Most of my publications are Open Access. However, if you can’t get any of my works, drop me a line and I will send you the PDF.
Journals
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, accepted.
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]
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]
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]
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]
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]
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]
E. Antezana, M. Egaña, B. De Baets, M. Kuiper and V. Mironov. ONTO-PERL: An API supporting the development and analysis of bio-ontologies. Bioinformatics 2008, 24(6):885-887. [Bioinformatics]
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]
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]
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]
Conference proceedings
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]
J.A. Miñarro-Giménez, M. Egaña Aranguren, F. García-Sánchez, J. T. Fernández-Breis. A Semantic Query Interface for the OGO Platform. A Semantic Query Interface for the OGO Platform. ITBAM (DEXA) 2010, LNCS 6266, pp. 128-142. [SpringerLink]
Mikel Egaña, Alan Rector, Robert Stevens, Erick Antezana. Applying Ontology Design Patterns in bio-ontologies. EKAW 2008, LNCS 5268, pp. 7-16. [SpringerLink]
Workshops
A Quality Evaluation Framework for Bio-Ontologies. Jesualdo Tomás Fernández-Breis, Mikel Egaña Aranguren and Robert Stevens. ICBO 2009, Buffalo, USA. http://dx.doi.org/10.1038/npre.2009.3479.1
Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language. Mikel Egaña, Robert Stevens, Erick Antezana. OWLed 2008, Washington DC, USA. http://dx.doi.org/10.1038/npre.2009.4006.1
Antezana E, Blonde W, Egana M, Rutherford A, Stevens R, De Baets B, Mironov V, Kuiper M: Structuring the life science resourceome for Semantic Systems Biology: lessons from the BioGateway project. SWAT4LS 2008, Edinburgh, Scotland, UK. http://ceur-ws.org/Vol-435/
Theses
[PhD] 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] 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]
Etc.
English
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 (2009 eta 2010) aurkeztutako artikuluak (Ez nuen saririk jaso):
- Informazio biologikoa web semantikoaren bidez kudeatzeko diseinu patroiak. Nire tesiaren euskarazko laburpena. [pdf]
- Datuen amarauna. Linked Data-ri buruzko artikulua [pdf]
Euskarazko wikipedian ere banabil, edukiak sartzen edo hobetzen, ahal dudan heinean.
Español
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]
OF THE GENE ONTOLOGY
