The Automatic Search Tool

In addition to addressing the practicalities of database maintenance, we also aim to enhance the range of the facilities available, to make the information within CHIRBASE more readily accessible to users. CHIRBASE contains two form-based applications for query building designed to help novice or expert users to formulate queries the query menu and the automatic search tool. 

Unfortunately, no software techniques exist currently to automatically search for additional roots. Instead, modelers must rely on their understanding of geochemistry to demonstrate uniqueness to their satisfaction. Activity-activity diagrams such as those presented in Figures 12.1-12.3 are the most useful tools for identifying additional roots. 

Information-retrieval tools Information retrieval offers a solution to tasks from text searches to the automatic categorization and summation of documents. Advanced search algorithms use thesauri and text mining to discover contexts that could not be found with simple queries. Semantic text analyses can also be implemented. 

Having said all this, we would like to alert the reader to the fact that the CCDC, is not a simply a body devoted to the permanent storage of crystallographic data but also very much an active research organisation, both in the analysis of structural data and in the development of new research and search tools for the CSD. Thus, for example, it is likely that we in the future will see search tools that can automatically recognise such features as nets, dimensionality and interpenetration. CCDC also have some more recent products called knowledge bases , IsoStar and Mogul, that may be quite useful as well. 

This collaborative database contains information on numerous usual metabolites. Including mass spectrometry data on metabohtes, it is the default database for automatic searches of the LC-MS statistical analysis tool Xcms online . 

The JME can also serve as a query input tool for structure databases by allowing creation of complex substructure queries (Figure 2-130), which are automatically translated into SMARTS [22]. With the help of simple HTML-format elements the creation of 3D structure queries is also possible, as were used in the 3D pharmacophore searches in the NCI database system [129]. Creation of reac-... 

Web in the life of the medicinal chemist. One may see the development of alerting services for the primary medicinal chemistry journals. The Web-based information search process could be replaced by a much more structured one based on metadata, derived by automated processing of the original full-text article. To discover new and potentially interesting articles, the user subscribes to the RSS feeds of relevant publishers and can simply search the latest items that appear automatically for keywords of interest. The article download is still necessary, but it may be possible for the client software to automatically invoke bibliographic tools to store the found references. Another application of the Chemical Semantic Web may be as alerting services for new additions to chemical databases where users get alerts for the new additions of structures or reactions. 

The second postprocessing step is the automated enhancement of the TrEMBL annotation to bring TrEMBL entries closer to SWISS-PROT standard. There is an increasing need for reliable automatic functional annotation to cope with the rapidly increasing amount of sequence data. Most of the current approaches are still based on sequence similarity searches against known proteins. Some groups try to collect the results of different prediction tools in a simple way, e.g., PEDANT (Frishman and Mewes, 1997) or GeneQuiz (Scharf et al., 1994). However, several pitfalls of these methods have been reported (Bork and Koonin, 1998). 

Raw data generated by the Phenotype Pfinder protocol is maintained in a dedicated database. The database automatically graphs the data, generates statistical analyses of assays, and flags those assays which show a statistically significant difference between WT and KO mice. The data can be searched and viewed by either specific KO line or assay. The database also offers a tool for analysis of historically accumulated control data sorted by genetic background. 

Once these ontological specifications are created, it is possible to apply reasoning tools to automatically create workflows of services that tackle tasks that require the involvement of multiple services. These are of particular interest, as they offer the possibility of on-the-fly aggregation of services and information in response to a scientist s (potentially complex) query, without the need for workflows to have been predefined. Such reasoning tools already exist, but they require exhaustive search of the Web services space (an NP-complete problem). Techniques and heuristics are being developed in the Semantic Web community to reduce the search spaces and effect efficient searches. We will participate in these efforts while tailoring the searches to cheminformatics. 

As time went on, computers were used for increasingly complex problems in chemistry, as will be shown. In this process, the early quantum chemistry users received competition from the theoretical chemists oriented toward a broader field of mathematical chemistry. Eventually many experimentalists started to use computational tools for quantum and classical mechanics, statistical mechanics, and database searching. Parallel to these applications, almost every experimental setup had a dedicated computer to run experiments and evaluate data automatically. Laboratory automation will not be treated in this chapter. Likewise, no attempt will be made to cover the impact of computers on experimental structure determination (e.g.. X-ray crystallography). 

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