Molecular-biological annotation data is continuously being collected, curated and made accessible in numerous public data sources. Integration of this data is a major challenge in bioinformatics. We developed the GenMapper system that physically integrates heterogeneous annotation data in a flexible way and supports large-scale analysis on the integrated data. It uses a generic data model to uniformly represent different kinds of annotations originating from different data sources. Existing associations between objects, which represent valuable biological knowledge, are explicitly utilized to drive data integration and combine annotation knowledge from different sources. To serve specific analysis needs, powerful operators are provided to derive tailored annotation views from the generic data representation. GenMapper is operational and has been successfully used for large-scale functional profiling of genes.
The current version of GenMapper is available here.

We also developed a hybrid approach to integrate annotation data for the expression analysis of genes and proteins. Expression data is materialized in a data warehouse while annotation data is integrated virtually according to analysis needs. To facilitate the access to many sources we utilize the commercial product SRS (Sequence Retrieval System) of LION bioscience.

BioFuice is a novel approach for integrating data from different private and public data sources and ontologies. BioFuice follows a peer-to-peer-like data integration based on bidirectional mappings. Sources and mappings are associated with a domain model to support a semantically meaningful interoperability. BioFuice extends the generic iFuice integration platform which utilizes specific operators for data fusion and workflow-like script programs. BioFuice supports explorative data analysis and query and search capabilities. We have applied BioFuice in different research projects, such as for integrating protein interactions, detection of non-coding RNA and gene annotations based on expression experiments.

Current Project Members:

• Erhard Rahm
• Toralf Kirsten

Previous Project Members:

• Hong-Hai Do
• Christine Körner (Diploma student)

Further and Related Information:

• about GenMapper on the IZBI homepage
• about BioFuice on the IZBI homepage
• about Gene Expression Warehousing
• about Networked Computing Resources for Biomedical Research (MediGRID)

Master Thesis:

• Christine Körner: Integration von Genannotationen aus Web-Datenquellen, 2005

Selected Publications:

Kirsten, T.; Thor, A.; Rahm, E. Instance-based matching of large life science ontologies Proc. DILS 2007, LNCS 2007-06 [14 citations]

Rahm, Erhard; Kirsten, Toralf; Lange, Jörg The GeWare data warehouse platform for the analysis of molecular-biological and clinical data Journal of Integrative Bioinformatics, 4(1):47, 2007 2007-01-20 [11 citations]

Kirsten, Toralf; Rahm, Erhard BioFuice: Mapping-based data integration in bioinformatics Proc. of 3rd Int. Workshop on Data Integration in the Life Sciences (DILS), Springer LNCS 4075, 2006 2006-07 [12 citations]

Kirsten, T.; Körner, C.; Do, H.H.; Rahm, E. Hybrid Integration of Molecular-biological Annotation Data Proc. 2nd International Workshop on Data Integration in the Life Sciences (DILS), Springer LNCS 3615, 2005 2005-07 [10 citations]

Rahm, E.; Thor, A.; Aumueller, D.; Do, H.H.; Golovin, N.; Kirsten, T. iFuice - Information Fusion utilizing Instance Correspondences and Peer Mappings 8th International Workshop on the Web and Databases (WebDB) 2005-06 [18 citations]

Körner, C.; Kirsten, T.; Do, H.H., Rahm, E. Hybride Integration von molekularbiologischen Annotationsdaten 11th Conf. of Database Systems for Business, Technology and Web (BTW) 2005-03

Do, H.H.; Rahm, E. Flexible Integration of Molecular-biological Annotation Data: The GenMapper Approach Proc. EDBT 2004, Heraklion, Greece, Springer LNCS, March 2004. 2004-03 [38 citations]

Posters and Talks:

Kirsten, T.; Rahm, E. BioFuice: A decentralized Approach to integrate molecular-biological Data Proc 4th Research Festival for Life Sciences, Leipzig, Dec. 2005 2005-12

Mützel, B.; Do, H.H.; Khaitovich, P.; Weiß, G.; Rahm, E.; Pääbo, S. Functional Profiling of Genes Differently Expressed in the Brains of Humans and Chimpanzees Proc. 2nd Biotech Day, Univ. Leipzig, May 2003, 264-265. 2003-05

Rahm, E.; Do, H.H.; Kirsten, T. Data Integration for Analyzing Gene Expression Data - Selected Projects Data Integration for Analyzing Gene Expression Data. Bonn, May 2003. 2003-05

Kirsten, T.; Do, H.H.; Sosna, D.; Rahm, E., Krohn, K.; Eszlinger, M.; Paschke, R. Gene Expression Warehousing in Leipzig Poster for the Workshop on Databases and Data Integration in Genome Research, Berlin, February 2002 2002-02

Kirsten, T.; Do, H.H.; Rahm, E.; Krohn, K. Gene Expression Warehousing in Leipzig. Poster/Abstract, Proc. Biotech Day, Univ. Leipzig, May 2002, pp. 152-153. 2002