Bibliography of Year: 1999

  1. 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


  2. Collado-Vides, J., Hofestadt, R., Mavrovouniotis, M.L., and Michal, G.. "Modeling and simulation of gene regulation and metabolic pathways." Biosystems. 49 (1). 1999. pp. 79-82.
    [ .pdf ] [ PubMed ]

    Keywords: *Gene Expression Regulation ; *Metabolism ; *Models Genetic


  3. Ellis, L.B., Hershberger, C.D., and Wackett, L.P.. "The University of Minnesota Biocatalysis/Biodegradation Database: specialized metabolism for functional genomics." Nucleic Acids Res. 27 (1). 1999. pp. 373-6.
    [ .pdf ] [ PubMed ]

    The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://www.labmed.umn.edu/umbbd/i nde x.html) first became available on the web in 1995 to provide information on microbial biocatalytic reactions of, and biodegradation pathways for, organic chemical compounds, especially those produced by man. Its goal is to become a representative database of biodegradation, spanning the diversity of known microbial metabolic routes, organic functional groups, and environmental conditions under which biodegradation occurs. The database can be used to enhance understanding of basic biochemistry, biocatalysis leading to speciality chemical manufacture, and biodegradation of environmental pollutants. It is also a resource for functional genomics, since it contains information on enzymes and genes involved in specialized metabolism not found in intermediary metabolism databases, and thus can assist in assigning functions to genes homologous to such less common genes. With information on >400 reactions and compounds, it is poised to become a resource for prediction of microbial biodegradation pathways for compounds it does not contain, a process complementary to predicting the functions of new classes of microbial genes.

    Keywords: Bacteria_genetics ; Bacteria_*metabolism ; Bacterial Proteins_metabolism ; *Biodegradation ; Biotechnology ; *Catalysis ; *Databases Factual_trends ; Environmental Pollution ; Enzymes_chemistry ; Enzymes_genetics ; Enzymes_metabolism ; Genes ; Bacterial_genetics ; Genes ; Bacterial_physiology ; Human ; Information Storage and Retrieval ; Internet ; Minnesota ; Universities


  4. Goss, P.J. and Peccoud, J.. "Analysis of the stabilizing effect of Rom on the genetic network controlling ColE1 plasmid replication." Pac Symp Biocomput. 1999. pp. 65-76.
    [ .pdf ] [ PubMed ]

    A stochastic model of ColE1 plasmid replication is presented. It is implemented by using UltraSAN, a simulation tool based on an extension of stochastic Petri nets (SPNs). It allows an exploration of the variation in plasmid number per bacterium, which is not possible using a deterministic model. In particular, the rate at which plasmid-free bacteria arise during bacterial division is explored in some detail since spontaneous plasmid loss is a widely observed empirical phenomenon. The rate of spontaneous plasmid loss provides an evolutionary explanation for the maintainance of Rom protein. The presence of Rom acts to reduce variance in plasmid copy number, thereby reducing the rate of plasmid loss at bacterial division. The ability of stochastic models to link biochemical function with evolutionary considerations is discussed.

    Keywords: Cell Division ; Computational Biology_*methods ; *DNA Replication ; Escherichia coli_*genetics ; Escherichia coli_growth and development ; *Models Genetic ; *Plasmids ; Stochastic Processes


  5. Karp, P.D., Riley, M., Paley, S.M., Pellegrini-Toole, A., and Krummenacker, M.. "Eco Cyc: encyclopedia of Escherichia coli genes and metabolism." Nucleic Acids Res. 27 (1). 1999. pp. 55-8.
    [ .pdf ] [ PubMed ]

    The EcoCyc database describes the genome and gene products of Escherichia coli, its metabolic and signal-transduction pathways, and its tRNAs. The database describes 4391 genes of E.coli, 695 enzymes encoded by a subset of these genes, 904 metabolic reactions that occur in E.coli, and the organization of these reactions into 129 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways. EcoCyc has many references to the primary literature, and is a (qualitative) computational model of E. coli metabolism. EcoCyc is available at URL http://ecocyc. PangeaSystems.com/ecocyc/

    Keywords: Classification ; *Databases Factual ; Enzymes_genetics ; Enzymes_metabolism ; Escherichia coli_*genetics ; Escherichia coli_*metabolism ; *Genes Bacterial ; Genome Bacterial ; Information Storage and Retrieval ; Internet ; Signal Transduction ; User-Computer Interface


  6. Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., and Kanehisa, M.. "KEGG: Kyoto Encyclopedia of Genes and Genomes." Nucleic Acids Res. 27 (1). 1999. pp. 29-34.
    [ .pdf ] [ PubMed ]

    Kyoto Encyclopedia of Genes and Genomes (KEGG) is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules. The major component of KEGG is the PATHWAY database that consists of graphical diagrams of biochemical pathways including most of the known metabolic pathways and some of the known regulatory pathways. The pathway information is also represented by the ortholog group tables summarizing orthologous and paralogous gene groups among different organisms. KEGG maintains the GENES database for the gene catalogs of all organisms with complete genomes and selected organisms with partial genomes, which are continuously re-annotated, as well as the LIGAND database for chemical compounds and enzymes. Each gene catalog is associated with the graphical genome map for chromosomal locations that is represented by Java applet. In addition to the data collection efforts, KEGG develops and provides various computational tools, such as for reconstructing biochemical pathways from the complete genome sequence and for predicting gene regulatory networks from the gene expression profiles. The KEGG databases are daily updated and made freely available (http://www.genome.ad.jp/kegg/).

    Keywords: Computational Biology ; *Databases Factual ; Gene Expression ; *Genes ; *Genome ; Ligands ; Metabolism ; Sequence Homology