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Generic Ontology Matching and Mapping Management (GOMMA)

GOMMA - top results at OAEI competition

The Ontology Alignment Evaluation Initiative (OAEI) yearly compares ontology and schema matching systems w.r.t. their efficiency and effectiveness. The evaluation covers different domains such as matching bibliographic or life science ontologies.

In OAEI 2012 GOMMA achieves the best results for the Anatomy and Library track. Overall GOMMA produced mappings of very high quality with good runtimes for all 6 SEALS tracks. For details, please check the OAEI results page and our paper GOMMA results for OAEI 2012.

The OAEI 2011.5 evaluation results appeared in April 2012. GOMMA is among the Top2 systems for matching anatomy and very large life science ontologies. For matching large biomedical ontologies (results), GOMMA achieves the best matching quality (F-measure >92%) for the “FMA-NCI small overlapping” subtask. The organizers of the track conclude that the Top2-Systems GOMMA and LogMap “are a bit ahead” w.r.t. the other participating systems (F-Measure <76%). Both systems also achieve very good execution times, even for matching full FMA against full NCIT each comprising more than 60,000 concepts. For the anatomy track, GOMMA is the best system w.r.t. F-Measure (91.2%) among all participating systems in 2011.5. In previous campaigns only Agreement Maker achieved a better F-Measure of 91.7%. Note that GOMMA was able to produce this result in less than one minute while Agreement Maker (as most other systems) run more than 10 minutes (see Runtimes and Scalability at result page).

Background

Ontologies are increasingly used to structure and semantically describe entities of domains, such as genes and proteins in life sciences. Their increasing size and the high frequency of updates resulting in a large set of ontology versions necessitates efficient management and analysis of this data.

System Architecture

GOMMA is a generic infrastructure for managing and analyzing life science ontologies and their evolution. The component-based infrastructure utilizes a generic repository to uniformly and efficiently manage many versions of ontologies and different kinds of mappings. Different functional components focus on matching life science ontologies, detecting and analyzing evolutionary changes and patterns in these ontologies. These components are used by several analysis and online applications, such as for ontology matching and the Ontology Evolution Explorer (OnEX). The figure below shows the system architecture of the component-based infrastructure.

This infrastructure enables scalable applications and analyses based on a generic data management of heterogeneous ontologies, entity sources and mappings. The modular design of the infrastructure components allows for a flexible extensibility of GOMMA’s functionalities to meet changed requirements and to realize further applications in future.

Applications

Project Members

Software

You can get access to GOMMA for non-commercial use. Please write an email containing detailed information on the name of your institution, the purpose of using GOMMA (Non-commercial research project, Commercial use, Other, …) to Anika Groß .

IMPORTANT: USE THE PROTOTYPE ON YOUR OWN RISK. THERE ARE NO GUARANTEES AND NO SUPPORT SERVICES. DISTRIBUTION OF THE SOFTWARE ONLY FOR EDUCATIONAL, RESEARCH AND NON-COMMERCIAL PURPOSES. IF YOU INTEND TO USE (RESULTS OF) THE PROTOTYPE FOR ANY KIND OF PUBLICATION YOU HAVE TO

  • INFORM US IN ADVANCE (write an email including detailed information to Anika Groß)
  • CITE OUR GOMMA PUBLICATIONS

The complete system is programmed in Java. After getting access, you can test the software using the GOMMA package and a MySQL database as backend. You will find instructions in the read-me as well as helping comments in an exemplary application. We welcome your feedback, but please have in mind, that GOMMA is an academic research prototype.

Publications

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Lee, L. H.; Groß, A.; Hartung, M.; Liou, D. M.; Rahm, E.
A Multi-Part Matching Strategy for Mapping LOINC with Laboratory Terminologies
Journal of the American Medical Informatics Association (JAMIA)
2014-09
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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.; Kolb, L.; Groß, A.; Rahm, E.
Optimizing Similarity Computations for Ontology Matching - Experiences from GOMMA
Proc. 9th Intl. Conference on Data Integration in the Life Sciences (DILS), 2013
2013-07
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Hartung, M.; Groß, A.; Rahm, E.
Composition Methods for Link Discovery
Proc. of 15. GI-Fachtagung für Datenbanksysteme in Business, Technologie und Web (BTW), 2013
2013-03
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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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Hartung, M.; Groß, A.; Kirsten, T.; Rahm, E.
Effective Composition of Mappings for Matching Biomedical Ontologies
The Semantic Web: ESWC 2012 Satellite Events. Revised Selected Papers.
2012-09
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Hartung, M.; Groß, A.; Kirsten, T.; Rahm, E.
Effective Mapping Composition for Biomedical Ontologies
Semantic Interoperability in Medical Informatics @ ESWC 2012
2012-05
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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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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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Kirsten, T.; Kolb, L.; Hartung, M.; Groß, A.; Köpcke, H.; Rahm, E.
Data Partitioning for Parallel Entity Matching
Proc. 8th Intl. Workshop on Quality in Databases (QDB), 2010
2010-09
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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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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