Semantic web infrastructure for fungal enzyme biotechnologists

The FungalWeb Ontology seeks to support various data integration needs of enzyme biotechnology from inception to product roll. Serving as a knowledgebase for decision support, the conceptualization seeks to link fungal species with enzymes, enzyme substrates, enzyme classifications, enzyme modifications, enzyme related intellectual property, enzyme retail and applications. The ontology, developed in the OWL language, is the result of the integration of numerous biological database schemas, web accessible text resources and components of existing ontologies. We assess the quantity of implicit knowledge in the FungalWeb Ontology by analyzing the range of tags in the OWL files and along with other description logic (DL) computable metrics of the ontology, contrast it with other publicly available bio-ontologies. Thereafter, we demonstrate how the FungalWeb Ontology supports its broad remit required in fungal biotechnology by (i) presenting application scenarios (ii) presenting the conceptualizations of the ontological frame able to support these scenarios and (iii) suggesting semantic queries typical of a fungal enzymologist involved in product development. Recognizing the complexity of the ontology query process for the non-technical manager we introduce a simplified query tool, Ontoligent Interactive Query (OntoIQ) that allows the user to browse and build queries from a selection of query patterns and ontology content. The OntoIQ interface supports users not familiar with writing DL syntax allowing them access to the ontology with expressive description logic reasoning tools. Finally we discuss the challenges encountered during the development of semantic infrastructure for fungal enzyme biotechnologists.

[1]  Birte Glimm.  Query Answering Systems in the Semantic Web , 2004 .

[2]  Amos Bairoch,et al.  NEWT, a new taxonomy portal , 2003, Nucleic Acids Res..

[3]  Peter Luginbühl,et al.  Discovery of Pectin-degrading Enzymes and Directed Evolution of a Novel Pectate Lyase for Processing Cotton Fabric* , 2005, Journal of Biological Chemistry.

[4]  Alan T. Bull,et al.  Search and Discovery Strategies for Biotechnology: the Paradigm Shift , 2000, Microbiology and Molecular Biology Reviews.

[5]  Yosuke Nishitani,et al.  Genotypic analyses of lactobacilli with a range of tannase activities isolated from human feces and fermented foods. , 2004, Systematic and applied microbiology.

[6]  Chan Huah Yong,et al.  Architecture of Agent-Based Healthcare Intelligent Assistant on Grid Environment , 2004, PDCAT.

[7]  Joanne S. Luciano,et al.  PAX of mind for pathway researchers. , 2005, Drug discovery today.

[8]  Volker Haarslev,et al.  The Ecology of Ontologies in the Public Domain , 2007 .

[9]  Michael Wessel,et al.  A High Performance Semantic Web Query Answering Engine , 2005, Description Logics.

[10]  M. Himmel,et al.  Enzymes, Energy, and the Environment: A Strategic Perspective on the U.S. Department of Energy's Research and Development Activities for Bioethanol , 1999, Biotechnology progress.

[11]  Carole A. Goble,et al.  TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources , 1998, ISMB.

[12]  Leila Kosseim,et al.  Using Selectional Restrictions to Query an OWL Ontology , 2006, FOIS.

[13]  S. Kroken,et al.  Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[14]  S. Burton,et al.  Metagenomics, gene discovery and the ideal biocatalyst. , 2004, Biochemical Society transactions.

[15]  Antje Chang,et al.  BRENDA , the enzyme database : updates and major new developments , 2003 .

[16]  Xiao Su,et al.  Ontoligent Interactive Query Tool , 2006, CSWWS.

[17]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[18]  A. Rector,et al.  Relations in biomedical ontologies , 2005, Genome Biology.

[19]  Amos Bairoch,et al.  The ENZYME database in 2000 , 2000, Nucleic Acids Res..

[20]  Gregory Butler,et al.  The FungalWeb Ontology: Semantic Web Challenges in Bioinformatics and Genomics , 2005, SEMWEB.

[21]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[22]  F. Rosetto,et al.  Role of Autochthonous Filamentous Fungi in Bioremediation of a Soil Historically Contaminated with Aromatic Hydrocarbons , 2006, Applied and Environmental Microbiology.

[23]  Stefan Decker,et al.  Creating Semantic Web Contents with Protégé-2000 , 2001, IEEE Intell. Syst..

[24]  Clayton H. Johnson,et al.  Redundancy, phylogeny and differential expression of Histoplasma capsulatum catalases. , 2002, Microbiology.

[25]  René Witte,et al.  Combining Biological Databases and Text Mining to Support New Bioinformatics Applications , 2005, NLDB.

[26]  Volker Haarslev,et al.  RACER System Description , 2001, IJCAR.

[27]  Barry Smith,et al.  On the Application of Formal Principles to Life Science Data: a Case Study in the Gene Ontology , 2004, DILS.