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HCLS new member: Mikel Egaña Aranguren (UPM, Spain)

From: Mikel Egaña Aranguren <megana@fi.upm.es>
Date: Sat, 21 May 2011 13:01:45 +0200
Message-ID: <4DD79B99.5060803@fi.upm.es>
To: public-semweb-lifesci@w3.org
CC: stephens_susie_m@lilly.com, marshall@science.uva.nl, eric@w3.org

My name is Mikel Egaña Aranguren, and I have just joined the HCLS IG on 
behalf of the UPM, Spain. Some of you already know me but a presentation 
is due, so that we can figure out in which areas of the HCLS IG I can be 
most useful.

I got a BSc in biology by the University of Basque Country (2004), 
Spain, and then I completed an MSc in bioinformatics at the Univesity of 
Manchester, UK. After that I joined the BioHealth Informatics Group, 
also at the University of Manchester, and obtained my PhD on 2009, 
supervised by Robert Stevens, advised by Alan Rector and examined by 
Michel Dumontier and Andy Brass. My thesis was entitled "Role and 
Application of Ontology Design Patterns in Bio-ontologies" (By the way, 
you can buy it at http://amzn.to/kPzlfa, I'm a poor post-doc :-). After 
that I worked for the University of Murcia (Spain) during 2 months in 
the OGO project (http://miuras.inf.um.es/~ogo/). Since 14 February of 
2011 I'm working in the Ontology Engineering Group (OEG) of the UPM 
(http://www.oeg-upm.net/), in Madrid, with a Marie Curie contract for a 
post-doc position for three years. You can see more detailed information 
about me, including publications, at 

During my short career I have been mainly working on the idea of 
developing best practices and methods so that biologists feel at ease 
with the subtetlies and power of OWL when it comes to build rich and 
functional biomedical ontologies. As part of that idea, I have done 
different things, ranging from building ontologies and semantic 
resources to building tools for bio-ontology development 

Now that I'm working at the OEG I would like to take advantage of the 
know-how of the OEG in Linked Data and further my career on the Linked 
Open Data realm. As part of such development my main activity within the 
group has been to seek funding for LOD/Life Sciences projects, specially 
focused in environmental data.

The lines I'm/I will be working on at the OEG can be summarised as:

- Best practices for publishing LD: how to build/maintain bio-ontologies 
for LD, emergent vocabularies in the LOD cloud, inference for LD.

- Using LD to publish environmental and biodiversity data.

- Documenting antipatterns that appear when building bio-ontologies.

The concrete projects I'm working on right now:

- Hypothesis management with semantic technologies: in this project I'm 
collaborating with Martin Kuiper of the NTNU. We are setting up a system 
in which hypotheses are generated from microarray data and validated 
against the LOD cloud (And other resources) to "trim" the search space 
for further experimentation. We have submitted a poster to the 
bio-ontologies workshop.

- Migrating the OGO system to the LOD cloud.

- Applying the methods developed by Corcho et al [1] to detect 
antipatterns in biomedical ontologies.

I also teach an OWL course in the 4th year of computer science degree 
here at UPM (As part of the Artificial Intelligence course).

Looking forward to contribute to the group,



[1] Catherine Roussey, Oscar Corcho, and Luis Manuel Vilches Blázquez. A
catalogue of OWL ontology antipatterns. In Proceedings of the fifth
international conference on Knowledge capture, K-CAP ’09, pages
205–206, New York, NY, USA, 2009. ACM.

Mikel Egaña Aranguren, PhD

Marie Curie post-doc at Ontology Engineering Group, UPM
Received on Monday, 23 May 2011 09:57:56 UTC

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