Database work

In systems presenting complex equilibria, not all the equilibria are, or even can be, determined experimentally. One of the advantages of calculated 

Four thermodynamic sub-databases have been created to enable the thermodynamic calculations for the OPTICORR project  

The database created especially for Ni-based alloys contains the thermodynamic data for all the phases significant in conunercial alloys, such as carbides M23C6, M3C2, MeC, M7C3, MC-eta, nitrides, silicides. Laves phases, P, R, mu and sigma phases. 

4 The assessed phase diagram Fe-Ce compared with experimental data [7]. 

5 The calculated activity coefficients of Ce in molten Fe (experimental points from references [8] and [9]). 

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It is to be emphasized that such database work is often complicated, and requires a team of professionals comprising physician and nonphysician pharmacoepidemiologists, statisticians and specialists in information technology. Perhaps one of the greatest contributions that a clinician can make to such a team is to provide relevance to the hypotheses that are tested and as a reality check on the results that the computers generate, and which those less close to the field tend to regard automatically as fact . 

NCBI Handbook Guide to Databases and Bioinformatics. 2003-. National Center for Biotechnology Information, NLM, NIH. URL http //www.ncbi.nlm.nih.gov/books/bv.fcgi call=bv.View.ShowSection rid=handbook. NCBI databases and search engines with information on how the databases work and how they can be leveraged for bioinformatics research on a larger scale. 

At the NEA Data Bank, Pierre Nagel and Eric Lacroix have provided excellent software and advice, which have eased the editorial and database work. Cynthia Picot, Solange Quarmeau and Amanda Costa from NEA Publications have provided considerable help in editing the present series. Their contributions and the support of many NEA staff members are highly appreciated. 

But large changes were in the offing. Proposals had been made to reorganise the SRC permanent laboratories, and these were about to be acted on. Their consequence for this story is the shifting of the computational chemistry focus from Atlas to Daresbury Laboratory, as mentioned above. But before going on to consider the developments after the change of location, it is useful to back-track a little and consider the chemical database work done at Atlas lab. 

Much more could be (and has been) written on this subject. Suffice it to say here that NIR is a proven route to the detection of counterfeit currency, and because of the relatively and unavoidably small database, work should be ongoing to thwart the efforts of counterfeiters. LANL offered this work as an R D 100 Contest entry in 1996 under the title SuperScan Counterfeit Currency Detector but it was not among the top 100. Moreover, the FBI and SS seemed disinterested, saying there is no problem. However, an invention disclosure was filed and a patent [9] issued. 

The implementation is distributed in that individual databases may reside on any network-accessible host. Apart from the added complexities of networks and communication software, co-ordination of combined searches over distributed databases works the same, independent of the physical location of the database. This effectively isolates the end-user from any requirement to know where data reside, and in what DBMS. 

Other geographical units (e.g. the Taxonomic Databases Working Group (TDWG) geographical categories) can be difficult. 

Multinational data management systems are the most use to the wider community as both personal and institutional systems are rarely widely known about or accessible (although some institutionally held datasets are made available via the World Wide Web). Although standards for the exchange of biodiversity data have been developed by Biodiversity Information Standards (a not-for-profit scientific and educational association formerly known as the Taxonomic Database Working Group), conditions of data submission and data retrieval from multinational systems vary. 

The techmque was first employed, in real-world conditions, for monitoring external corrosion in the large diameter steel tubing used for oil well casings. In the late fifties, T.R. Schmidt at Shell Developments, pioneered the technique in those demanding applications, although the technique itself was invented, by W.R. MacLean, (Ref. 1) somewhat earlier. T.R Schmidt has written a history (Ref. 2) of much of the early work in the technology, which contains many references, others which may be of interest are held on the NTIAC database (Ref 3). 

It was reahzed quite some decades ago that the amount of information accumulated by chemists can, in the long run, be made accessible to the scientific community only in electronic form in other words, it has to be stored in databases. This new field, which deals with the storage, the manipulation, and the processing of chemical information, was emerging without a proper name. In most cases, the scientists active in the field said they were working in "Chemical Information . However, as this term did not make a distinction between librarianship and the development of computer methods, some scientists said they were working in "Computer Chemistry to stress the importance they attributed to the use of the computer for processing chemical information. However, the latter term could easily be confused with Computational Chemistry, which is perceived by others to be more limited to theoretical quantum mechanical calculations. 

In 1967, work was presented from a Sheffield group on indexing chemical reactions for database budding. In 1969, a Harvard group presented its first steps in the development of a system for computer-assisted synthesis design. Soon afterwards, groups at Brandeis University and TU Munich, Germany, presented their work in this area. 

Unfortunately, in most cases not all the available information on a reaction is given in the reaction equation in a publication, and even less so in reaction databases. To obtain a fuller picture of the reaction that was performed, the text describing the experimental procedure in the publication or a lab journal) would have to be consulted. Reaction products that are considered as trivial, such as water, alcohol, ammonia, nitrogen, etc., are generally not included in the reaction equation or mentioned in the text describing the experimental work. This poses serious problems for the automatic identification of the reaction center. It is highly desirable to have the full stoichiometry of a reaction specified in the equation. 

We shall discuss here the methods that have been developed for enabling the computer to perceive both complete chemical structures and fragments of them, as well as their mutual similarity. This is very important in many fields of chemistry, The recognition of flill structures is required routinely in everyday work with large databases. 

A number of other software packages are available to predict NMR spectra. The use of large NMR spectral databases is the most popular approach it utilizes assigned chemical structures. In an advanced approach, parameters such as solvent information can be used to refine the accuracy of the prediction. A typical application works with tables of experimental chemical shifts from experimental NMR spectra. Each shift value is assigned to a specific structural fragment. The query structure is dissected into fragments that are compared with the fragments in the database. For each coincidence, the experimental chemical shift from the database is used to compose the final set of chemical shifts for the... 

In spite of the importance of reaction prediction, only a few systems have been developed to tackle this problem, largely due to its complexity it demands a huge amount of work before a system is obtained that can make predictions of sufficient quality to be useful to a chemist. The most difficult task in the development of a system for the simulation of chemical reactions is the prediction of the course of chemical reactions. This can be achieved by using knowledge automatically extracted from reaction databases (see Section 10.3.1.2). Alternatively, explicit models of chemical reactivity will have to be included in a reaction simulation system. The modeling of chemical reactivity is a very complex task because so many factors can influence the course of a reaction (see Section 3.4). 

The reasons for this lack of work are manifold The problem is quite complex and difficult to tackle. The information in reaction databases is inherently biased only known reactions, no reactions that failed, are stored. However, any learning also needs information on situations where a certain event will not happen or will fad. The quality of information stored in reaction databases often leaves something to be desired reaction equations are incomplete, certain detads on a reaction are often incomplete or missing, the coverage of the reaction space is not homogeneous, etc. Nevertheless, the challenge is there and the merits of success should be great ... 

The maximum dissimilarity algorithm works in an iterative manner at each step one compormd is selected from the database and added to the subset [Kennard and Stone 1969]. The compound selected is chosen to be the one most dissimilar to the current subset. There are many variants on this basic algorithm which differ in the way in which the first compound is chosen and how the dissimilarity is measured. Three possible choices for fhe initial compormd are (a) select it at random, (b) choose the molecule which is most representative (e.g. has the largest sum of similarities to the other molecules) or (c) choose the molecule which is most dissimilar (e.g. has the smallest sum of similarities to the other molecules). 

A second scheme uses a database of known chemical reactions. This more often results in synthesis routes that will work. However, this occurs at the expense of not being able to suggest any new chemistry. This method can also give many possible synthesis routes, not all of which will give acceptable yield or be easily carried out. The quality of results will depend on the database of known reactions and the means for determining which possible routes are best. These are often retro synthetic algorithms, which start with the desired product and let the researcher choose from a list of possible precursors. 

The functionality available in MedChem Explorer is broken down into a list of available computational experiments, including activity prediction, align/ pharmacophore, overlay molecules, conformer generation, property calculation, and database access. Within each experiment, the Web system walks the user through a series of questions that must be answered sequentially. The task is then submitted to a remote server, where it is performed. The user can view the progress of the work in their Web browser at any time. Once complete, the results of the calculation are stored on the server. The user can then run subsequent experiments starting with those results. The Web interface includes links to help pages at every step of the process. 

Bibliographic/Technical. The principal databases in which bibhographic chemical information is stored are hsted in Table 1. Examples of the use of these databases include searching the CA file to find the pubhshed work of a certain author, or the World Textiles file to determine the extent of weft knitting machinery use in Europe. 

Numeric. Researchers routinely use reported numeric measurements and data in thek work. Handbooks have been the primary source for locating this type of information, but numeric databases are now increasing in availabiUty. Advantages of searching numeric databases on-line include ease of use, dkect access to desked data, and abiUty to manipulate the information in the answer set. 

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