Other Databases

Factual databases may provide the electronic version of printed catalogs on chemical compoimds. The catalogs of different suppliers of chemicals serve to identify chemical compounds with their appropriate synonyms, molecular formulas, molecular weight, structure diagrams, and - of course - the price. Sometimes the data are linked to other databases that contain additional information. Structure and substructure search possibihties have now been included in most of the databases of chemical suppliers. 

These are databases that provide links to other databases or data sources. In this case, records describe objects that are other databases. The "Gale Directory of Databases" [14] is one of them. The connection between the databases flows through the meta-data of each database. 

Besides structure and substructure searches, Gmclin provides a special search strategy for coordiuation compouuds which is found in no other database the ligand search system, This superior search method gives access to coordination compounds from a completely different point of view it is possible to retrieve all coordination compounds with the same ligand environment, independently of the central atom or the empirical formula of the compound. 

The SWISS-PROT database [36] release 40.44 (February, 2003) contains over 120 000 sequences of proteins with more than 44 million amino adds abstracted from about 100 000 references. Besides sequence data, bibHographical references, and taxonomy data, there are highly valuable annotations of information (e.g., protein function), a minimal level of redundancy, and a high level of integration with other databases (EMBL, PDB, PIR, etc.). The database was initiated in 1987 by a partnership between the Department of Medicinal Biochemistry of the University of Geneva, Switzerland, and the EMBL. Now SWISS-PROT is driven as a joint project of the EMBL and the Swiss Institute of Bioinformatics (SIB). 

Metadatabases are databases which describe other databases in a comprehensive and stnretured way [51], A prominent example is the DAIN Metadatabase of Internet Resources for Environmental Chemicals kctp //wwMmz.uni-ka el.de/dain) which in 2002 comprised more than 700 entries. This metadatabase is documented in Chapter V, Section 10 of the Handbook, on Databa.scs on Enviromnental Information", It supports the user in finding the right database(s) for their purposes. 

HypcrCliem provides two form s of param eter sets an. ASCII text form and the Td/ / database form eonsistent with dB.ASH IV and a large n iini her of other database packages. Since the prin cipal diffi-ctilty with using molecular mechan ics is having or obtaining appropriate pa ram eters, you may wan t to explore parameter sets as a database in the Tc// /form. 

Nuclear Magnetic Resonance Spectroscopy. Bmker s database, designed for use with its spectrophotometers, contains 20,000 C-nmr and H-nmr, as weU as a combined nmr-ms database (66). Sadder Laboratories markets a PC-based system that can search its coUection of 30,000 C-nmr spectra by substmcture as weU as by peak assignments and by fiiU spectmm (64). Other databases include one by Varian and a CD-ROM system containing polymer spectra produced by Tsukuba University, Japan. CSEARCH, a system developed at the University of Vieima by Robien, searches a database of almost 16,000 C-nmr. Molecular Design Limited (MDL) has adapted the Robien database to be searched in the MACCS and ISIS graphical display and search environment (63). Projects are under way to link the MDL system with the Sadder Hbrary and its unique search capabiHties. 

CHEMINFORMRX from FlZ-Chemie Berlin and CHEMRE CT from Springer-Vedag Infochem GmbH are other databases covering reaction information area. Reaction information is also available from Bedstein, Gmelin, and CA. 

MACCS-II enables direct interface with other database management systems, such as the Relational Database Management System (RDBMS) and Oracle, so that databases which contain text and numeric data for which special interfaces are normally needed can be constmcted. Eor example, an Oracle MACCS-II linked system is currendy being used by the National Institute on Dmg Abuse (113) to develop a database that will allow scientists to determine the molecular stmctures of cocaine and other controlled substances as well as designer dmgs. 

Other Databases with Patent Information. The APIPAT database has been discussed, as have the unique capabihties of the merged WPI—APIPAT file on ORBIT. Many other databases contain substantial amounts of patent information, notable among them are Derwent s biotechnology Abstracts the TULSA database (petroleum exploration and production), several specialized pharmaceutical files, PAPERCHEM, and METADEX. A very complete listing of databases containing patent information circa 1990 has been prepared (38). 

In the biosciences, a database is a curated repository of raw data containing annotations, further analysis, and links to other databases. Examples of databases are the SWISSPROT database for annotated protein sequences or the FlyBase database of genetic and molecular data for Drosophila melanogaster. 

Database What is the underlying database Can it integrate data from other databases Can it convert the database to a different database type ... 

Maintains the EMBL Nucleotide and SWISS-PROT databases as well as other databases.)... 

MSDB (ftp //ftp.ncbi.nih.gov/repository/MSDB), database created especially for MS applications. Contains nonidentical protein sequences obtained from other databases (PIR, TrEMBL, SwissProt). At http // www.matrixscience.com/help/seq db setup msdb.html, a guidebook for MSDB users can be found. 

The latter are vast sites with links to other databases for pharmaceutical support sites—http //www.MedsiteNavigator.com... 

NIOSH 2001. NIOSH Pocket Guide to Chemical Hazards and Other Databases. U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health. DHHS (NIOSH) Publication No. 2001-145. August. 

This is, in our opinion, the primary source of thermochemical values and therefore it should be the starting point of all the other databases. The selections have been made by the Task Group on Key Values for Thermodynamics appointed in 1968 by the Committee on Data for Science and Technology (CODATA) of the International Council of Scientific Unions. Unfortunately, the number of species for which data are recommended in the final report is rather small ( 150). 

The NBS 82 tables are still widely used, mainly because they contain data (e.g., solution enthalpies) not easily found in other databases. 

Prosite is perhaps the best known of the domain databases (Hofmann et al., 1999). The Prosite database is a good source of high quality annotation for protein domain families. Prosite documentation includes a section on the functional meaning of a match to the entry and a list of example members of the family. Prosite documentation also includes literature references and cross links to other databases such as the PDB collection of protein structures (Bernstein et al., 1977). For each Prosite document, there is a Prosite pattern, profile, or both to detect the domain family. The profiles are the most sensitive detection method in Prosite. The Prosite profiles provide Zscores for matches allowing statistical evaluation of the match to a new protein. Profiles are now available for many of the common protein domains. Prosite profiles use the generalized profile software (Bucher et al., 1996). 

The BLOCKS database contains blocks for each family (Henikoff and Henikoff, 1991 Henikoff et al., 1999). Blocks are ungapped multiple sequence alignments that are exacdy equivalent to the motifs found in the PRINTS database. The families in BLOCKS are currently derived from Prosite and PRINTS families. The bulk of BLOCKS entries are constructed from Prosite, using the lists of true positive members they provide. Motifs are automatically derived from the members of the Prosite family. Note that BLOCKS does not use the Prosite patterns to construct its motifs. BLOCKS provides functionality to search motifs against motifs this feature is not provided by other databases. 

Databases, generally available for a fee, often together with software packages, have been prepared for several types of materials and systems. Typical examples are a database developed for Fe-rich alloys containing data for up to 15 components, and 55 types of phases or similar databases for Mg-rich, Al-rich, Ni-rich, Ti-rich alloys. Other databases are available for different types of materials semiconductors, solder alloys, ceramic systems, slag, molten salts, etc. 

In addition to resources maintained by official agencies, other databases exist that are commercial ventures addressing medical professionals. Here are some examples that may interest you ... 

Other databases, including DNA and protein databases, the Human Genome Database (GDB), and Medline. Two relatively new query systems in OMIM, OMIM Gene Map and OMDVt Morbid Map, provide cytogenetic map locations of diseases and gene lists organized by diseases, respectively. 

All WDI entries include similar and related functions. Similar shows structures within WDI and related gives a list of other databases where this substance or related structures appear. 

When the related button above the structure is selected, a list of similar structures in other databases is shown. Empath, Planet, TCM and WOMBAT are found. In Planet, the closest structure is IHWK. Selecting it brings up the Planet version of the PDB... 

One method of enhancing safety knowledge is to learn from the experience of others. (See Chapter 15.) A sampling of industry databases that contain information about incidents is presented below in Table 11-3. An internet search can help the user in locating and evaluating these and other databases. 

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