Ellis, L.B., Hershberger, C.D., Bryan, E.M., and Wackett, L.P.. "The University of Minnesota Biocatalysis/Biodegradation Database: emphasizing enzymes." Nucleic Acids Res. 29
(1).
2001.
pp. 340-3.
[ .pdf ] [ PubMed ]
The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.ahc.umn.edu/) provides curated information on microbial catabolic enzymes and their organization into metabolic pathways. Currently, it contains information on over 400 enzymes. In the last year the enzyme page was enhanced to contain more internal and external links; it also displays the different metabolic pathways in which each enzyme participates. In collaboration with the Nomenclature Commission of the International Union of Biochemistry and Molecular Biology, 35 UM-BBD enzymes were assigned complete EC codes during 2000. Bacterial oxygenases are heavily represented in the UM-BBD; they are known to have broad substrate specificity. A compilation of known reactions of naphthalene and toluene dioxygenases were recently added to the UM-BBD; 73 and 108 were listed respectively. In 2000 the UM-BBD is mirrored by two prestigious groups: the European Bioinformatics Institute and KEGG (the Kyoto Encyclopedia of Genes and Genomes). Collaborations with other groups are being developed. The increased emphasis on UM-BBD enzymes is important for predicting novel metabolic pathways that might exist in nature or could be engineered. It also is important for current efforts in microbial genome annotation.
Keywords: Bacteria_genetics ; Bacteria_metabolism ; Biodegradation ; Catalysis ; *Databases Factual ; Enzymes_genetics ; Enzymes_*metabolism ; Fungi_genetics ; Fungi_metabolism ; Information Storage and Retrieval ; Internet
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
Kanehisa, M., Goto, S., Kawashima, S., and Nakaya, A.. "The KEGG databases at GenomeNet." Nucleic Acids Res. 30
(1).
2002.
pp. 42-6.
[ .pdf ] [ PubMed ]
The Kyoto Encyclopedia of Genes and Genomes (KEGG) is the primary database resource of the Japanese GenomeNet service (http://www.genome.ad.jp/) for understanding higher order functional meanings and utilities of the cell or the organism from its genome information. KEGG consists of the PATHWAY database for the computerized knowledge on molecular interaction networks such as pathways and complexes, the GENES database for the information about genes and proteins generated by genome sequencing projects, and the LIGAND database for the information about chemical compounds and chemical reactions that are relevant to cellular processes. In addition to these three main databases, limited amounts of experimental data for microarray gene expression profiles and yeast two-hybrid systems are stored in the EXPRESSION and BRITE databases, respectively. Furthermore, a new database, named SSDB, is available for exploring the universe of all protein coding genes in the complete genomes and for identifying functional links and ortholog groups. The data objects in the KEGG databases are all represented as graphs and various computational methods are developed to detect graph features that can be related to biological functions. For example, the correlated clusters are graph similarities which can be used to predict a set of genes coding for a pathway or a complex, as summarized in the ortholog group tables, and the cliques in the SSDB graph are used to annotate genes. The KEGG databases are updated daily and made freely available (http://www.genome.ad.jp/kegg/).
Keywords: Computational Biology ; Computer Graphics ; *Databases Genetic ; *Databases Protein ; Gene Expression Profiling ; *Genome ; Human ; Information Storage and Retrieval ; Internet ; Macromolecular Systems ; Metabolism_genetics ; Multigene Family ; Protein Conformation ; Proteins_chemistry ; Proteins_genetics ; Proteins_metabolism ; Sequence Homology
Kawashima, T., Kawashima, S., Kohara, Y., Kanehisa, M., and Makabe, K.W.. "Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags." Nucleic Acids Res. 30
(1).
2002.
pp. 119-20.
[ .pdf ] [ PubMed ]
MAGEST is a database for maternal gene expression information for an ascidian, Halocynthia roretzi. The ascidian has become an animal model in developmental biological research because it shows a simple developmental process, and belongs to one of the chordate groups. Various data are deposited into the MAGEST database, e.g. the 3'- and 5'-tag sequences from the fertilized egg cDNA library, the results of similarity searches against GenBank and the expression data from whole mount in situ hybridization. Over the last 2 years, the data retrieval systems have been improved in several aspects, and the tag sequence entries have increased to over 20 000 clones. Additionally, we constructed a database, translated MAGEST, for the amino acid fragment sequences predicted from the EST data sets. Using this information comprehensively, we should obtain new information on gene functions. The MAGEST database is accessible via the Internet at http://www.genome.ad.jp/magest/.
Keywords: Amino Acid Sequence ; DNA Complementary_genetics ; *Databases Genetic ; *Expressed Sequence Tags ; Forecasting ; *Gene Expression Regulation ; Developmental ; Gene Library ; In Situ Hybridization ; Information Storage and Retrieval ; Internet ; RNA Messenger Stored_biosynthesis ; Urochordata_*embryology ; Urochordata_*genetics ; Urochordata_metabolism ; Zygote_metabolism
Karp, P.D., Riley, M., Paley, S.M., and Pellegrini-Toole, A.. "The MetaCyc Database." Nucleic Acids Res. 30
(1).
2002.
pp. 59-61.
[ .pdf ] [ PubMed ]
MetaCyc is a metabolic-pathway database that describes 445 pathways and 1115 enzymes occurring in 158 organisms. MetaCyc is a review-level database in that a given entry in MetaCyc often integrates information from multiple literature sources. The pathways in MetaCyc were determined experimentally and are labeled with the species in which they are known to occur based on literature references examined to date. MetaCyc contains extensive commentary and literature citations. Applications of MetaCyc include pathway analysis of genomes, metabolic engineering and biochemistry education. MetaCyc is queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools. MetaCyc is available via the World Wide Web at http://ecocyc.org/ecocyc/metacyc.html, and is available for local installation as a binary program for the PC and the Sun workstation, and as a set of flatfiles. Contact metacyc-info
Keywords: Comparative Study ; Database Management Systems ; *Databases Protein ; Enzymes_chemistry ; Enzymes_*metabolism ; Genome ; Human ; Information Storage and Retrieval ; Internet ; *Metabolism
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
Karp, P.D., Riley, M., Saier, M., Paulsen, I.T., Collado-Vides, J., Paley, S.M., Pellegrini-Toole, A., Bonavides, C., and Gama-Castro, S.. "The EcoCyc Database." Nucleic Acids Res. 30
(1).
2002.
pp. 56-8.
[ .pdf ] [ PubMed ]
EcoCyc is an organism-specific pathway/genome database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, its transport proteins and its mechanisms of transcriptional control of gene expression. EcoCyc is queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools. EcoCyc is available at http://ecocyc.org/.
Keywords: Database Management Systems ; *Databases Genetic ; Escherichia coli_*genetics ; Escherichia coli_*metabolism ; Escherichia coli Proteins_*genetics ; Escherichia coli Proteins_*physiology ; Gene Expression Regulation Bacterial ; *Genome Bacterial ; Information Storage and Retrieval ; Internet ; Protein Transport ; Signal Transduction
Karp, P.D.. "Pathway databases: a case study in computational symbolic theories." Science. 293
(5537).
2001.
pp. 2040-4.
[ .pdf ] [ PubMed ]
A pathway database (DB) is a DB that describes biochemical pathways, reactions, and enzymes. The EcoCyc pathway DB (see http://ecocyc.org) describes the metabolic, transport, and genetic-regulatory networks of Escherichia coli. EcoCyc is an example of a computational symbolic theory, which is a DB that structures a scientific theory within a formal ontology so that it is available for computational analysis. It is argued that by encoding scientific theories in symbolic form, we open new realms of analysis and understanding for theories that would otherwise be too large and complex for scientists to reason with effectively.
Keywords: Artificial Intelligence ; *Computational Biology ; Culture Media ; *Databases Factual ; Escherichia coli_enzymology ; Escherichia coli_*genetics ; Escherichia coli_growth and development ; Escherichia coli_*metabolism ; *Genome Bacterial ; Internet ; Software