Logical and Semantic Database Integration. - Jacob Köhler; Matthias Lange 001; Ralf Hofestädt; Steffen Schulze-Kremer (BIBE, 2000)

The biology Petri net markup language. - Ming Chen; Andreas Freier; Jacob Köhler; Alexander Rüegg (Promise, 2002)

The Semantic Metadatabase (SEMEDA): Ontology Based Integration of Federated Molecular Biological Data Sources. - Jacob Köhler; Steffen Schulze-Kremer (Silico Biol., 2002)

SEMEDA: ontology based semantic integration of biological databases. - Jacob Köhler; Stephan Philippi; Matthias Lange 001 (Bioinform., 2003)

SEMEDA (semantic meta database): ontology based semantic integration of biological databases. - Jacob Köhler (2003)

On the Application of Formal Principles to Life Science Data: a Case Study in the Gene Ontology. - Barry Smith 001; Jacob Köhler; Anand Kumar 005 (DILS, 2004)

Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalized Data Structures. - Jacob Köhler; Christopher J. Rawlings; Paul Verrier; Rowan A. C. Mitchell; Andre Skusa; Alexander Rüegg; Stephan Philippi (Silico Biol., 2004)

Using XML Technology for the Ontology-Based Semantic Integration of Life Science Databases. - Stephan Philippi; Jacob Köhler (IEEE Trans. Inf. Technol. Biomed., 2004)

Extraction of biological interaction networks from scientific literature. - Andre Skusa; Alexander Rüegg; Jacob Köhler (Briefings Bioinform., 2005)

Graph-based analysis and visualization of experimental results with ONDEX. - Jacob Köhler; Jan Baumbach; Jan Taubert; Michael Specht; Andre Skusa; Alexander Rüegg; Christopher J. Rawlings; Paul Verrier; Stephan Philippi (Bioinform., 2006)

Quality control for terms and definitions in ontologies and taxonomies. - Jacob Köhler; Katherine Munn; Alexander Rüegg; Andre Skusa; Barry Smith 001 (BMC Bioinform., 2006)

Ontology based text indexing and querying for the semantic web. - Jacob Köhler; Stephan Philippi; Michael Specht; Alexander Rüegg (Knowl. Based Syst., 2006)

PHI-base: a new database for pathogen host interactions. - Rainer Winnenburg; Thomas K. Baldwin; Martin Urban; Christopher J. Rawlings; Jacob Köhler; Kim E. Hammond-Kosack (Nucleic Acids Res., 2006)

Automated Structure Extraction and XML Conversion of Life Science Database Flat Files. - Stephan Philippi; Jacob Köhler (IEEE Trans. Inf. Technol. Biomed., 2006)

The OXL format for the exchange of integrated datasets. - Jan Taubert; Klaus Peter Sieren; Matthew Hindle; Berend Hoekman; Rainer Winnenburg; Stephan Philippi; Christopher J. Rawlings; Jacob Köhler (J. Integr. Bioinform., 2007)

Graph-based sequence annotation using a data integration approach. - Robert Pesch; Artem Lysenko; Matthew Hindle; Keywan Hassani-Pak; Ralf Thiele; Christopher J. Rawlings; Jacob Köhler; Jan Taubert (J. Integr. Bioinform., 2008)

PHI-base update: additions to the pathogen-host interaction database. - Rainer Winnenburg; Martin Urban; Andrew M. Beacham; Thomas K. Baldwin; Sabrina Holland; Magdalen Lindeberg; Hilde Hansen; Christopher J. Rawlings; Kim E. Hammond-Kosack; Jacob Köhler (Nucleic Acids Res., 2008)

Linking Life Sciences Data Using Graph-Based Mapping. - Jan Taubert; Matthew Hindle; Artem Lysenko; Jochen Weile; Jacob Köhler; Christopher J. Rawlings (DILS, 2009)

Molecular Information Fusion in Ondex. - Jan Taubert; Jacob Köhler (Approaches in Integrative Bioinformatics, 2014)