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Relations in biomedical ontologies
To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in suchExpand
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PHI-base: a new database for pathogen host interactions
To utilize effectively the growing number of verified genes that mediate an organism's ability to cause disease and/or to trigger host responses, we have developed PHI-base. This is a web-accessibleExpand
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Graph-based analysis and visualization of experimental results with ONDEX
TLDR
We present a database system that combines the features of semantic database integration and text mining with methods for graph-based analysis. Expand
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PHI-base update: additions to the pathogen–host interaction database
TLDR
The pathogen–host interaction database (PHI-base) is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and Oomycete pathogens, which infect human, animal, plant, insect, fish and fungal hosts. Expand
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SEMEDA: ontology based semantic integration of biological databases
TLDR
MOTIVATION Many molecular biological databases are implemented on relational Database Management Systems, which provide standard interfaces like JDBC and ODBC for data and metadata exchange. Expand
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Addressing the problems with life-science databases for traditional uses and systems biology
A prerequisite to systems biology is the integration of heterogeneous experimental data, which are stored in numerous life-science databases. However, a wide range of obstacles that relate to access,Expand
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On the Application of Formal Principles to Life Science Data: a Case Study in the Gene Ontology
TLDR
Formal principles governing best practices in classification and definition have for too long been neglected in biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. Expand
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Integration of life science databases
TLDR
An overview of the sources of database heterogeneity and a review of different database integration methods. Expand
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Ontology based text indexing and querying for the semantic web
TLDR
This publication shows how the gap between the HTML based internet and the RDF based vision of the semantic web might be bridged, by linking words in texts to concepts of ontologies. Expand
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Extraction of biological interaction networks from scientific literature
TLDR
Biology can be regarded as a science of networks: interactions between various biological entities (eg genes, proteins, metabolites) on different levels (eg gene regulation, cell signalling) can be represented as graphs. Expand
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