Queries software design

Both the nucleic acid sequences and the protein sequences derived from the biological information are collected in most such databases. Large amounts of data in these databases need to be sorted, stored, retrieved, and analyzed. Selection of subsets of data for particular analysis should also be done. IT providers designed such a data warehouse and developed an interface that provides an important benefit to researchers by making it easy to access the existing information and also to submit new entries (i.e., datamining) (Table 5.6). Middlewares and structured query language (SQL) softwares were developed for this purposes. The former one is used... 

Figure 6 Total number of papers in the 12-year period covered by CJACS for three molecular modeling software vendors. Abbreviations are MSI for Molecular Simulations Inc. and CMD for Cambridge Molecular Design. These searches were structured to identify the vendors by the city in which their headquarters is (or was) located. For MSI, three cities were used. The queries were (1) tripos and st(w)louis, (2) biosym and san(w)diego, and (3a) biodesign and pasadena, (3b) polygen and Waltham, (3c) (molecular(w)simulations(w)inc and waltham) or (molecular(w)sim-ulations(w)inc and burlington), (3d) cambridge(w)molecular(w)design.

PESTIDOC has been designed and created as a quick and easy retrieval of documentation on pesticides. The relational database allows the user to find information on the various issues on pesticides and commercial products, to get data needed for the human and environmental risk assessment. So, the database could provide operational guidance and problem solving in case of response and recovery from environmental, human contamination episodes. Furthermore the flexibility of the software allows the implementation of country-specific information and knowledge, such as pesticide commercial names, national MRLs, producers and so on. So the information currently spread in different data repositories could be unified under one ontology, managed by proper content management workflows and published for user-friendly query purposes. 

A graphic-oriented interpreter has been designed to control the input of the query structures, the retrieval procedure and the presentation of the answers. This software technology enables the user to customise the menu and to introduce new commands. A hierarchic multiwindow technique facilitates the construction of complex Markush queries. 

Each of the aforementioned data sources was created and evolved independently over time based on the needs and demands associated with each individual system. In many cases, each system had its own interface in addition to its own data and queries across systems and data sources were difficult or impossible. Most of the data were available in Oracle databases although a significant amount existed only in Excel workbooks and other non-database files. The Oracle data were spread across over 100 database schemas stored on 24 individual database instances. Because of time and resource constraints and our design philosophy, a decision was made to employ a federated approach in which data would be accessed from its original location whenever possible but integrated into a unified view via the Mobius software. 

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