Schultes; Eleni Mina; Ivo Fokkema; Johan T. den Dunnen; Marco Roos; Jeroen F. J. Laros; Barend Mons; Kristina M. Hettne; et al. (SWAT4LS, 2015)

Nanopublications for exposing experimental data in the life-sciences: a Huntington's Disease case study. - Eleni Mina; Mark Thompson 002; Rajaram Kaliyaperumal; Jun Zhao 003; Eelke van der Horst; Zuotian Tatum; Kristina M. Hettne; Erik A. Schultes; Barend Mons; Marco Roos (J. Biomed. Semant., 2015)

The Organisation of Bring Your Own Data (BYOD) Workshops to Make Life Science Data Linkable at the Source. - Mascha Jansen; Claudio Carta; Marco Roos; Luiz Olavo Bonino da Silva Santos (SWAT4LS, 2016)

Registries of Domain-Relevant Semantic Reference Models Help Bootstrap Interoperability in Domains with Fragmented Data Resources. - Marco Roos; Mark D. Wilkinson; Rajaram Kaliyaperumal; Mark Thompson 002; Claudio Carta; Ronald Cornet; Luiz Olavo Bonino da Silva Santos (SWAT4LS, 2016)

The FAIRification of Data and the Potential of FAIR Resources Demonstrated, in Practice, at the Rome Bring Your Own Data Workshop. - Claudio Carta; Marco Roos; Annika Jacobsen; Rajaram Kaliyaperumal; Mark Thompson 002; Mark D. Wilkinson; Ronald Cornet; Andra Waagmeester; David van Enckevort; Mascha Jansen; Luana Licata; Allegra Via; et al. (SWAT4LS, 2017)

Semantic Knowledge Graph Network Features for Drug Repurposing. - Tareq B. Malas; Roman Kudrin; Sergei Starikov; Dorien Peters; Marco Roos; Peter A. C. 't Hoen; Kristina M. Hettne (SWAT4LS, 2017)

Overview of a Suite of Tools and Training Material for Implementing FAIR Data Principles. - Mark Thompson 002; Luiz Olavo Bonino da Silva Santos; Kees Burger; Rajaram Kaliyaperumal; Erik A. Schultes; Annika Jacobsen; Claudio Carta; Richard Finkers; David van Enckevort; Mascha Jansen; Barend Mons; Marco Roos (SWAT4LS, 2017)

OSSE Goes FAIR - Implementation of the FAIR Data Principles for an Open-Source Registry for Rare Diseases. - Jannik Schaaf; Dennis Kadioglu; Jens Goebel; Christian-Alexander Behrendt; Marco Roos; David van Enckevort; Frank Ückert; Fatlume Sadiku; Thomas O. F. Wagner; Holger Storf (GMDS, 2018)

Wikidata as an intuitive resource towards semantic data modeling in data FAIRification. - Annika Jacobsen; Andra Waagmeester; Rajaram Kaliyaperumal; Gregory S. Stupp; Lynn M. Schriml; Mark Thompson 002; Andrew I. Su; Marco Roos (SWAT4LS, 2018)

FAIR Data Management to Access Patient Data. - Núria Queralt Rosinach; Rajaram Kaliyaperumal; César Henrique Bernabé; Qinqin Long; Henk Jan van der Wijk; Barend Mons; Marco Roos (DaMaLOS, 2020)

Applying the FAIR Data Principles to the Registry of Vascular Anomalies (VASCA). - Bruna dos Santos Vieira; Karlijn H. J. Groenen; Peter A. C. 't Hoen; Annika Jacobsen; Marco Roos; Rajaram Kaliyaperumal; Martijn G. Kersloot; Ronald Cornet; Leo J. Schultze Kool (dHealth, 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)

A Generic Workflow for the Data FAIRification Process. - Annika Jacobsen; Rajaram Kaliyaperumal; Luiz Olavo Bonino da Silva Santos; Barend Mons; Erik Schultes; Marco Roos; Mark Thompson 002 (Data Intell., 2020)

The "A" of FAIR - As Open as Possible, as Closed as Necessary. - Annalisa Landi; Mark Thompson 002; Viviana Giannuzzi; Fedele Bonifazi; Ignasi Labastida; Luiz Olavo Bonino da Silva Santos; Marco Roos (Data Intell., 2020)

Making FAIR Easy with FAIR Tools: From Creolization to Convergence. - Mark Thompson 002; Kees Burger; Rajaram Kaliyaperumal; Marco Roos; Luiz Olavo Bonino da Silva Santos (Data Intell., 2020)

Enabling FAIR Discovery of Rare Disease Digital Resources. - Rajaram Kaliyaperumal; Núria Queralt Rosinach; Kees Burger; Luiz Olavo Bonino da Silva Santos; Marc Hanauer; Marco Roos (dHealth, 2021)

LUMC Clinical Ontology for Biomedical Research. - Núria Queralt-Rosinach; César Henrique Bernabé; Qinqin Long; Rajaram Kaliyaperumal; Marco Roos (ICBO, 2021)

Reuse of Design Pattern Measurements for Health Data. - Núria Queralt-Rosinach; Mark D. Wilkinson; Rajaram Kaliyaperumal; César Henrique Bernabé; Qinqin Long; Michel Dumontier; Paul N. Schofield; Marco Roos (JOWO, 2021)

De-novo FAIRification via an Electronic Data Capture system by automated transformation of filled electronic Case Report Forms into machine-readable data. - Martijn G. Kersloot; Annika Jacobsen; Karlijn H. J. Groenen; Bruna dos Santos Vieira; Rajaram Kaliyaperumal; Ameen Abu-Hanna; Ronald Cornet; Peter A. C. 't Hoen; Marco Roos; Leo J. Schultze Kool; Derk L. Arts (J. Biomed. Informatics, 2021)

The Use of Foundational Ontologies in Bioinformatics. - César Henrique Bernabé; Núria Queralt-Rosinach; Vítor E. Silva Souza; Luiz Olavo Bonino da Silva Santos; Annika Jacobsen; Barend Mons; Marco Roos (SWAT4HCLS, 2022)

Phenopackets for the Semantic Web. - Rajaram Kaliyaperumal; Gurnoor Singh; Núria Queralt-Rosinach; Jumamurat Bayjanov; Peter Bram 't Hoen; Marco Roos (SWAT4HCLS, 2022)

Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data. - Rajaram Kaliyaperumal; Mark D. Wilkinson; Pablo Alarcón Moreno; Nirupama Benis; Ronald Cornet; Bruna dos Santos Vieira; Michel Dumontier; César Henrique Bernabé; Annika Jacobsen; Clémence M. A. Le Cornec; Mario Prieto Godoy; Núria Queralt-Rosinach; et al. (J. Biomed. Semant., 2022)

Applying the FAIR principles to data in a hospital: challenges and opportunities in a pandemic. - Núria Queralt-Rosinach; Rajaram Kaliyaperumal; César Henrique Bernabé; Qinqin Long; Simone A. Joosten; Henk Jan van der Wijk; Erik Flikkenschild; Kees Burger; Annika Jacobsen; Barend Mons; Marco Roos (J. Biomed. Semant., 2022)

FAIR Digital Twins for Data-Intensive Research. - Erik Schultes; Marco Roos; Luiz Olavo Bonino da Silva Santos; Giancarlo Guizzardi; Jildau Bouwman; Thomas Hankemeier; Arie Baak; Barend Mons (Frontiers Big Data, 2022)

A goal-oriented method for FAIRification planning. - César Henrique Bernabé; Tiago Prince Sales; Erik Schultes; Niek van Ulzen; Annika Jacobsen; Luiz Olavo Bonino da Silva Santos; Barend Mons; Marco Roos (ER (Companion), 2023)

A Method to Facilitate the Identification of FAIRification Objectives. - César Henrique Bernabé; Annika Jacobsen; Luiz Olavo Bonino da Silva Santos; Marco Roos (ICBO, 2023)

Surveyed common data access policies preferences amongst European Reference Networks. - Alberto Cámara Ballesteros; Nirupama Benis; César Henrique Bernabé; Inés de Oliveira Coelho; Clémence M. A. Le Cornec; Aylin Demir; Bruna dos Santos Vieira; Jose Antonio Ramírez; K. Joeri van der Velde; Shuxin Zhang; Ronald Cornet; Annika Jacobsen; et al. (SWAT4HCLS, 2023)

Structured review on Huntington's disease iron hypothesis. - Karolis Cremers; Marco Roos; Katy Wolstencroft; Eleni Mina; Núria Queralt-Rosinach (SWAT4HCLS, 2023)

FAIRification and semantic modelling for Duchenne and Becker Muscular Dystrophy rare diseases. - Pablo Perdomo-Quinteiro; Sergiu Siminiuc; Paraskevi Sakellariou; Marco Roos; Pietro Spitali; Núria Queralt-Rosinach (SWAT4HCLS, 2023)

Updating the CEMO ontology for future epidemiological challenges. - Núria Queralt-Rosinach; Paul N. Schofield; Marco Roos; Robert Hoehndorf (SWAT4HCLS, 2023)

The FAIR Data Point Populator: collaborative FAIRification and population of FAIR Data Points. - Daphne Wijnbergen; Rajaram Kaliyaperumal; Marco Roos; Eleni Mina (SWAT4HCLS, 2023)

A Resource for Guiding Data Stewards to Make European Rare Disease Patient Registries FAIR. - Philip van Damme; Pablo Alarcón Moreno; César Henrique Bernabé; Alberto Cámara Ballesteros; Clémence M. A. Le Cornec; Bruna dos Santos Vieira; K. Joeri van der Velde; Shuxin Zhang; Claudio Carta; Ronald Cornet; Peter A. C. 't Hoen; Annika Jacobsen; et al. (Data Sci. J., 2023)

The use of foundational ontologies in biomedical research. - César Henrique Bernabé; Núria Queralt-Rosinach; Vítor E. Silva Souza; Luiz Olavo Bonino da Silva Santos; Barend Mons; Annika Jacobsen; Marco Roos (J. Biomed. Semant., 2023)

FAIR Software as a Service: Combining tools to implement FAIR for clinical data platforms. - Rick Overkleeft; Sander van Boom; Eric Prud'hommeaux; Kees Burger; Jip Fransen; Teus H. Kappen; Luiz Olavo Bonino da Silva Santos; Rajaram Kaliyaperumal; Marco Roos (SWAT4HCLS, 2024)

Designing a FAIRification game for Research Software. - Rohitha Ravinder; Dhwani Solanki; Claudio Carta; Bruna dos Santos Vieira; Johannes Keller 006; Marco Roos; Leyla Jael Castro (SWAT4HCLS, 2024)

FAIR for automatic federated omics analysis. - Daphne Wijnbergen; Georgios Malamas; Marco Roos; Eleni Mina (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)

Restructuring Knowledge Graphs with Conceptual Models: Implications for Machine Learning Predictions in Drug Repurposing. - César Bernabé; Rosa Zwart; Pablo Perdomo-Quinteiro; Annika Jacobsen; Tiago Prince Sales; Núria Queralt-Rosinach; Katherine Wolstencroft; Luiz Olavo Bonino da Silva Santos; Barend Mons; Marco Roos (CAiSE (2), 2025)

GO-Plan: A goal-oriented method for FAIRification planning. - César Bernabé; Isadora Valle Sousa; Tiago Prince Sales; Erik Schultes; Niek van Ulzen; Vítor E. Silva Souza; Annika Jacobsen; Luiz Olavo Bonino da Silva Santos; Barend Mons; Marco Roos (Inf. Serv. Use, 2025)

The FAIR data point populator: collaborative FAIRification and population of FAIR data points. - Daphne Wijnbergen; Rajaram Kaliyaperumal; Kees Burger; Luiz Olavo Bonino da Silva Santos; Barend Mons; Marco Roos; Eleni Mina (BMC Medical Informatics Decis. Mak., 2025)