Journals

Mikel Val-Calvo, Mikel Egaña Aranguren, Juan Mulero-Hernández, Ginés Almagro-Hernández, Prashant Deshmukh, José Antonio Bernabé-Díaz, Paola Espinoza-Arias, José Luis Sánchez-Fernández, Juergen Mueller, Jesualdo Tomás Fernández-Breis. OntoGenix: Leveraging Large Language Models for enhanced ontology engineering from datasets. Information Processing & Management 2025: 62 (3). [Information Processing & Management]

Mikel Egaña Aranguren, Mark D. Wilkinson. Enhanced reproducibility of SADI web service workflows with Galaxy and Docker. GigaScience 2015: 4(59). [GigaScience][ADDI][DOI]

Pawluczyk, M., Weiss, J., Links, M. G., Aranguren, M. E., Wilkinson, M. D., and Egea-Cortines, M. Quantitative evaluation of bias in PCR amplification and Next Generation Sequencing derived from metabarcoding samples. Analytical and Bioanalytical Chemistry 2015: 407(7):1841–1848. [Analytical and Bioanalytical Chemistry][pdf][DOI]

Alejandro Rodríguez González, Alison Callahan, José Cruz-Toledo, Adrian Garcia, Mikel Egaña Aranguren, Michel Dumontier, Mark D. Wilkinson. Automatically exposing OpenLifeData via SADI semantic Web Services. Journal of Biomedical Semantics 2014, 5(1):46+. [Journal of Biomedical Semantics][ADDI][DOI]

Mikel Egaña Aranguren, Alejandro Rodríguez González, Mark D. Wilkinson. Executing SADI services in Galaxy. Journal of Biomedical Semantics 2014, 5(1):42+. [Journal of Biomedical Semantics][ADDI][DOI]

Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Michel Dumontier. Special issue on Linked Data for Health Care and the Life Sciences (Editorial). Semantic Web Journal 2014, 5(2): 99-100. [pdf][IOS press][Semantic Web Journal]

José Antonio Miñarro-Giménez, Mikel Egaña Aranguren, Boris Villazón-Terrazas, Jesualdo Tomás Fernández Breis. Translational research combining orthologous genes and human diseases with the OGOLOD dataset. Semantic Web Journal 2014, 5(2): 145-149. [IOS press][Semantic Web Journal]

Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Erick Antezana, Chris Mungall, Alejandro Rodríguez González, Mark D. Wilkinson. OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. Journal of Biomedical Semantics 2013, 4 (1):2+. [Journal of Biomedical Semantics][DOI]

Astrid Duque-Ramos, Jesualdo T. Fernández-Breis, Miguela Iniesta, Michel Dumontier, Mikel Egaña Aranguren, Stefan Schulz, Nathalie Aussenac-Gilles, and Robert Stevens. Evaluation of the OQuaRE framework for ontology quality. Expert Systems with Applications 2013, 40(7):2696–2703. [Science Direct][pdf][ADDI][DOI]

José Antonio Miñarro-Giménez, Mikel Egaña Aranguren, Boris Villazón-Terrazas and Jesualdo Tomás Fernández-Breis. Publishing Orthology and Diseases Information in the Linked Open Data cloud. Current Bioinformatics 2012, 7 (3), 255-266. [Bentham science][pdf][DOI]

Vladimir Mironov, Erick Antezana, Mikel Egaña, Ward Blondé, Bernard De Baets, Robert Stevens and Martin Kuiper. Flexibility and utility of the cell cycle ontology. Applied Ontology 2011, 6 (3), 247-261. [IOS Press][pdf][ADDI][DOI]

Jose Antonio Miñarro Gimenez; Mikel Egaña Aranguren, Rodrigo Martínez Béjar, Jesualdo Tomás Fernández Breis, Marisa Madrid. Semantic integration of information about orthologs and diseases: The OGO system. Journal of Biomedical Informatics 2011, 44, 1020-1031. [Science Direct][pdf][ADDI][DOI]

Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov, Martin Kuiper. BioGateway: a semantic systems biology tool for the life sciences. BMC bioinformatics 2009, 10(Suppl 10):S11. [BMC bioinformatics][ADDI][DOI]

Erick Antezana, Mikel Egaña, Bernard De Baets, Ward Blondé, Aitzol Illarramendi, Iñaki Bilbao, Bernard De Baets, Robert Stevens, Vladimir Mironov and Martin Kuiper. The Cell Cycle Ontology: An application ontology for the representation and integrated analysis of the cell cycle process. Genome Biology 2009, 10:R58. [Genome Biology][ADDI][DOI]

Mikel Egaña Aranguren, Erick Antezana, Martin Kuiper, Robert Stevens. Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology. BMC bioinformatics 2008, 9(Suppl 5):S1. [BMC bioinformatics][ADDI][DOI]

Mikel Egaña Aranguren, Chris Wroe, Carole Goble, Robert Stevens. In situ migration of handcrafted ontologies to Reason-able Forms. Data & Knowledge Engineering 2008, 66, 147-162. [Science Direct][pdf][ADDI][DOI]

Erick Antezana, Mikel Egaña Aranguren, Bernard De Baets, Martin Kuiper, Vladimir Mironov. ONTO-PERL: An API supporting the development and analysis of bio-ontologies. Bioinformatics 2008, 24(6):885-887. [Bioinformatics][ADDI][DOI]

Mikel Egaña Aranguren, Sean Bechoffer, Phillip Lord, Ulrike Sattler and Robert Stevens. Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL. BMC Bioinformatics 2007, 8:57. [BMC bioinformatics][ADDI][DOI]

Robert Stevens, Mikel Egaña Aranguren, Katy Wolstencroft, Ulrike Sattler, Nick Drummond and Mathew Horridge. Using OWL to Model Biological Knowledge. International Journal of Human Computer Studies 2006, 65:7, 583-594. [Science Direct][pdf][DOI]

Chapters in books

Mikel Egaña Aranguren, Robert Stevens, Erick Antezana, Jesualdo Tomás Fernández-Breis, Martin Kuiper, Vladimir Mironov. Technologies and best practices for building bio-ontologies. In Marco Ramoni and Gil Alterovitz (Eds), Knowledge-based Bioinformatics: From Analysis to Interpretation. ISBN: 978-0-470-74831-2. [Wiley][pdf]

Conference proceedings

Alejandro Rodríguez González, Marcos Martínez Romero, Mikel Egaña Aranguren, Mark D. Wilkinson. Nanopublishing clinical diagnoses: tracking diagnostic knowledge base content and utilization. 27th International Symposium on Computer-Based Medical Systems (CBMS 2014): 335-340. [IEEE Xplore][pdf]

Alejandro Rodríguez Iglesias, Mikel Egaña Aranguren, Alejandro Rodríguez González, Mark D. Wilkinson. Plant-Pathogen Interactions Ontology (PPIO). International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2013), pages 695-702. [iwbbio.ugr.es][pdf]

Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Erick Antezana. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL.  In Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences, SWAT4LS 2011, pages 12–19, ACM 2012. [ACM][pdf]

J.A. Miñarro-Giménez, M. Egaña Aranguren, F. García-Sánchez, J. T. Fernández-Breis. A Semantic Query Interface for the OGO Platform. ITBAM (DEXA) 2010, LNCS 6266, pp. 128-142. [SpringerLink][pdf]

Mikel Egaña, Alan Rector, Robert Stevens, Erick Antezana. Applying Ontology Design Patterns in bio-ontologies. EKAW 2008, LNCS 5268, pp. 7-16. [SpringerLink][pdf]

Preprints, Workshops and other publications

Joel Garcia-Escribano, Arkaitz Carbajo, Mikel Egaña Aranguren, Unai Lopez-Novoa. Using GPT to build a Project Management assistant for Jira environments. [Arxiv][pdf]

Aranguren, Mikel Egaña and Fernández Breis, Jesualdo Tomás and Balentzia, Bidane Leon and Garcia Castro, Alexander and Rompe, Markus, A Comprehensive View of Software Vulnerability Risks Through Enterprise Knowledge Graphs. [SSRN][pdf]

Aranguren, M. E. (2024). The Transparent Relations Ontology (TRO): a vocabulary to describe conflicts of interest. [Arxiv][pdf]

Aranguren, M. E., Breis, J. T. F., Castro, A. G., and Rompe, M. (2024). The Cybersecurity Ontology Network: the first building block for a comprehensive Cybersecurity Knowledge Graph. In OK4I - Ontologies and Knowledge Graphs for Industry (Co-located with FOIS), Enschede, Netherlands. [CEUR workshops volume 3882][pdf]

Aranguren, M. E. (2015). Merging OpenLifeData with SADI services using Galaxy and Docker (DOI 10.1101/013615). BioRxiv, Cold Spring Harbor Labs. [Biorxiv][pdf]

Marshall, M., Boyce, R., Deus, H., Zhao, J., Willighagen, E., Samwald, M., Pichler, E., Hajagos, J., Aranguren, M., Miller, M., Prudhommeaux, E., Dumontier, M., and Stephens, S. (2012). Health Care and Life Science (HCLS) Linked Data Guide (http://www.w3.org/2001/sw/hcls/notes/hcls-rdf-guide/)

Horridge, M., Aranguren, M., Mortensen, J., Musen, M., and Noy, N. (2012). Ontology Design Pattern Language Expressivity Requirements. In WOP (Co-located with ISWC), Boston, USA. [pdf]

Gimenez, J., Aranguren, M., and Tomas, J. (2012). NCBO-Galaxy: bridging the BioPortal web services and the Galaxy platform. In ICBO, Graz, Austria. [pdf]

Fernandez-Breis, J., Aranguren, M., and Stevens, R. (2009). A quality evaluation framework for bio-ontologies. In ICBO, Buffalo, USA. [pdf]

Aranguren, M., Stevens, R., and Antezana, E. (2008b). Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language. In OWL Experiences and Directions (OWLEd), Washington DC, USA.

Iannone, L., Egana, M., Rector, A., and Stevens, R. (2008). Augmenting the expressivity of the ontology pre-processor language. In OWL Experiences and Directions (OWLEd), co-located with ISWC, Karlsruhe, Germany. [pdf]

Antezana, E., Blondé, W., Egana, M., Rutherford, A., Stevens, R., De Baets, B., Mironov, V., and Kuiper, M. (2008a). Structuring the life science resourceome for semantic systems biology: lessons from the BioGateway Project. In Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS): November 28, 2008; Edinburgh, United Kingdom. [pdf]

Etc.

English

PhD thesis: Role and Application of Ontology Design Patterns in Bio-ontologies. Mikel Egaña Aranguren, 2009, University of Manchester, Faculty of Engineering and Physical Sciences, School of Computer Science. [pdf]

MSc thesis: Improving the structure of the Gene Ontology. Mikel Egaña Aranguren, 2004, University of Manchester, Faculty of Engineering and Physical Sciences, School of Biological Sciences. [pdf]

Content created for the Ontogenesis KnowledgeBlog meeting: a paper and two reviews.

Content created for the Bioinformatics KnowledgeBlog: a tutorial describing how to publish information in Linked Open Data.

Basic introduction to the shell. This is a very basic tutorial on how to use the UNIX shell for non-geeks, e.g. biologists doing a bioinformatics course ;-). [pdf]

Euskara

CAF-Elhuyar sarietara aurkeztutako artikuluak (Ez nuen saririk jaso):

  • (2023) Bitcoin eta Troika: ideologia non-nahi. [pdf]
  • (2021) Datu zientifikoen argitalpen eraginkorra FAIR printzipioen bidez. [pdf]
  • (2010) Datuen amarauna. Linked Data-ri buruzko artikulua [pdf]
  • (2009) Informazio biologikoa web semantikoaren bidez kudeatzeko diseinu patroiak. Nire tesiaren euskarazko laburpena. [pdf]

Berria fundazioak antolatutako leihaketa batera aurkeztutako proiektua, argitaletxe digital bat sortzeko ideiekin. [pdf]

Euskarazko wikipedian ere banabil, edukia sortzen edo hobetzen, ahal dudan heinean.

Español

Pliego técnico proyecto Hércules. [pdf].

Video divulgativo sobre Linked Data para el concurso On Zientzia 2012.

Software libre (GNU/linux) para biólogos. BioGaia 3, 2003 (COBE). [pdf]

¿Qué puede hacer la web semántica por la biología? BioGaia 7, 2009 (COBE). [pdf]

Breve introducción a TeXshade, un paquete LaTeX para representar alineamientos de secuencias. [pdf1, pdf2]