Hofestadt, R.. "Grammatical formalization of metabolic processes." Proc Int Conf Intell Syst Mol Biol.
vol. 1.
1993.
pp. 181-9.
[ PubMed ]
In the field of biotechnology and medicine it is of interest to model and simulate metabolic processes. The usual methods to model metabolic pathways are chemical descriptions and differential equations. Moreover, the graph theoretical aspect is discussed and the development of expert systems is in process. In this paper we present the formalization of metabolic processes. Our formalization is based on the theory of formal languages. This formalization is called genetic grammar and represents an expansion of the Semi-Thue-System.
Keywords: *Computer Simulation ; *Expert Systems ; Gene Expression ; *Metabolism ; *Models Biological ; Programming Languages
Kanehisa, M. and Goto, S.. "KEGG: kyoto encyclopedia of genes and genomes." Nucleic Acids Res. 28
(1).
2000.
pp. 27-30.
[ .pdf ] [ PubMed ]
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. The genomic information is stored in the GENES database, which is a collection of gene catalogs for all the completely sequenced genomes and some partial genomes with up-to-date annotation of gene functions. The higher order functional information is stored in the PATHWAY database, which contains graphical representations of cellular processes, such as metabolism, membrane transport, signal transduction and cell cycle. The PATHWAY database is supplemented by a set of ortholog group tables for the information about conserved subpathways (pathway motifs), which are often encoded by positionally coupled genes on the chromosome and which are especially useful in predicting gene functions. A third database in KEGG is LIGAND for the information about chemical compounds, enzyme molecules and enzymatic reactions. KEGG provides Java graphics tools for browsing genome maps, comparing two genome maps and manipulating expression maps, as well as computational tools for sequence comparison, graph comparison and path computation. The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/).
Keywords: *Databases Factual ; Gene Expression ; *Genome ; Human ; Information Storage and Retrieval ; Proteins_genetics ; Proteins_metabolism
Kawashima, T., Kawashima, S., Kanehisa, M., Nishida, H., and Makabe, K.W.. "MAGEST: MAboya gene expression patterns and sequence tags." Nucleic Acids Res. 28
(1).
2000.
pp. 133-5.
[ .pdf ] [ PubMed ]
MAGEST is a database for newly identified maternal cDNAs of the ascidian, Halocynthia roretzi, which aims to examine the population of the mRNAs. We have collected 3' and 5' tag sequences of mRNAs and their expression data from whole-mount in situ hybridi-zation in early embryos. To date, we have determined more than 2000 tag-sequences of H.roretzi cDNAs and input them into public databases. The tag sequences and the expression data as well as additional information can be obtained through MAGEST via the WWW at http://www.genome.ad.jp/magest/
Keywords: DNA Complementary ; *Databases Factual ; *Expressed Sequence Tags ; *Gene Expression ; Information Storage and Retrieval ; Urochordata_*genetics
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