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MediGRID: Networked Computing Resources for Biomedical Research

Grid computing is regarded as one of the critical success factors in biomedical research. The joint project MediGRID unifies well known research institutes in the area of medicine, biomedical informatics and life sciences into a consortium. Numerous associated partners from industry, healthcare and research facilities ensure a broad representation of these communities.

The main goal of MediGRID is the development of a Grid middleware integration platform enabling eScience services for biomedical life science. Therefore the consortium allocated the tasks in different modules. The four methodological modules (middleware, ontology, resource fusion and eScience) plan to incrementally develop and provide a Grid infrastructure while taking into account the need of the biomedical users. The user communities are represented in three research modules for biomedical informatics, image processing and clinical research.

MediGRID is initially funded for three years. Within this time period our goal is to demonstrate the benefit of Grid computing in use cases covering different areas of biomedical informatics. The first cases will cover highly grid enabled projects from biomedical informatics in order to develop best practices for grid-enabling other biomedical projects.

Whereas Grid projects are pretty similar in the lower layers, the biomedical community has to face particular challenges in the upper layers. The top layer represents the heterogeneous biomedical data sources. Beyond the problem to find the relevant data sets via metadata description, access control to the data is of paramount interest, as the owner of the data are foremost patients. Due to the heterogeneity of the data we need an additional ontology layer to homogenize the data. Given semantic interoperability the researcher can correlate and analyze the data with biomedical informatics methods. Finally the result data can be presented.

The successful usage of services, data and physical resources in a Grid environment requires beside technical a semantic interoperability between organisations and nodes. Ontologies are an elementary instrument for describing different resources in a semantic unique way.

The module ontology tools focuses on two purposes:

  • The OntoBuilder tool will be provided to manage and build simple ontologies (controlled vocabularies) used by selected MediGRID applications.
  • Existing biomedical ontologies (e.g. GeneOntology) are integrated and utilized for MediGRID applications. This fusion service is based on the existing GenMapper tool

An ontology provides the conceptualisation of a domain. With a system of semantically unique defined terms an ontology can be used to structure the knowledge in the domain and to describe it for the exchange between applications clearly. Instances of ontologies vary from standardized vocabularies, taxonomies (is-a hierarchies) up to complex networks of concepts including different types of relations.

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Hartung, M; Loebe, F; Herre, H.; Rahm, E.
Management of Evolving Semantic Grid Metadata Within a Collaborative Platform
Information Sciences, Volume 180, Issue 10, 15 May 2010, Pages 1837-1849
2010-05
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Groß, A.; Hartung, M.; Kirsten, T.; Rahm, E.
Estimating the Quality of Ontology-based Annotations by Considering Evolutionary Changes
Proc. 6th Data Integration in the Life Sciences (DILS) Conf., Springer LNCS 5647, 2009
2009-07
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Hartung, M.; Kirsten, T.; Groß, A.; Rahm, E.
Exploring changes in life science ontologies with OnEX
Poster at 7th Leipzig Research Festival for Life Sciences 2008 and 6th Intl. Workshop on Data Integration in the Life Sciences (DILS) 2009
2009-07
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Krefting, D.; Bart, J.; Beronov, K.; Dzhimova, O.; Falkner, J.; Hartung, M.; Hoheisel, A.; Knoch, T.A.; Lingner, T.; Mohammed, Y.; Peter, K.; Rahm, E.; Sax, U.; Sommerfeld, D.; Steinke, T.; Tolxdorff, T.; Vossberg, M.; Viezens, F.; Weisbecker, A.
MediGRID: Towards a user friendly secured grid infrastructure
Future Generation Computer Systems, Volume 25, Issue 3, March 2009, Pages 326-336
2009-03
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Thor, A.; Hartung, M.; Groß, A.; Kirsten, T.; Rahm, E.
An Evolution-based Approach for Assessing Ontology Mappings - A Case Study in the Life Sciences
Proc. of 13. GI-Fachtagung für Datenbanksysteme in Business, Technologie und Web (BTW), 2009
2009-03
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Groß, A.; Hartung, M.; Kirsten, T.; Rahm, E.
Evolution-based analysis of functional protein annotation
Poster at 7th Leipzig Research Festival for Life Sciences 2008
2008-12
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Hartung, M.; Loebe, F.; Herre, H.; Rahm, E.
A Platform for Collaborative Management of Semantic Grid Metadata
Proc. of 2nd Intl. Symposium on Intelligent Distributed Computing (IDC) 2008
2008-09
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Hartung, M.; Kirsten, T.; Rahm, E.
Analyzing the Evolution of Life Science Ontologies and Mappings
Proc. of 5th Int. Workshop on Data Integration in the Life Sciences (DILS), Springer LNCS 5109, 2008
2008-06

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Hartung, M.
Management von Ontologien in den Lebenswissenschaften
Tagungsband zum 20. GI-Workshop über Grundlagen von Datenbanken (20th GI-Workshop on the Foundations of Databases), Apolda (Thüringen)
2008-05
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Hartung, M.; Herre, H.; Loebe, F.; Rahm, E.
D-Grid Ontology - Semantic description of the D-Grid initiative
Poster for the D-Grid All Hands Meeting (AHM), Göttingen, September 2007
2007-09
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Kirsten, T.; Thor, A.; Rahm, E.
Instance-based matching of large life science ontologies
Proc. of 4th Intl. Workshop on Data Integration in the Life Sciences (DILS), 2007
2007-06
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Hartung, M.; Rahm, E.
A Grid Middleware for Ontology Access
1st German e-Science Conference, 2007. Baden-Baden, Germany
2007-05

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Sax, U.; Weisbecker, A.; Falkner, J.; Viezens, F.; Mohammed, Y.; Hartung, M.; Bart, J.; Krefting, D.; Knoch, T.A.; Semler, S.C.
Auf dem Weg zur individualisierten Medizin - Grid-basierte Services für die EPA der Zukunft
Telemed 2007 - Electronic Health Record und Gesundheitsportale, Berlin, 2007
2007-04
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Sax, U.; Mohammed, Y.; Viezens, F.; Lingner, T.; Morgenstern, B.; Hartung, M.; Rienhoff, O.
MediGRID - Medical Grid Computing
Poster for International Supercomputer Conference ISC2006, Dresden
2006-07

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