Bibliography of Author: Bechhofer, S.

  1. Baker, P.G., Brass, A., Bechhofer, S., Goble, C.A., Paton, N.W., and Stevens, R.. "TAMBIS--Transparent Access to Multiple Bioinformatics Information Sources." Proc Int Conf Intell Syst Mol Biol. vol. 6. 1998. pp. 25-34.
    [ .pdf ] [ .ps ] [ PubMed ] [ WebSite ]

    The TAMBIS project aims to provide transparent access to disparate biological databases and analysis tools, enabling users to utilize a wide range of resources with the minimum of effort. A prototype system has been developed that includes a knowledge base of biological terminology (the biological Concept Model), a model of the underlying data sources (the Source Model) and a 'knowledge-driven' user interface. Biological concepts are captured in the knowledge base using a description logic called GRAIL. The Concept Model provides the user with the concepts necessary to construct a wide range of multiple-source queries, and the user interface provides a flexible means of constructing and manipulating those queries. The Source Model provides a description of the underlying sources and mappings between terms used in the sources and terms in the biological Concept Model. The Concept Model and Source Model provide a level of indirection that shields the user from source details, providing a high level of source transparency. Source independent, declarative queries formed from terms in the Concept Model are transformed into a set of source dependent, executable procedures. Query formulation, translation and execution is demonstrated using a working example.

    Keywords: Artificial Intelligence ; *Computational Biology ; Databases Factual ; User-Computer Interface


  2. Baker, P.G., Goble, C.A., Bechhofer, S., Paton, N.W., Stevens, R., and Brass, A.. "An ontology for bioinformatics applications." Bioinformatics. 15 (6). 1999. pp. 510-20.
    [ .pdf ] [ .ps ] [ PubMed ] [ WebSite ]

    MOTIVATION: An ontology of biological terminology provides a model of biological concepts that can be used to form a semantic framework for many data storage, retrieval and analysis tasks. Such a semantic framework could be used to underpin a range of important bioinformatics tasks, such as the querying of heterogeneous bioinformatics sources or the systematic annotation of experimental results. RESULTS: This paper provides an overview of an ontology [the Transparent Access to Multiple Biological Information Sources (TAMBIS) ontology or TaO] that describes a wide range of bioinformatics concepts. The present paper describes the mechanisms used for delivering the ontology and discusses the ontology's design and organization, which are crucial for maintaining the coherence of a large collection of concepts and their relationships. AVAILABILITY: The TAMBIS system, which uses a subset of the TaO described here, is accessible over the Web via http://img.cs.man.ac.uk/tambis (although in the first instance, we will use a password mechanism to limit the load on our server). The complete model is also available on the Web at the above URL.

    Keywords: Classification ; *Computational Biology ; Databases Factual ; Expert Systems ; Models Biological


  3. Goble, C.A., Stevens, R., Ng, G., Bechhofer, S., Paton, N.W., Baker, P.G., Peim, M., and Brass, A.. "Transparent access to multiple bioinformatics information sources" IBM Systems Journal. 40 (2). 2001. pp. 532--551.
    [ .pdf ]

    This paper describes the Transparent Access to Multiple Bioinformatics Information Sources project, known as TAMBIS, in which a domain ontology for molecular biology and bioinformatics is used in a retrieval-based information integration system for biologists. The ontology, represented using a description logic and managed by a terminology server, is used both to drive a visual query interface and as a global schema against which complex intersource queries are expressed. These source-independent declarative queries are then rewritten into collections of ordered source-dependent queries for execution by a middleware layer. In bioinformatics, the majority of data sources are not databases but tools with limited accessible interfaces. The ontology helps manage the interoperation between these resources. The paper emphasizes the central role that is played by the ontology in the system. The project distinguishes itself from others in the following ways: the ontology, developed by a biologist, is substantial; the retrieval interface is sophisticated; the description logic is managed by a sophisticated terminology server. A full pilot application is available as a JavaTM applet integrating five sources concerned with proteins. This pilot is currently undergoing field trials with working biologists and is being used to answer real questions in biology, one of which is used as a case study throughout the paper.


  4. Stevens, R., Baker, P.G., Bechhofer, S., Ng, G., Jacoby, A., Paton, N.W., Goble, C.A., and Brass, A.. "TAMBIS: transparent access to multiple bioinformatics information sources." Bioinformatics. 16 (2). 2000. pp. 184-5.
    [ PubMed ] [ WebSite ]

    SUMMARY: TAMBIS (Transparent Access to Multiple Bioinformatics Information Sources) is an application that allows biologists to ask rich and complex questions over a range of bioinformatics resources. It is based on a model of the knowledge of the concepts and their relationships in molecular biology and bioinformatics. AVAILABILITY: TAMBIS is available as an applet from http://img.cs.man.ac.uk/tambis SUPPLEMENTARY: A full manual tutorial and videos can be found at http://img.cs.man.ac.uk/tambis. CONTACT: tambis

    Keywords: Computational Biology ; *Information Storage and Retrieval ; *Software