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mikeleganaaranguren039sblog.wordpress.2020-10-02.001.xml
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<?xml version="1.0" encoding="UTF-8" ?>
<!-- This is a WordPress eXtended RSS file generated by WordPress as an export of your site. -->
<!-- It contains information about your site's posts, pages, comments, categories, and other content. -->
<!-- You may use this file to transfer that content from one site to another. -->
<!-- This file is not intended to serve as a complete backup of your site. -->
<!-- To import this information into a WordPress site follow these steps: -->
<!-- 1. Log in to that site as an administrator. -->
<!-- 2. Go to Tools: Import in the WordPress admin panel. -->
<!-- 3. Install the "WordPress" importer from the list. -->
<!-- 4. Activate & Run Importer. -->
<!-- 5. Upload this file using the form provided on that page. -->
<!-- 6. You will first be asked to map the authors in this export file to users -->
<!-- on the site. For each author, you may choose to map to an -->
<!-- existing user on the site or to create a new user. -->
<!-- 7. WordPress will then import each of the posts, pages, comments, categories, etc. -->
<!-- contained in this file into your site. -->
<!-- generator="WordPress.com" created="2020-10-02 08:30"-->
<rss version="2.0"
xmlns:excerpt="http://wordpress.org/export/1.2/excerpt/"
xmlns:content="http://purl.org/rss/1.0/modules/content/"
xmlns:wfw="http://wellformedweb.org/CommentAPI/"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:wp="http://wordpress.org/export/1.2/"
>
<channel>
<title>Mikeleganaaranguren's Blog</title>
<link>https://mikeleganaaranguren.wordpress.com</link>
<description>Just another WordPress.com weblog</description>
<pubDate>Fri, 02 Oct 2020 08:30:22 +0000</pubDate>
<language>en</language>
<wp:wxr_version>1.2</wp:wxr_version>
<wp:base_site_url>http://wordpress.com/</wp:base_site_url>
<wp:base_blog_url>https://mikeleganaaranguren.wordpress.com</wp:base_blog_url>
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<title>Mikeleganaaranguren's Blog</title>
<link>https://mikeleganaaranguren.wordpress.com</link>
</image>
<item>
<title>Publications</title>
<link>https://mikeleganaaranguren.wordpress.com/publications/</link>
<pubDate>Fri, 08 Jan 2010 23:06:36 +0000</pubDate>
<dc:creator>mikeleganaaranguren</dc:creator>
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<content:encoded><![CDATA[A list of my most important publications follows (To see all of them, please refer to my <a href="http://mikeleganaaranguren.wordpress.com/curriculum-vitae-2/">CV</a>). Many of them are <a href="http://en.wikipedia.org/wiki/Open_access_%28publishing%29">Open Access</a>; a PDF is attached to the ones that are not.
<h2>Journals</h2>
Mikel Egaña Aranguren, Mark D. Wilkinson. Enhanced reproducibility of SADI web service workflows with Galaxy and Docker. GigaScience 2015: 4(59). [<a href="https://gigascience.biomedcentral.com/articles/10.1186/s13742-015-0092-3">GigaScience</a>]
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. <em>Analytical and Bioanalytical Chemistry</em> 2015: 407(7):1841–1848. [<a href="http://link.springer.com/article/10.1007%2Fs00216-014-8435-y#">Analytical and Bioanalytical Chemistry</a>][<a href="http://mikeleganaaranguren.files.wordpress.com/2015/02/pawluczyk_abc1.pdf">pdf</a>]
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. <em>Journal of Biomedical Semantics</em> 2014, 5(1):46+. [<a href="http://www.jbiomedsem.com/content/5/1/46/abstract">Journal of Biomedical Semantics</a>]
Mikel Egaña Aranguren, Alejandro Rodríguez González, Mark D. Wilkinson. Executing SADI services in Galaxy. <em>Journal of Biomedical Semantics</em> 2014, 5(1):42+. [<a href="http://www.jbiomedsem.com/content/5/1/42/abstract">Journal of Biomedical Semantics</a>]
Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Michel Dumontier. Special issue on Linked Data for Health Care and the Life Sciences (Editorial). <em>Semantic Web Journal</em> 2014, 5(2): 99-100. [<a href="http://iospress.metapress.com/content/c6k06713136134q2/">IOS press</a>][<a href="http://www.semantic-web-journal.net/content/special-issue-linked-data-health-care-and-life-sciences">Semantic Web Journal</a>]
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. <em>Semantic Web Journal</em> 2014, 5(2): 145-149. [<a href="http://iospress.metapress.com/content/clv840273574688k/">IOS press</a>][<a href="http://www.semantic-web-journal.net/content/translational-research-combining-orthologous-genes-and-human-diseases-ogolod-dataset">Semantic Web Journal</a>]
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. <em>Journal of Biomedical Semantics</em> 2013, 4 (1):2+. [<a href="http://www.jbiomedsem.com/content/4/1/2/abstract">Journal of Biomedical Semantics</a>]
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. <em>Expert Systems with Applications</em> 2013, 40(7):2696–2703. [<a href="http://www.sciencedirect.com/science/article/pii/S0957417412012146">Science Direct</a>][<a href="http://mikeleganaaranguren.files.wordpress.com/2013/01/eswa8231.pdf">pdf</a>]
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.<em> Current Bioinformatics</em> 2012, 7 (3), 255-266. [<a href="http://www.benthamscience.com/contents-JCode-CBIO-Vol-00000007-Iss-00000003.htm">Bentham science</a>][<a href="http://mikeleganaaranguren.files.wordpress.com/2013/01/currentbioinformatics-ogolod.pdf">pdf</a>]
Vladimir Mironov, Erick Antezana, Mikel Egaña, Ward Blondé, Bernard De Baets, Robert Stevens and Martin Kuiper. Flexibility and utility of the cell cycle ontology. <em>Applied Ontology</em> 2011, 6 (3), 247-261. [<a href="http://iospress.metapress.com/content/g1754121847215j2/">IOS Press</a>][<a href="http://mikeleganaaranguren.files.wordpress.com/2013/01/247-261.pdf">pdf</a>]
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. <em>Journal of Biomedical Informatics </em>2011, 44, 1020-1031. [<a href="http://dx.doi.org/10.1016/j.jbi.2011.08.002">Science Direct</a>][<a href="http://mikeleganaaranguren.files.wordpress.com/2013/01/jbi-ogo.pdf">pdf</a>]
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. <em>BMC bioinformatics</em> 2009, 10(Suppl 10):S11. [<a href="http://www.biomedcentral.com/1471-2105/10/S10/S11">BMC bioinformatics</a>]
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. <em>Genome Biology </em>2009, 10:R58. [<a href="http://genomebiology.com/2009/10/5/R58">Genome Biology</a>]
Mikel Egaña Aranguren, Erick Antezana, Martin Kuiper, Robert Stevens. Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology.<em> BMC bioinformatics</em> 2008, 9(Suppl 5):S1. [<a href="http://www.biomedcentral.com/1471-2105/9/S5/S1">BMC bioinformatics</a>]
Mikel Egaña Aranguren, Chris Wroe, Carole Goble, Robert Stevens. <em>In situ</em> migration of handcrafted ontologies to Reason-able Forms. <em>Data & Knowledge Engineering</em> 2008, 66, 147-162. [<a href="http://dx.doi.org/10.1016/j.datak.2008.02.002">Science Direct</a>][<a href="http://mikeleganaaranguren.files.wordpress.com/2013/01/in_situ.pdf">pdf</a>]
Erick Antezana, Mikel Egaña Aranguren, Bernard De Baets, Martin Kuiper, Vladimir Mironov. ONTO-PERL: An API supporting the development and analysis of bio-ontologies. <em>Bioinformatics</em> 2008, 24(6):885-887. [<a href="https://doi.org/10.1093/bioinformatics/btn042">Bioinformatics</a>]
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. <em>BMC Bioinformatics</em> 2007, 8:57. [<a href="http://www.biomedcentral.com/1471-2105/8/57">BMC bioinformatics</a>]
Robert Stevens, Mikel Egaña Aranguren, Katy Wolstencroft, Ulrike Sattler, Nick Drummond and Mathew Horridge. Using OWL to Model Biological Knowledge. <em>International Journal of Human Computer Studies</em> 2006, 65:7, 583-594. [<a href="http://dx.doi.org/10.1016/j.ijhcs.2007.03.006">Science Direct</a>][<a href="http://mikeleganaaranguren.files.wordpress.com/2013/01/using_owl.pdf">pdf</a>]
<h2>Chapters in books</h2>
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. [<a href="http://eu.wiley.com/WileyCDA/WileyTitle/productCd-0470748311,descCd-description.html">Wiley</a>][<a href="http://mikeleganaaranguren.files.wordpress.com/2013/01/c03.pdf">pdf</a>]
<h2>Conference proceedings</h2>
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. [<a href="http://mikeleganaaranguren.files.wordpress.com/2014/08/4435a335.pdf">pdf</a>]
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. [<a href="http://mikeleganaaranguren.files.wordpress.com/2013/04/iwbbio2013_submission_27.pdf">pdf</a>]
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. [<a href="http://dx.doi.org/10.1145/2166896.2166903">ACM</a>][<a href="http://mikeleganaaranguren.files.wordpress.com/2013/01/p12-aranguren.pdf">pdf</a>]
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. [<a href="http://www.springerlink.com/content/a8462053566297l1/">SpringerLink</a>][<a href="http://mikeleganaaranguren.files.wordpress.com/2013/01/dexa.pdf">pdf</a>]
Mikel Egaña, Alan Rector, Robert Stevens, Erick Antezana. Applying Ontology Design Patterns in bio-ontologies. EKAW 2008, LNCS 5268, pp. 7-16. [<a href="http://www.springerlink.com/content/d2lp476v0p281q73/">SpringerLink</a>][<a href="http://mikeleganaaranguren.files.wordpress.com/2013/01/ekaw.pdf">pdf</a>]
<h2>Preprints, Workshop Proceedings and other publications</h2>
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/)
<h2>Etc.</h2>
<strong>English</strong>
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. [<a href="http://mikeleganaaranguren.files.wordpress.com/2010/01/thesis.pdf">pdf</a>]
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. [<a href="http://mikeleganaaranguren.files.wordpress.com/2010/01/msc_thesis.pdf">pdf</a>]
Content created for the Ontogenesis KnowledgeBlog meeting: <a href="http://ontogenesis.knowledgeblog.org/tag/mikel-egana-aranguren/">a paper and two reviews</a>.
Content created for the Bioinformatics KnowledgeBlog: <a href="http://bioinformatics.knowledgeblog.org/2011/07/05/publishing-information-in-the-linked-open-data-cloud/">a tutorial describing how to publish information in Linked Open Data</a>.
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 ;-). [<a href="http://mikeleganaaranguren.files.wordpress.com/2010/01/basic_shell.pdf">pdf</a>]
<strong>Euskara</strong>
CAF-Elhuyar sarietara (2009 eta 2010) aurkeztutako artikuluak (Ez nuen saririk jaso):
<ul>
<li>Informazio biologikoa web semantikoaren bidez kudeatzeko diseinu patroiak. Nire tesiaren euskarazko laburpena. [<a href="http://mikeleganaaranguren.files.wordpress.com/2010/03/mikelegana_websembio_cafelhuyar.pdf">pdf</a>]</li>
<li>Datuen amarauna. <a href="http://eu.wikipedia.org/wiki/Datu_estekatuak">Linked Data</a>-ri buruzko artikulua [<a href="http://mikeleganaaranguren.files.wordpress.com/2011/05/caf_elhuyar_2010_datuen_amarauna.pdf">pdf</a>]</li>
</ul>
Berria fundazioak antolatutako leihaketa batera aurkeztutako proiektua, argitaletxe digital bat sortzeko ideiekin. [<a href="https://mikeleganaaranguren.files.wordpress.com/2015/03/mikel_egac3b1a_aranguren_txostena.pdf">pdf</a>]
<a href="http://eu.wikipedia.org/wiki/Azala">Euskarazko wikipedian</a> ere banabil, edukia sortzen edo hobetzen, ahal dudan heinean.
<strong>Español</strong>
Pliego técnico <a href="https://www.um.es/web/hercules/proyectos">proyecto Hércules</a>. [<a href="https://mikeleganaaranguren.files.wordpress.com/2020/05/01678941.pdf">pdf</a>]. También disponible en:
<ul>
<li>https://contrataciondelestado.es/wps/wcm/connect/12ede981-14f4-4993-9696-d0b7e41f2265/DOC20190403143712Informe+Hercules.pdf?MOD=AJPERES</li>
<li>https://sede.um.es/perfilcontratante/uploads/01678941.PDF</li>
</ul>
<a href="https://vimeo.com/42962819">Video divulgativo</a> sobre <a href="http://es.wikipedia.org/wiki/Datos_enlazados">Linked Data</a> para el concurso <a href="http://www.onzientzia.tv/bideoa-ikusi.asp?Kodea=332&lang=ES">On Zientzia 2012</a>.
Software libre (GNU/linux) para biólogos. BioGaia 3, 2003 (<a href="http://www.cobeuskadi.es/">COBE</a>). [<a href="http://mikeleganaaranguren.files.wordpress.com/2010/01/linuxbiologos.pdf">pdf</a>]
¿Qué puede hacer la web semántica por la biología? BioGaia 7, 2009 (<a href="http://www.cobeuskadi.es/">COBE</a>). [<a href="http://mikeleganaaranguren.files.wordpress.com/2010/01/biogaialssw.pdf">pdf</a>]
Breve introducción a <a href="http://www.ctan.org/tex-archive/macros/latex/contrib/texshade/">TeXshade</a>, un paquete LaTeX para representar alineamientos de secuencias. [<a href="http://mikeleganaaranguren.files.wordpress.com/2010/01/texshade_es.pdf">pdf1</a>, <a href="http://mikeleganaaranguren.files.wordpress.com/2010/01/texshade_es_ejemplos.pdf">pdf2</a>]
<div id="_mcePaste" style="overflow:hidden;position:absolute;left:-10000px;top:845px;width:1px;height:1px;">IMPROVING THE STRUCTURE
OF THE GENE ONTOLOGY</div>]]></content:encoded>
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<title>Research and development</title>
<link>https://mikeleganaaranguren.wordpress.com/projects/</link>
<pubDate>Fri, 08 Jan 2010 23:21:21 +0000</pubDate>
<dc:creator>mikeleganaaranguren</dc:creator>
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<content:encoded><![CDATA[I am interested in the exploitation of <a href="http://www.w3.org/standards/semanticweb/">Semantic Web</a> technology (<a href="www.w3.org/standards/techs/rdf">RDF</a>, <a href="http://www.w3.org/standards/techs/owl">OWL</a>, <em>etc.</em>) to improve knowledge management in several domains, most importantly Life Sciences and Open Data. The realisation of this interest involves the creation of semantic resources (<a href="http://en.wikipedia.org/wiki/Ontology_%28information_science%29">Ontologies</a>, <a href="http://en.wikipedia.org/wiki/Knowledge_base">Knowledge Bases</a>, <a href="http://www.w3.org/standards/semanticweb/data">Linked Data</a> datasets, <a href="http://sadiframework.org/">Semantic Web Services</a>, <em>etc.</em>), and the development of tools for creating and using such resources.
I have been involved in the following funded projects:
<ul>
<li>2018. <a href="http://www.ejie.eus/y79-contgen/es/contenidos/anuncio_contratacion/expx74j30109/es_doc/es_arch_expx74j30109.html?ruta=/y79-appcontr/es/v79aWar/comunJSP/v79aSuscribirRSS.do?=R01HPortal=y79&R01HPage=appcontr&R01HLang=es&widget=true&p01=AC&p02=&p03=8&p04=&p05=&p06=&p07=&p08=&p09=&p10=&p11=&p12=&p13=&p14=&p15=05%2F04%2F2018&p16=&p17=AMPLIADO&p18=false&p19=false&p20=false&p21=es&p22=ultimos30dias&p23=&p24=y79-appcontr&p25=y79-contgen&p45=true&p48=&p51=1">Servicios Directorio Linked Open Data</a>. Basque Government, Spain. (70.000 EUR)</li>
<li>2016 - 2018. <a href="http://replicate-project.eu/">REPLICATE: Renaissance of Places with Innovative Citizenship And TEchnology</a> (Project 691735). EU. (Consortium: 24M EUR; Eurohelp: 300.000 EUR)</li>
<li>2016 - 2018. <a href="http://www.contratacion.euskadi.eus/w32-1084/es/contenidos/anuncio_contratacion/expx74j21656/es_doc/es_arch_expx74j21656.html">Servicios OpenLinkedData</a> (Linked Data implementation of Open Data Euskadi). Basque Government, Spain. (90.000 EUR)</li>
<li>2015 - 2016. Linking Open Domains, Plataforma para la generación de datos enlazados (LODGen). Ministerio de Industria, Energia y Turismo, Acción Estratégica Economía y Sociedad Digital (AEESD) 1/2015, Spain (TSI-100105-2015-0012). (40.000 EUR)</li>
<li>2017 - 2018. SOLDAGE (Semantic Open Linked DAta GEnerator), a <a href="https://www.nature.com/articles/sdata201618">FAIR</a> data generator. Hazitek, Basque Government. (150.000 EUR)</li>
<li>2015. Enlazando Gipuzkoa con el Mundo (ENGIMU). Gipuzkoako Foru Aldundia, Gipuzkoa IKT: Innovación digital Empresas, Spain. (40.000 EUR)</li>
</ul>
I have done freelance work:
<ul>
<li>I wrote the <span class="background-details"><span class="lt-line-clamp__line lt-line-clamp__line--last"><a href="https://sede.um.es/perfilcontratante/uploads/01678941.PDF">Public tender</a> for two projects under the <a href="http://hercules.um.es/">Hércules initiative</a>, a federation of University research data through Linked Open Data (5 million EUR).
</span></span></li>
<li><a href="https://www.cogni.zone">Cognizone</a> (Ontology Engineering).</li>
<li>Intellimedis (Ontology Engineering).</li>
</ul>
I am or have been involved in the following technical developments:
<ul>
<li>Linked Open Data Euskadi: migration of current Open Data Euskadi to Linked Open Data. [<a href="https://github.com/opendata-euskadi">https://github.com/opendata-euskadi</a>]</li>
<li>Guerra Civil en Euskadi: this resource integrates data about the spanish civil war in Euskadi, through RDF graphs, and it offers nice visualisations. [<a href="http://guerracivileuskadi.eurohelp.es/">http://guerracivileuskadi.eurohelp.es/</a>]</li>
<li>Linked Data Test Suite:Tests and reporting for Linked Data systems. [<a href="https://github.com/mikel-egana-aranguren/LinkedDataTestSuite">https://github.com/mikel-egana-aranguren/LinkedDataTestSuite</a>]</li>
<li>ALDAPA: Assistant for Linked DAta Production Automation. [<a href="https://github.com/mikel-egana-aranguren/ALDAPA">https://github.com/mikel-egana-aranguren/ALDAPA</a>]</li>
<li>SADI-Galaxy is a wrapper of <a href="http://sadiframework.org/content/about-sadi/">SADI</a> services for <a href="http://galaxyproject.org/">Galaxy</a>. [<a href="http://github.com/mikel-egana-aranguren/SADI-Galaxy">http://github.com/mikel-egana-aranguren/SADI-Galaxy</a>]. There are also two <a href="https://www.docker.com/">Docker</a> versions for easy deployment, each of them with a different approach: <a href="https://github.com/mikel-egana-aranguren/SADI-Docker-Galaxy">SADI-Docker-Galaxy</a> provides the SADI tools as a Docker image and how to configure Galaxy to run Docker images; <a href="http://github.com/mikel-egana-aranguren/SADI-Galaxy-Docker">SADI-Galaxy-Docker</a> provides the whole Galaxy server, preconfigured with SADI tools, as a Docker image.</li>
<li>OpenLifeData2SADI is a set of SADI services that wraps the Linked Data resources from Open Life Data (formerly known as Bio2RDF). I wrote the Galaxy pipelines to demonstrate how to use the SADI services. [<a href="http://github.com/wilkinsonlab/OpenLifeData2SADI">http://github.com/wilkinsonlab/OpenLifeData2SADI</a>]</li>
<li>BIOM-LD is a mapping of the <a href="http://biom-format.org/">BIOM format</a> to a <a href="http://lod-cloud.net/">Linked Open Data</a> setting, including an ontology defining the mapping (<a href="http://bioportal.bioontology.org/ontologies/BIOMO">BIOMO</a>). This is a very preliminary development. [<a href="http://github.com/mikel-egana-aranguren/biom-ld">http://github.com/mikel-egana-aranguren/biom-ld</a>]</li>
<li>Life Sciences Linked Data: This is a standalone, light-weight, configuration-free bundle to publish Linked Data. It is meant as an educational tool that students can use to become familiar with Linked Data, by publishing their own dataset at localhost with only the necessary hassle, but still being aware of the overal technical setting. It can also be used for rapid prototyping and deployment of a Linked Data system. [<a href="http://github.com/mikel-egana-aranguren/LSLD">http://github.com/mikel-egana-aranguren/LSLD</a>]</li>
<li>Linked Data Server: a different version of Life Sciences Linked Data, using Stardog as a triple store and a custom NodeJS script instead of Pubby. The script is technically worse than Pubby, obviously, but the overall configuration is way easier. [<a href="https://github.com/mikel-egana-aranguren/LinkedDataServerNodeJSStardog">https://github.com/mikel-egana-aranguren/LinkedDataServerNodeJSStardog</a>]</li>
<li>DDx2NP: This programme can be used to add Nanopublications to a given medical Knowledge Base. [<a href="http://github.com/wilkinsonlab/DDx2NP">http://github.com/wilkinsonlab/DDx2NP</a>]</li>
<li>PPIO: The Plant-Pathogen Interactions Ontology (<a href="http://purl.oclc.org/PPIO">http://purl.oclc.org/PPIO</a>) offers an axiomisation of plant-pathogen interactions in order to annotate, query and reason over such domain of knowledge. [<a href="https://github.com/wilkinsonlab/PPIO">https://github.com/wilkinsonlab/PPIO</a>]</li>
<li>NCBO-Galaxy: NCBO-Galaxy provides graphical interfaces for the NCBO web services available at <a href="http://bioportal.bioontology.org/">BioPortal</a>, to access and exploit biomedical ontologies as part of <a href="http://galaxy.psu.edu/">Galaxy</a> workflows. It can be found in Ontology Manipulation in the Galaxy Toolshed. [<a href="http://toolshed.g2.bx.psu.edu/">http://toolshed.g2.bx.psu.edu/</a>]</li>
<li>OGO: OGO integrates orthology information with diseases from OMIM, exploiting OWL, SPARQL and OBO ontologies. [<a href="http://miuras.inf.um.es:9080/OGO-1.0/">http://miuras.inf.um.es:9080/OGO-1.0/</a>]</li>
<li>OGOLOD is a Linked Data version of OGO. [<a href="http://miuras.inf.um.es/%7Eogo/ogolod.html">http://miuras.inf.um.es/~ogo/ogolod.html</a>]</li>
<li>ODPs catalogue: A repository of ontology engineering best practices, focused on biological knowledge. [<a href="http://odps.sf.net">http://odps.sf.net</a>]</li>
<li>BioGateway: An RDF store holding information integrated from different bioinformatics resources, like the OBO ontologies, GOA files and SwissProt. [<a href="http://www.semantic-systems-biology.org/biogateway">http://www.semantic-systems-biology.org/biogateway</a>]</li>
<li>CCO: The Cell Cycle Ontology is an application ontology that describes different aspects of the cell cycle, integrating information from UniProt, IntAct, GOA, NCBI taxonomy and GO. [<a href="http://cellcycleontology.org">http://cellcycleontology.org</a>]</li>
<li>OPPL: The Ontology Pre-Processor Language is a scripting language for defining and performing axiomatic changes in OWL ontologies, thus offering an abstraction of the OWL API that works directly with axioms instead of programmatic procedures. [<a href="http://oppl.sourceforge.net/">http://oppl.sourceforge.net/</a>]</li>
<li>OPPL-Galaxy: this tool can be used to execute <a href="http://oppl2.sourceforge.net/">OPPL</a> scripts as part of <a href="http://galaxy.psu.edu/">Galaxy</a>. It can be found in Ontology Manipulation in the Galaxy Toolshed. [<a href="http://toolshed.g2.bx.psu.edu/">http://toolshed.g2.bx.psu.edu/</a>]</li>
<li>ONTO-PERL: An API for manipulating OBO ontologies, written in Perl. [<a href="http://search.cpan.org/%7Eeasr/">http://search.cpan.org/~easr/</a>]</li>
<li>GONG: Gene Ontology Next Generation is a methodology for enriching OBO ontologies by adding OWL axioms based on dissecting the structure of the term names with regular expressions. [<a href="http://www.gong.manchester.ac.uk">http://www.gong.manchester.ac.uk</a>]</li>
<li>Linked Data Open Data Euskadi: pack para publicar Linked Data con un dataset de Open Data Euskadi, como demostración de como implementar Linked Data apropiadamente, desarrollado en el <a href="http://dev.morelab.deusto.es/hackathon/index.php/P%C3%A1gina_principal">Open Data Day Deusto 2014</a>. [<a href="http://github.com/OpenDataDayBilbao/Linked-Data-Open-Data-Euskadi">http://github.com/OpenDataDayBilbao/Linked-Data-Open-Data-Euskadi</a>]</li>
</ul>]]></content:encoded>
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<title>Ihes ederra</title>
<link>https://mikeleganaaranguren.wordpress.com/?p=29</link>
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<dc:creator>mikeleganaaranguren</dc:creator>
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<content:encoded><![CDATA[Lehen eleberri grafikoa
ideia onak, baina experimental egia
esan ohi denez, maisu izatera heldu dena bakarrik apur ditzake arauak (eg umbral)
gainera hasierako ingelesa txarra
dena den, alan moore euskaldun bat izan arte bide oso luzea aurretik badaukagu ere, hasiera ez da txarra]]></content:encoded>
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<title>MSc thesis</title>
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<pubDate>Wed, 13 Jan 2010 14:25:02 +0000</pubDate>
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<pubDate>Wed, 13 Jan 2010 14:31:33 +0000</pubDate>
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<title>DEXA 2010 - Bilbo</title>
<link>https://mikeleganaaranguren.wordpress.com/2010/01/20/dexa-2010-bilbo/</link>
<pubDate>Wed, 20 Jan 2010 13:05:21 +0000</pubDate>
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<content:encoded><![CDATA[DEXA 2010 (<a href="http://www.dexa.org/">http://www.dexa.org/</a>) will take place in Bilbo, my home city.]]></content:encoded>
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<title>KnowledgeBlog: bloging a book about ontologies</title>
<link>https://mikeleganaaranguren.wordpress.com/2010/01/21/knowledgeblog-bloging-a-book-about-ontologies/</link>
<pubDate>Thu, 21 Jan 2010 15:47:11 +0000</pubDate>
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<content:encoded><![CDATA[I'm participating on an <a href="http://ontogenesis.knowledgeblog.org/">experiment</a> about using blogs to create a book about bio-ontologies. <a href="http://duncan.hull.name/2010/01/21/ontogenesis/">Duncan Hull</a> has a more in depths explanation.]]></content:encoded>
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<wp:comment_author><![CDATA[Ontogenesis: Who’s here? | Ontogenesis]]></wp:comment_author>
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<wp:comment_content><![CDATA[[...] Mikel Egana-Aranguren [...]]]></wp:comment_content>
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<wp:comment_author><![CDATA[Mikel]]></wp:comment_author>
<wp:comment_author_email>[email protected]</wp:comment_author_email>
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<wp:comment_author_IP>85.85.58.89</wp:comment_author_IP>
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<wp:comment_content><![CDATA[Photos:
http://www.flickr.com/photos/dullhunk/4309532104/
http://www.flickr.com/photos/dullhunk/4309532104/]]></wp:comment_content>
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<title>Why linked data for data.gov.uk?</title>
<link>https://mikeleganaaranguren.wordpress.com/2010/01/26/why-linked-data-for-data-gov-uk/</link>
<pubDate>Tue, 26 Jan 2010 15:44:17 +0000</pubDate>
<dc:creator>mikeleganaaranguren</dc:creator>
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<content:encoded><![CDATA[Very nice post on why RDF is a good idea for the UK's <a href="http://data.gov.uk/">open data initiative</a>, and, by extension, for the whole web: <a href="http://www.jenitennison.com/blog/node/140">http://www.jenitennison.com/blog/node/140</a>.]]></content:encoded>
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<title>linuxbiologos</title>
<link>https://mikeleganaaranguren.wordpress.com/linuxbiologos/</link>
<pubDate>Wed, 27 Jan 2010 16:26:23 +0000</pubDate>
<dc:creator>mikeleganaaranguren</dc:creator>
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<title>BioGaiaLSSW</title>
<link>https://mikeleganaaranguren.wordpress.com/biogaialssw/</link>
<pubDate>Wed, 27 Jan 2010 16:30:07 +0000</pubDate>
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<title>texshade_es</title>
<link>https://mikeleganaaranguren.wordpress.com/texshade_es/</link>
<pubDate>Wed, 27 Jan 2010 16:52:27 +0000</pubDate>
<dc:creator>mikeleganaaranguren</dc:creator>
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<title>texshade_es_ejemplos</title>
<link>https://mikeleganaaranguren.wordpress.com/texshade_es_ejemplos/</link>
<pubDate>Wed, 27 Jan 2010 16:52:30 +0000</pubDate>
<dc:creator>mikeleganaaranguren</dc:creator>
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<title>basic_shell</title>
<link>https://mikeleganaaranguren.wordpress.com/basic_shell/</link>
<pubDate>Wed, 27 Jan 2010 16:54:12 +0000</pubDate>
<dc:creator>mikeleganaaranguren</dc:creator>
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<title>Why use OWL?</title>
<link>https://mikeleganaaranguren.wordpress.com/2010/01/28/why-use-owl/</link>
<pubDate>Thu, 28 Jan 2010 16:58:32 +0000</pubDate>
<dc:creator>mikeleganaaranguren</dc:creator>
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<content:encoded><![CDATA[A very succint and nice answer: <a href="http://www.xfront.com/why-use-owl.html">http://www.xfront.com/why-use-owl.html</a>]]></content:encoded>
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<title>OWL as RDF validator</title>
<link>https://mikeleganaaranguren.wordpress.com/2010/02/02/owl-as-rdf-validator/</link>
<pubDate>Tue, 02 Feb 2010 21:02:52 +0000</pubDate>
<dc:creator>mikeleganaaranguren</dc:creator>
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<content:encoded><![CDATA[Very nice explanation on the <a href="http://clarkparsia.com/pellet/icv">Pellet Integrity Constraint Validator</a>. Pellet ICV allows to use OWL to validate RDF data with CWA and weak UNA.]]></content:encoded>
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<title>Calling International Rescue: knowledge lost in literature and data landslide!</title>
<link>https://mikeleganaaranguren.wordpress.com/2010/02/10/calling-international-rescue-knowledge-lost-in-literature-and-data-landslide/</link>
<pubDate>Wed, 10 Feb 2010 09:15:28 +0000</pubDate>
<dc:creator>mikeleganaaranguren</dc:creator>
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<content:encoded><![CDATA[Very interesting article by <a href="http://www.biochemj.org/bj/424/bj4240317.htm">Attwood et al</a>, relevant to <a href="http://ontogenesis.knowledgeblog.org/">Ontogenesis Knowledge Blog</a>.
<p style="padding-left:30px;">“It is quite depressive to
think that we are spending millions in grants for people to perform
experiments, produce new knowledge, hide this knowledge in a
often badly written text and then spend some more millions trying
to second guess what the authors really did and found”</p>]]></content:encoded>
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<wp:post_id>88</wp:post_id>
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