Database query

To evaluate the performance of the descriptors one needs a database of compoimds for which the biological activities are known, e.g.. either the MDDR or the NCI databases. Queries are selected that are typical of a drug-hke molecule and from therapeutic categories that... 

Data mining in chemistry focuses on the extraction and evaluation of information in chemical data sets. In contrast to other fields of data mining applications, chemical data mining does not confine itself to conventional database queries but rather generates new information from the data. 

A most important task in the handling of molecular data is the evaluation of "hidden information in large chemical data sets. One of the differences between data mining techniques and conventional database queries is the generation of new data that are used subsequently to characterize molecular features in a more general way. Generally, it is not possible to hold all the potentially important information in a data set of chemical structures. Thus, the extraction of relevant information and the production of reliable secondary information are important topics. 

Another important feature of a LIMS DBMS is the abiUty to perform ad hoc database queries. It is impossible to predict all the forms in which LIMS users will want to display their data while the LIMS is being designed. As a result, it is desirable to select a LIMS which allows users to define their own reports. Most commercial DBMS have a standard query language (SQL) interface. SQL is a simple database query tool which is based on... 

J. H. van Drie, Strategies for the determination of pharmacophoric 3D database queries,... 

If a protein mixture was digested, the database query may give an ambiguous result because there is no single protein that produces, on digestion, the measured set of peptides. Sometimes this can be compensated for by sequentially subtracting the peptide masses of the first identified protein from the mass set and rerunning the database search (Jensen et al., 1997) but if one protein was less abundant, it is likely to be missed completely in the database search. 

The unit of a wrapper with its associated program or database query is called an analyzer. Analyzers are often highly specific. The correctness of their results depends partially on certain conditions, such as the taxonomic specification. Annotation added by an analyzer is often in turn exploited by other analyzers executed later. EDITtoTrEMBL uses the conditions, which are stored in the RuleBase, for the execution of analyzers. Dispatchers, programs that coordinate the flow of entries between different analyzers, evaluate these conditions. 

CA EPA 1998. USEPA/OPP Pesticide related database queries OPP s registered and cancelled pesticide product database. California Environmental Protection Agency. Internet http //www.cdpr.ca.gov/docs/epa/epamenu.htm. Accessed on Nov. 6, 1998. 

Hall et al. (1985) reported that no 1,2-diphenylhydrazine (less than pg/L) was detected in the Nanticoke River near the Chesapeake Bay. The analytical method involved liquid-liquid extraction, concentration, and. analysis by GC/MS. The Contract Laboratory Program statistical database (queried April 13, 1987) reported that 1 2-diphenylhydrazine has been detected n water at i of 357 hazardous waste sites at a concentration of (96 ppb (CLPSDB 1987), and has been reported at 7 of 117, sites. n the national Priority List database (ATSDR 1990) The U.S. EPA Contract laboratory Program uses GC methods to analyze the contaminants of interest. Since 1,2-diphenylhydrazine oxidize, to azobenzene in the GC injector port and both 1,2-diphenylhydrazine and azobenzene, have the same GC retention time and mass spectra, reports of 1,2-diphenylhydrazine from the Contract Laboratory Program may actually represent detections of 1,2-diphenylhydrazine, azobenzene, or both (see Chapter 6 for more details). 

Diphenylhydrazine has been identified in soil only at hazardous waste sites. The Contract Laboratory Program statistical database (queried April 13, 1987) reported that 1,2-diphenylhydrazine has been detected in the soil at 2 of 357 hazardous waste sites in both cases at 18,200 ppm (CLPSDB 1987). The Contract Laboratory Program uses GC methods to analyze the contaminants of interest. As discussed in Section 5.4.2, this may actually represent detections of either... 

The TSCATS database of EPA is part of CIS , and included when this chapter was written more than 24000 documents about over 8400 substances, usually supplied by big industrial enterprises. They mostly relate to toxicological, environmental and other safety issues. Entries of Table 1 carrying note / are included in this database. Queries about TSCATS can be sent to cissupport nisc.com. 

The registry object, defined as an instance variable of the AbstractMapper class, caches the entity objects in a map, the primary key of the object as the key and the object as the value. The abstractFind() method performs a lookup in the registry and returns the object being searched if it is already in the cache. Otherwise it performs a database query, calls the load() method to build tlie entity object, and returns it. 

Information Retrieval and Reporting. Ad hoc retrieval and reporting of data using Datatrieve and other VAX languages is an important feature of LIMS as it is impossible to foresee all the future requirements for reports. The Database Query Language utility (DBQ) is used to retrieve, update and report data from compiled BASIC, PASCAL or other VAX languages. Data Manipulation Language (DML) is used by FORTRAN to access the data. 

VanDrie, J.H. Strategies for the determination ofpharmacophoric 3D database queries, J. Comput.-AidedMol. Des., 1997,11,39-52. 

Data archiving limits the growth of databases allowing database queries, report generation, data writes, and amendments to be completed within the performance requirements for ongoing operation. 

An example of where field definition can improve the database integrity is simply date format, which is especially critical for data shared between organizations in the United States and other parts of the world. If a database query is entered for records between 1/4/02 and 7/4/02, should the database interpret this as January 4 to July 4 or April 1 to April 7 If the field is defined to display dates in a dd-mm-yy format, 04-Jul-02 will be unambiguously interpreted. 

Markush Structure. Essentially a generic structure, in which a root or parent structure plus Rgroups and their members can represent an entire combinatorial library. Markush structures were developed for patent purposes, and the specification of substituents are often more general than in the case of generic structures or database queries. Markush structures are also used to represent generic reactions, in which the reactants and products are represented by generic structures. 

Experience Matters. In every aspect of SBDD, as in all technical fields, there is no substitute for experience. Given the variety of different techniques that must be incorporated, this means that experience from several different people will be needed for optimal function of a discovery project team. Essential expertise is needed in X-ray crystallographic studies, graphical display of experimental results, initial and iterative design of compounds and synthetic tactics, the creation of databases and database queries, and the analyses of search outputs and of the results of computational simulation experiments. 

On 30 November 2000,1.4 million doses of vaccine had been distributed. From January 1999 to the time of the database query, there was no evidence that the incidence of these arthritic conditions was higher than reported in the general population or that they were associated with an autoimmune process (7). 

Tripos mainly contains StereoPlex that is designed specifically to address the need for additional stereomers in your 3D databases. StereoPlex functions as a 3D database-extender and can be used either by itself or as a CON CORD pre-processor. What is more, when compounds have more than a single stereocenter, StereoPlex actually increases the 3D shape diversity of the databases, thus becoming a data-hase-diversifier. While diastereomers and enantiomers often look the same to distance-based pharmacophores or database queries, to biological receptors they are as different as night and day. StereoPlex has several features ... 

The Green Synthetic Reactions module is database query module to find references related to selected synthetic processes, particularly those that act as examples of... 

As well as the usual indices, link indices can be built which allow for navigation between databases or cross-database queries. Two fields from different databanks must be specified as having a link between them. 

This program takes the S. cerevisiae reference sequence for each locus and runs a Blast search against the Rfam database. If there is a hit with an expectation value below some cutoff (default E < 10 the name of the matching database query is added as a new field to the data file. Please note that the locations of the sequence data files and the blast index files on the command-line must be specified. 

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