Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL. - Mikel Egaña Aranguren; Sean Bechhofer; Phillip W. Lord; Ulrike Sattler; Robert D. Stevens 001 (BMC Bioinform., 2007)

Using OWL to model biological knowledge. - Robert Stevens 001; Mikel Egaña Aranguren; Katy Wolstencroft; Ulrike Sattler; Nick Drummond; Matthew Horridge; Alan L. Rector (Int. J. Hum. Comput. Stud., 2007)

Applying Ontology Design Patterns in Bio-ontologies. - Mikel Egaña; Alan L. Rector; Robert Stevens 001; Erick Antezana (EKAW, 2008)

Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language. - Mikel Egaña; Robert Stevens 001; Erick Antezana (OWLED (Spring), 2008)

Augmenting the Expressivity of the Ontology Pre-Processor Language. - Luigi Iannone; Mikel Egaña Aranguren; Alan L. Rector; Robert Stevens 001 (OWLED, 2008)

Structuring the Life Science Resourceome for Semantic Systems Biology: Lessons from the BioGateway Project. - Erick Antezana; Ward Blondé; Mikel Egaña; Alistair Rutherford; Robert Stevens 001; Bernard De Baets; Vladimir Mironov; Martin Kuiper (SWAT4LS, 2008)

BioGateway: Integrated RDF for Life Science Queries. - Erick Antezana; Ward Blondé; Mikel Egaña; Alistair Rutherford; Robert Stevens 001; Bernard De Baets; Vladimir Mironov; Martin Kuiper (SWAT4LS, 2008)

The Cell Cycle Ontology: An Application Ontology Supporting the Life Sciences. - Erick Antezana; Mikel Egaña; Ward Blondé; Robert Stevens 001; Bernard De Baets; Vladimir Mironov; Martin Kuiper (SWAT4LS, 2008)

ONTO-PERL: An API for supporting the development and analysis of bio-ontologies. - Erick Antezana; Mikel Egaña; Bernard De Baets; Martin Kuiper; Vladimir Mironov (Bioinform., 2008)

Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology. - Mikel Egaña Aranguren; Erick Antezana; Martin Kuiper; Robert Stevens 001 (BMC Bioinform., 2008)

In situ migration of handcrafted ontologies to reason-able forms. - Mikel Egaña Aranguren; Chris Wroe; Carole A. Goble; Robert Stevens 001 (Data Knowl. Eng., 2008)

BioGateway: a semantic systems biology tool for the life sciences. - Erick Antezana; Ward Blondé; Mikel Egaña; Alistair Rutherford; Robert Stevens 001; Bernard De Baets; Vladimir Mironov; Martin Kuiper (BMC Bioinform., 2009)

A Semantic Query Interface for the OGO Platform. - José Antonio Miñarro-Giménez; Mikel Egaña Aranguren; Francisco García-Sánchez 001; Jesualdo Tomás Fernández-Breis (ITBAM, 2010)

OPPL-Galaxy: enhancing ontology exploitation in galaxy with OPPL. - Mikel Egaña Aranguren; Jesualdo Tomás Fernández-Breis; Erick Antezana (SWAT4LS, 2011)

Flexibility and utility of the cell cycle ontology. - Vladimir Mironov; Erick Antezana; Mikel Egaña; Ward Blondé; Bernard De Baets; Martin Kuiper; Robert Stevens 001 (Appl. Ontology, 2011)

Semantic integration of information about orthologs and diseases: The OGO system. - José Antonio Miñarro-Giménez; Mikel Egaña Aranguren; Rodrigo Martínez-Béjar; Jesualdo Tomás Fernández-Breis; Marisa Madrid (J. Biomed. Informatics, 2011)

NCBO-Galaxy: bridging the BioPortal web services and the Galaxy platform. - José Antonio Miñarro-Giménez; Mikel Egaña Aranguren; Jesualdo Tomás Fernández-Breis; Erick Antezana (ICBO, 2012)

Ontology Design Pattern Language Expressivity Requirements. - Matthew Horridge; Mikel Egaña Aranguren; Jonathan Mortensen; Mark A. Musen; Natalya Fridman Noy (WOP, 2012)

Plant Pathogen Interactions Ontology (PPIO). - Alejandro Rodriguez Iglesias; Mikel Egaña Aranguren; Alejandro Rodríguez González; Mark D. Wilkinson (IWBBIO, 2013)

OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. - Mikel Egaña Aranguren; Jesualdo Tomás Fernández-Breis; Erick Antezana; Chris Mungall; Alejandro Rodríguez González; Mark D. Wilkinson (J. Biomed. Semant., 2013)

Evaluation of the OQuaRE framework for ontology quality. - Astrid Duque-Ramos; Jesualdo Tomás Fernández-Breis; Miguela Iniesta-Moreno; Michel Dumontier; Mikel Egaña Aranguren; Stefan Schulz 001; Nathalie Aussenac-Gilles; Robert Stevens 001 (Expert Syst. Appl., 2013)

Nanopublishing Clinical Diagnoses: Tracking Diagnostic Knowledge Base Content and Utilization. - Alejandro Rodríguez González; Marcos Martínez Romero; Mikel Egaña Aranguren; Mark D. Wilkinson (CBMS, 2014)

Executing SADI services in Galaxy. - Mikel Egaña Aranguren; Alejandro Rodríguez González; Mark D. Wilkinson (J. Biomed. Semant., 2014)

Automatically exposing OpenLifeData via SADI semantic Web Services. - Alejandro Rodríguez González; Alison Callahan; José Cruz-Toledo; Adrian Garcia; Mikel Egaña Aranguren; Michel Dumontier; Mark D. Wilkinson (J. Biomed. Semant., 2014)

Special issue on Linked Data for Health Care and the Life Sciences. - Mikel Egaña Aranguren; Jesualdo Tomás Fernández-Breis; Michel Dumontier (Semantic Web, 2014)

Translational research combining orthologous genes and human diseases with the OGOLOD dataset. - José Antonio Miñarro-Giménez; Mikel Egaña Aranguren; Boris Villazón-Terrazas; Jesualdo Tomás Fernández-Breis (Semantic Web, 2014)

The cybersecurity ontology network: The first building block for a comprehensive cybersecurity knowledge graph (short paper). - Mikel Egaña Aranguren; Jesualdo Tomás Fernández-Breis; Alexander García Castro; Markus Rompe (JOWO, 2024)

The Transparent Relations Ontology (TRO): a vocabulary to describe conflicts of interest. - Mikel Egaña Aranguren (CoRR, 2024)

OntoGenix: Leveraging Large Language Models for enhanced ontology engineering from datasets. - Mikel Val-Calvo; Mikel Egaña Aranguren; Juan M. Martínez-Hernández; Ginés Almagro-Hernández; Prashant Deshmukh; José Antonio Bernabé-Díaz; Paola Espinoza-Arias; José Luis Sánchez-Fernández; Juergen Mueller; Jesualdo Tomás Fernández-Breis (Inf. Process. Manag., 2025)