Integrated database

The IntegrS portal (http //ebi.ac.uk/integr8) offers an overview of information about organism with completely sequenced genomes, statistical analysis of their genomes/ proteomes individually and comparatively. The database is build on three main sources (Kersey et al, 2005)  

genome reviews of annoted genome sequences from multiple sources  

nonredundant sets of UniProt entries representing completed proteomes and 

IPI (International Protein Index) with comprehensive protein sets for certain higher metazoan species. 

InterPro http //www.ebi.ac.uk/interpro Integration of aU the domain families from established databases such as Pfam, PRINTS, SMART, Tigrfam, SCOP and CATH and mapping them onto the genome sequences. 

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A strict separation of these three types of databases is difficult hence most databases contain a mixture of data types. Therefore the classification given here is based on the predominating data type. For example, the major emphasis of a patent database is on hterature, whereas it also comprises numeric and structural data. Another type is the integrated database, which provides a supplement of additional information, especially bibhographic data. Thus, different database types are merged, a textual database and one or more factual databases. 

One of the more prominent integrated databases is provided by CAS - the Registry CAPLUS, CA, CAOLD. All of these diverse databases are based on the... 

Compounds are stored in reaction databases as connection tables (CT) in the same manner as in structure databases (see Section 5.11). Additionally, each compound is assigned information on the reaction center and the role of each compound in the specific reaction scheme (educt, product, etc.) (see Chapter 3). In addition to reaction data, the reaction database also includes bibliographic and factual information (solvent, yield, etc.). All these different data types render the integrated databases quite complex. The retrieval software must be able to recall all these different types of information. 

Patent databases are therefore integrated databases because facts, text, tables, graphics, and structures are combined. In patents that include chemical aspects (mostly synthesis or processing), the chemical compounds are often represented by Markush structures (see Chapter 2, Section 2.7.1). These generic structures cover many compound families in a very compact maimer. A Markush structure has a core structure diagram with specific atoms and with variable parts (R-groups), which are defined in a text caption. The retrieval of chemical compounds from Markush structures is a complicated task that is not yet solved completely satisfactorily. 

Integrated DataBase for 1993 U.S. Spent Fuel and Raidioactive Waste Inventories, Projections, and Characteristics, DOE/RW-0006, Rev. 9, Oak Ridge National Laboratory, Oak Ridge, Term., Feb. 1994. 

Whether there are any possibilities of developing integrated databases between customer and major contractors. If not, the customer to provide reporting guidelines. 

Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y., and Kanehisa, M. (1998). DBGET/LinkDB an Integrated Database Retrieval System. Pacific Symp. Biocomputing 98. R. B. Altman, A. K. Dunker, L. Hunter, and T. E. Klein, eds.), pp. 683-694, World Scientific, Singapore. 

Bahl, a., et al. PlasmoDB the Plasmodium genome resource. An integrated database that provides tools for accessing, analysing and mapping expression and sequence data (both finished and unfinished). Nucl. Acids Res. 

Roter AH. (2005) Large-scale integrated databases supporting drug discovery. Curr. Opin. Drug Discov. Devel. 8 309-315. 

In terms of more conventional modelling it is surprising to find that there is still incompatibility between databases that handle complex metallic materials and slags. Sound databases exist for both separately but as yet there is no major integrated database that can handle the very important area of overlap. In terms of a total materials modelling capability it is clearly of benefit to have one self-consistent database rather than a series of separate ones to span a greater range of applications. 

Science, P. (2003) Poms Science, Integrity database http //www.prous.com. 

Singh AV et al (2007) Integrative database management for mouse development systems and concepts. Birth Defects Res C Embryo Today 81 1-19. doi 10.1002/bdrc.20089... 

Dan S, Tsunoda T, Kitahara O et al. An integrated database of ehemosensitivity to 55 antieancer drugs and gene expression profiles of 39 human cancer cell lines. Cancer Res 2002 62 1139-1147. 

Networked systems with integrated databases are used extensively in the pharmaceutical industry. These are computerized systems, and as such, must be qualified and validated to demonstrate suitability of their intended use. While validation of stand-alone computer systems is well described [8] and understood, there is still uncertainty on how to qualify networks and networked systems. On the other hand, inspectors are looking more and more into such systems, and validation of... 

Matejicek L (2005) Spatial modeling of air pollution in urban areas with GIS a case study on integrated database development. Adv Geosci 4 63-68... 

The amino acid sequences of proteins and nucleotide sequences of DNA can be retrieved from the integrated database retrieval systems Entrez (http //... 

Nakamura, R., Teshima, R., Takagi, K., and Sawada, J. 2005. Development of Allergen Database for Food Safety (ADFS) An integrated database to search allergens and predict allergenicity. Kokuritsu lyakuhin Shokuhin Eisei Kenkyusho Hokoku 123 32-36. 

Coutinho, P., and Henrissat, B. 1999. The modular structure of cellulases and other carbohydrate-active enzymes an integrated database approach. In Ohmiya, K., Hayashi, K., Sakka, K., Kobayashi, Y., Karita, S., and Kimura, T. (Eds.), Genetics, Biochemistry and Ecology of Cellulose Degradation. Tokyo Uni Publishers Co., Ltd. 

Security protection is provided to assure data integrity. Database access is controlled to prevent unauthorized user access (for example, to sensitive areas) and to prevent unauthorized operations (for example, delete a record). 

Kulp, D Haussler, D Reese, M. G. Eeckman, F. H. (1997). Integrating database homology in a probabilistic gene structure model. Pac Symp Biocomput, 232-44. 

Kersey, P. )., Duarte, )., Williams, A., Karavidopoulou, Y, Birney, E., Apweiler, R. (2004). The International Protein Index an integrated database for proteomics experiments. Proteomics 4, 1985-1988. 

Hu, Z., Barker, W. C. (2004). The iProClass integrated database for protein functional analysis. Comput. Biol. Chem. 28, 87-96. 

Coutinho, P.M. and Henrissat, B. (1999) Carbohydrate-active enzymes an integrated database approach, in Recent Advances in Carbohydrate Bioengineering... 

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