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ELISA - Evolution of Semantic Annotations

The new research project “ELISA - Evolution of Semantic Annotations” is a collaborative project between the Luxembourg Institute of Science and Technology (LIST), the University of Paris-Sud, and the Database Group, Universität Leipzig. ELISA is granted by the German Research Foundation (DFG) and the National Research Fund Luxembourg (FNR). The project aims at the development and evaluation of new methods for creating and maintaining semantic annotations.

Project Objectives:

The use of ontologies has shown great possibilities to tackle semantic interoperability issues in the medical domain. Often ontology elements are used to annotate information in order to make their semantics explicit for machines and to facilitate the retrieval of the annotated information. However, the medical domain is highly dynamic by nature. Since 50% of the knowledge of this field is renewed every 10 years, the content of ontologies, representing this knowledge, has to smoothly follow the evolution of the domain to remain exploitable by underlying software applications. As a consequence, the modifications made in these ontologies must also be propagated to all elements that depend on them, such as ontology-based semantic annotations.

In this context, ELISA will develop innovative concepts and tools to:

  • understand the quality of annotations through manual and automatic annotation processes,
  • identify and characterize the evolution occurring in ontologies, and
  • exploit this information to define algorithms to maintain semantic annotations affected by ontology evolution.

Two cases will be distinguished:

  • direct migration of the annotation in the case where those are modifiable, and
  • an ad-hoc migration process in the case where annotations are not modifiable. This will be done through the design of a query enrichment mechanism reflecting the evolution of ontology in order to keep annotated data searchable over time.

The proposed technology will help companies in managing the ever-increasing quantity of data they have to deal with. Moreover, it will be implemented in two real cases borrowed from the field of life sciences. First, we plan to apply our maintenance approach to annotations that serve to enrich patient data in the Luxembourgish national health platform. Second, we will investigate the semantic annotation maintenance problem that arises from the annotation of Case Report Forms used in clinical trial research.

Project Overview

ELISA - Evolution of Semantic Annotations

German Research Foundation ELISA - Evolution of Semantic Annotations - Grant RA 497/22-1

People

Partners

  • Silvio Domingos Cardoso

The website of ELISA project in LIST (ELISA in LIST)

ELISA researchers

(Dr. Cédric Pruski, Ying-Chi Lin, Dr. Marcos Da Silveira, Dr. Anika Groß, Prof. Dr. Erhard Rahm, Victor Christen, Silvio Domingos Cardoso)

Related publications

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Christen, Victor; Hartung, Michael; Groß, Anika
Region Evolution eXplorer - A tool for discovering evolution trends in ontology regions
Journal of Biomedical Semantics 2015, 6:26
2015-06
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Christen, Victor; Groß, Anika; Hartung, Michael
REX - a tool for discovering evolution trends in ontology regions
Proc. 10th Intl. Conference on Data Integration in the Life Sciences (DILS), Lisbon, July 2014
2014-07
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Groß, A.
Evolution von ontologiebasierten Mappings in den Lebenswissenschaften
Dissertation, Universität Leipzig
2014-03
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Groß, A.; Dos Reis, J.C.; Hartung, M.; Pruski, C.; Rahm, E.
Semi-Automatic Adaptation of Mappings between Life Science Ontologies
Proc. 9th Intl. Conference on Data Integration in the Life Sciences (DILS), Montreal, July 2013
2013-07
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Hartung, M.; Groß, A.; Rahm, E.
COnto-Diff : Generation of Complex Evolution Mappings for Life Science Ontologies
Journal of Biomedical Informatics 46 (1): 15-32
2013-02-01
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Groß, A.; Hartung, M.; Kirsten, T.; Rahm, E.
GOMMA Results for OAEI 2012
Seventh International Workshop on Ontology Matching @ ISWC 2012
2012-11
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Groß, A.; Hartung, M.; Thor, A.; Rahm, E.
How do computed ontology mappings evolve? - A case study for life science ontologies
Joint Workshop on Knowledge Evolution and Ontology Dynamics @ ISWC 2012
2012-11

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Groß, A.; Hartung, M.; Prüfer, K.; Kelso, J.; Rahm, E.
Impact of Ontology Evolution on Functional Analyses
Bioinformatics 28 (20): 2671-2677
2012-10-10
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Christen, Victor
REx – eine Webapplikation zur Visualisierung der Evolution von Ontologien in den Lebenswissenschaften
Studentenkonferenz Informatik Leipzig (SKIL) 2012
2012-09
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publication iconGroß, A.; Hartung, M.; Thor, A.; Rahm, E.
How do Ontology Mappings Change in the Life Sciences?
Selected Poster @ Intl. Conference on Data Integration in the Life Sciences (DILS)
2012-06
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publication iconHartung, M.; Groß, A.; Rahm, E.
Determining and Analyzing Semantic Ontology Changes with CODEX
Demo @ Intl. Conference on Data Integration in the Life Sciences (DILS)
2012-06
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Groß, A.; Hartung, M.; Thor, A.; Rahm, E.
How do Ontology Mappings Change in the Life Sciences?
CoRR abs/1204.2731
2012-04
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Hartung, M.; Groß, A.; Rahm, E.
CODEX: Exploration of semantic changes between ontology versions
Bioinformatics 28 (6): 895-896
2012-03
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Kirsten, T.; Groß, A.; Hartung, M.; Rahm, E.
GOMMA: A Component-based Infrastructure for managing and analyzing Life Science Ontologies and their Evolution
Journal of Biomedical Semantics 2011, 2:6
2011-11
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Groß, A.; Hartung, M.; Kirsten, T.; Rahm, E.
Mapping Composition for Matching Large Life Science Ontologies
2nd International Conference on Biomedical Ontology (ICBO 2011)
2011-07
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Hartung, M.
Evolution von Ontologien in den Lebenswissenschaften
Dissertation, Universität Leipzig
2011-05


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Kropp, H.
Berechnung von Diff-Evolution-Mappings zwischen geänderten Produktkatalogen
BTW Studierendenprogramm 2011
2011-03

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Bellahsene, Z.; Bonifati, A.; Rahm, E. (eds.)
Schema Matching and Mapping
Springer-Verlag, Data-Centric Systems and Applications
2011-02
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Hartung, M.; Terwilliger, J.; Rahm, E.
Recent advances in schema and ontology evolution
Schema Matching and Mapping, Springer-Verlag
2011-02
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Hartung, M.; Groß, A.; Rahm, E.
Rule-based Generation of Diff Evolution Mappings between Ontology Versions
CoRR abs/1010.0122
2010-10
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Groß, A.; Hartung, M.; Kirsten, T.; Rahm, E.
On Matching Large Life Science Ontologies in Parallel
7th International Conference on Data Integration in the Life Sciences (DILS 2010)
2010-08
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Hartung, M.; Groß, A.; Kirsten, T.; Rahm, E.
Discovering Evolving Regions in Life Science Ontologies
7th International Conference on Data Integration in the Life Sciences (DILS 2010)
2010-08
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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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Kirsten, T.; Hartung, M.; Groß, A.; Rahm, E.
Efficient Management of Biomedical Ontology Versions
LNCS 5872, pp.574-583, 4th Intl. Workshop on Ontology Content (Part of the OTM Conferences & Workshops)
2009-11
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Hartung, M.; Kirsten, T.; Groß, A.; Rahm, E.
OnEX: Exploring changes in life science ontologies
BMC Bioinformatics 2009, 10:250
2009-08
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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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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.; 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