O. Ritter, P. Kocab, M. Senger, D. Wolf, and S. Suhai. Prototype implementation of the integrated genomic database. Computers and Biomedical Research, 27:97--115, 1994.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....the promise of Biomatrix. A rough categorization of the approaches that can be applied to fill in its missing parts is given as follows. Data warehousing, in which data from various data sources are converted, merged, and stored in a centralized DBMS, e.g. Integrated Genomic Database (IGD) [32] and SRS [5] Middleware approaches, in which data are combined from multiple sources without creating a physical warehouse, e.g. BioKleisli [10] TAMBIS [1] and DiscoveryLink [16] etc. Due to the popularity of the Web, many online biological databases provide services through the Web and ....

O. Ritter, P. Kocab, M. Senger, D Wold, and S. Suhai. Prototype implementation of the integrated genomic database. Computers and Biomedical Research, 27:97--115, 1994.

....judge the likelihood of the occurrence of a particular pathway in an organism. Additional ASCII reports contain lists and tables that can be used for a quick overview (executive reports) database submission forms, or export files that can be imported by other systems, e.g. Subtilist [11] or IGD [12]. 14 Making Logical Decisions about Genome Features In order to reason about features of a genome, the output from each remote and local analysis tool is digested into a set of Prolog [13] facts. Each fact represents a statement about a region of the genome. Conclusions about properties of the ....

Ritter O, Kocab P, Senger M, Wolf D, Suhai S (1994) Prototype implementation of the integrated genomic database. Computational Biomedical Research 27, 97-115

....for the Interoperation of Information Sources 1.1 Heterogeneity Most information sources have been independently constructed and are autonomously maintained. Attempts have been made to integrate information from these various information sources into a monolithic information source [1] [2]. Such an approach creates maintenance and scalability problems. When an information source is to be added, the large information source must be restructured. Often such maintenance leads to substantial delays [3] Some researchers have tried to first build a standard ontology or global schema ....

O. Ritter, P. Kocab, M. Senger, D. Wolf, and S. Suhai. Prototype implementation of the integrated genomic database. Computers and Biomedical Research, 27:97--115, 1994.

....easily. Once annotations are generated, each sequence s owner must be contacted to request a modi cation to their data entry, a frustrating and arduous process. Other large comprehensive databases include the Genome Sequence Database (GSDB) 61] EMBL [68] the Integrated Genomic Database (IGD) [58], the Protein Data Bank (PDB) 9] GenoTopographer [14] and Genome Database (GDB) 42] While these databases are often excellent in their primary role as canonical repositories of nucleotide and protein sequence, they are less adept at dealing with annotations. 1.2.2 Curatorial Databases With ....

O. Ritter et al. Prototype implementation of the integrated genomic database. Comput. Biomed Res., 27(2):97-115, 1994.

....generated has, if anything, exceeded the expectations of that report, but fortunately the data is mostly available online, overcoming at least one of the major hurdles in creating the Biomatrix. However, despite substantial efforts at creating unified databases for genomic data (see for example [25]) we have to ask in what sense the ultimate goal of the creating the Biomatrix as a unified database for biological knowledge is attainable. We see a number of very serious obstacles to this: ffl As new experimental techniques are developed and as new generalizations and . laws are ....

....barrier, it provides an important mechanism for practical data source coordination and integration that can substantially affect the overall cost of integration. 4 Sample Solutions and Cost Tight Materialized Autonomous Integration: The Integrated Genome Database (IGD) developed by Ritter [25] represents the most demanding approach to integration: it is an example of a tightly federated, fully materialized database, where each of the twenty or so individual 10 July 12, 1995 resources is fully autonomous with respect to the integration. IGD uses an ACeDB schema and front end. The ....

Ritter, O., Kocab, P., Senger, M., Wolf, D., and Suhai, S. Prototype implementation of the integrated genomic database. Computers and Biomedical Research 27 (1994), 97--115.

....between those two notions of gene but both continue to be used interchangeably causing misunderstanding and making the integration of databases non trivial. The problem of bridging differing semantics exists for both the data warehousing approach of integrating molecular biology databases [Ritter et al. 1994], which physically collects the data to be integrated and stores it into one central database, as for the distributed approach [Fischman, 1996] which provides tools for on line interfacing autonomous databases on different hosts over the Internet or on a local host with a common interface and or ....

Ritter, O., Kocab, P., Senger, M., Wolf, D., and Suhai, S. (1994). Prototype Implementation of the Integrated Genomic Database. Computers and Biomedical Research, 27:97--115.

.... use grammars to translate information records, this approach is relevant to NCBI promotion of standards for database interchanges [4] It is a prerequisite for projects integrating and rediffusing genomic and molecular informations at a large scale, such as shown with GenInfo Backbone [5] or IGD [6]. As used in reference [7] we program with lex (lexical analyzer) and yacc (yet another compiler of compiler) generators for lexical and syntactic analyzers. These standard portable tools were formerly designed to specify programming languages [8] They allow us to describe and analyze rich ....

Ritter O., P. Kocab, M. Senger, D. Wolf& S. Suhai (1994). Prototype Implementation of the Integrated Genomic Database. Computers and Biomedical Research 27, 97--115.

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O. Ritter, P. Kocab, M. Senger, D. Wolf, and S. Suhai. Prototype implementation of the integrated genomic database. Computers and Biomedical Research, 27:97--115, 1994.

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