Core database

GORE. The CORE Electronic Chemistry Library is a joint project of Cornell University, OCLC (On-line Computer Library Center), Bell Communications Research (Bellcore), and the American Chemical Society. The CORE database will contain the full text of American Chemical Society Journals from 1980, associated information from Chemical Abstracts Service, and selected reference texts. It will provide machine-readable text that can be searched and displayed, graphical representations of equations and figures, and full-page document images. The project will examine the performance obtained by the use of a traditional printed index as compared with a hypertext system (SUPERBOOK) and a document retrieval system (Pixlook) (6,116). 

The user employs a graphical workflow builder to compose an analytic workflow built from a core database of statistical tasks or from the domain-specific modules. 

The LIMS manager is typically responsible for the daily administration of the entire LIMS (core database, LIMS servers, peripheral devices [e.g., printers, user PCs, etc.], networks). The manager must respond to user requests and problems in agreed-on timescales as he or she is providing a service to the laboratory. The duties include... 

The modem process information system is shown in Fig. 2-9. The basis of the whole system is the core database of process variables. Typical variables which are stored in such database are flows, inventories, temperatures, laboratory data, etc. The other data needed for balancing are in a databank of physical properties needed for setting up energy balances. The system is based on a Local Area Network (LAN) which makes possible the use of the database by other software and plant staff (clients of the information system). 

The data input to the core database can be from Distributed Control Systems (DCS), laboratory systems or other process databases. In practice also the manual entries must be available as DCS are usually not available in all plants of the company. 

For a comparison of PLA ecoprofiles with traditional petrochemical-based polymers the same methodology, software, and core databases were developed as used in the Association of Plastics Manufacturers of Europe (APME) analyses. The APME has over the last ten years published a series of ecoprofiles for traditional petrochemical-based polymers [12]. 

The air and water emissions, waste generations, and pollution can be calculated based on the software developed with Plastics Europe and a series of published EcoProfiles for traditional petroleum-based polymers. The same methodology, software, and core databases developed an Ecoprohle for Ingeo. All calculahons followed ISO 14040 and 14044 requirements (Vink et al. 2010). 

GeoScienceworld http //www.geoscienceworld.org/ (accessed June 9, 2010). A comprehensive Internet resource for research and communications in the geosciences, built on a core database aggregation of peer-reviewed journals indexed, linked, and interoperable with GeoRef... 

An analysis of the ORAC CORE reaction database of over 50,000 reactions shows that approximately 15% of the reactions are linked to other reactions via implicit links. We estimate that there are about 25,000 implicit links between reactions in the ORAC CORE database. However, implicit links between reactions in different selective databases are much less common due to the variation in the type of chemistry and examples used. The distribution of links between reactions is very dependent on the reactant and product structures. Common reactants, such as benzaldehyde, may account for a relatively high percentage of implicit links in a reaction database. 

This is a combined archival database with 171629 reactions originating predominantly from about 300 Journals and some patents. It comprises the Theilheimer databa.se (46785 reactions 1946-1980), the core database from the former ORAC system (about 65 000 reactions, mainly 1980-1991), and several databases produced by MDL (CLF Current Literature File 36600 general synthetic reactions 1983-1991. CHIRAS 13 200 asymmetric reactions 1975-1991. Metalysis 12000 metal-mediated reactions 1974-1991). Although the time coverage of RefLib does really start at 1946, the onset of Theilheimer, there are almost 4000 reactions with pre-1946 references (2600 with literature only before that year). 

ORAC was developed by A. P. Johnson et al., at Leeds University, and was later produced by ORAC Ltd. Since the takeover by MDL, ORAC has no longer been upgraded, but its core database (about 65000 reactions, coverage mainly since 1980, but with a significant number of earlier reactions) survives as part of MDL s RefLib (.see Section 3.2.3). ORAC had a few outstanding features that appeared only later in other reaction-retrieval systems, or are still missing in them thesaurus-based reaction classification (see Section 4.11), both bonds or atoms definable as reaction centers, both explicit... 

Hash codes of molecules which are already pre-computed are suitable for use in fiill structure searches in database applications. The compression of the code of a chemical structure into only one number also makes it possible to compute in advance the transformation results for a whole catalog. The files can be stored and kept complete in the core memory during execution of the program, so that a search can be accomplished within seconds. 

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. 

Ithough knowledge-based potentials are most popular, it is also possible to use other types potential function. Some of these are more firmly rooted in the fundamental physics of iteratomic interactions whereas others do not necessarily have any physical interpretation all but are able to discriminate the correct fold from decoy structures. These decoy ructures are generated so as to satisfy the basic principles of protein structure such as a ose-packed, hydrophobic core [Park and Levitt 1996]. The fold library is also clearly nportant in threading. For practical purposes the library should obviously not be too irge, but it should be as representative of the different protein folds as possible. To erive a fold database one would typically first use a relatively fast sequence comparison lethod in conjunction with cluster analysis to identify families of homologues, which are ssumed to have the same fold. A sequence identity threshold of about 30% is commonly... 

The most successful and user-friendly approach, which is now adopted by virtually all commercial systems, is the fill-in-the-forms or table-driven process control languages (PCLs). The core of these languages is a number of basic functional blocks or software modules. AU modules are defined as database points. Using a module is analogous to calhng a subroutine in conventional programs. 

There are two main classes of loop modeling methods (1) the database search approaches, where a segment that fits on the anchor core regions is found in a database of all known protein structures [62,94], and (2) the conformational search approaches [95-97]. There are also methods that combine these two approaches [92,98,99]. 

Homologous proteins have similar three-dimensional structures. They contain a core region, a scaffold of secondary structure elements, where the folds of the polypeptide chains are very similar. Loop regions that connect the building blocks of the scaffolds can vary considerably both in length and in structure. From a database of known immunoglobulin structures it has, nevertheless, been possible to predict successfully the conformation of hyper-variable loop regions of antibodies of known amino acid sequence. 

Similar residues in the cores of protein structures especially hydrophobic residues at the same positions, are responsible for common folds of homologous proteins. Certain sequence profiles of conserved residue successions have been identified which give rise to a common fold of protein domains. They are organized in the smart database (simple modular architecture research tool) http //smait.embl-heidelberg.de. 

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