Publications

A list of my most important publications follows (To see all of them, please refer to my CV). Many of them are Open Access; a PDF is attached to the ones that are not.

Journals

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

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]

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]

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]

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. [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]

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]

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]

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]

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]

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][pdf]

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]

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][pdf]

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. [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. [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, Workshop Proceedings and other publications

Aranguren, M. E. (2015). Merging OpenLifeData with SADI services using Galaxy and Docker (DOI 10.1101/013615). BioRxiv, Cold Spring Harbor Labs (http://dx.doi.org/10.1101/013615)

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

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

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

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

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

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/)

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 (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]

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

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]

IMPROVING THE STRUCTURE
OF THE GENE ONTOLOGY
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