Structure retrieval systems

Willett P (1987) A review of chemical structure retrieval systems. J Chemometrics 1 139—155. 

The structure correlation approach thus provides a link between the statics of crystals and the dynamics of reacting chemical systems. The first steps could be made without the help of computer-assisted structure retrieval systems but today the only practicable way to find details of particular structures or classes of structures is through the various databases, of which... 

Willett, P. A Review of Chemical Structure Retrieval Systems . J. Chemometrics. In the press. 

The same canonical name matching used for chemical structure retrieval systems works very well also in reaction indexing systems and provides rapid retrieval. 

The reaction database compiled on Biochemical Pathways can be accessed on the web and can be investigated with the retrieval system C ROL (Compound Access and Retrieval On Line) [211 that provides a variety of powerful search techniques. The Biochemical Pathways database is split into a database of chemical structures and a database of chemical reactions that can be searched independently but which have been provided with efficient crosslinks between these two databases. 

And last not least, we will have to see further improvements in the graphical user interfaces of software systems and the retrieval systems of databases in order to make software and databases more acceptable to the chemical community at large. Software and databases should speak the language a chemist is used to, with hand-drawn chemical structures and reaction equations, or even imderstand the spoken word - and only provide the desired information selectively, not buried in a phe of unnecessary output. 

In a further case relating to the structure of data stored on or in a record carrier used in a picture retrieval system, the European Patent Office s Boards of Appeal have considered the issue of patentability of a data structure [22]. Initially the patent application had been rejected on the grounds that the presentation of data was excluded from patentability (see above). However, in accepting an appeal filed by the patent applicant, the Board pointed out that there was a difference between the functional data, which controlled the technical working of the system, and the cognitive information, which represented the picture that could be retrieved and displayed. The Board stated that functional data relates to data that control the technical operation of the system. These data do not relate to the presentation of information, and thus data structures containing this information should be patentable. On the other hand, the cognitive information relates to the picture that could be retrieved and displayed. 

In the bioinformatics realm, SRS (Sequence Retrieval System) [2] is a popular system, which uses a centralized collection of data resources primarily in flat text file form and, more recently, handles XML (Extensible Markup Language) files as well. Data resources are treated in a federated manner since each is maintained in its original form. However, SRS contains a large number of cross-references between corresponding fields in various data sources, so that keyword searches can be done across them. SRS thus performs more structured searches across the information than what a simple text search provides (such as web indexes perform, for example). Even though the data model implicit in the cross-reference tables is not very deep, SRS provides a useful way for users to browse and do simple queries across a large number of data sources as well as to integrate results from some computational methods. 

Data Retrieval System (DRS)(2). We find it particularly important to have the plotting programs readily available since this is, as I will illustrate by several examples, an important first step in analysis of structure-activity data. 

A Chemically Oriented Information Storage and Retrieval System II. Computer Generation of the Wiswesser Notation of Complex Polycyclic Structures," Journal of Chemical Documentation, (3), 133-138 (1968). 

Searches for similar protein and nucleic acid sequences Protein structures on moving 3D coordinates Sequence retrieval system for cross-referencing databases Searches for similar protein sequences Database of gene sequences... 

BLAST Chime Entrez (NCBI) FASTA GenBank (NCBI) Molecules R Us RasMol (Ras Mac) SRS (EMBL) Searches for similar protein and nucleic acid sequences Protein structures on moving 3D coordinates Sequence retrieval system for cross-referencing databases Searches for similar protein sequences Database of gene sequences Provides coordinates for protein 3D structure and manipulation Provides coordinates for protein 3D structure and manipulation Sequence retrieval system for cross referencing databases... 

The Sequence Retrieval System (Etzold et ah, 1996) is a network browser for databases at EBI. The system allows users to retrieve, link, and access entries from all the interconnected resources such as nucleic acid, EST, protein sequence, protein pattern, protein structure, specialist/boutique, and/or bibliographic databases. The SRS is also a database browser of DDBJ, ExPASy, and a number of servers as the query system. The SRS can be accessed from EBI Tools server at http // www2.ebi.ac.uk/Tools/index.html or directly at http //srs6.ebi.ac.uk/. The SRS permits users to formulate queries across a range of different database types via a single interface in three different methods (Figure 3.4) ... 

PubChem is organized as three linked databases within the NC8I s Entrez information retrieval system. These are PubChem Substance. PubChem Compound, and PubChem BioAssay. Pubchem also provides a fast chemical structure similarity search tool. More information about using each component database may be found using the links above. 

Widely used treatises and monographs on the theory and the applications of MRR-spectroscopy are available [8-//], also comprehensive reviews on all aspects of obtaining molecular structure from MRR-spectra [6,12,13], including rovib interactions [14] and the reliability of the results [15-17], Molecular structural and other data obtained from MRR spectroscopy have been compiled over the past decades [18,19], The most recent compilation is MOGADOC (short for Molecular Gas Phase Documentation ), a computerized database and retrieval system that is updated periodically and today contains more than 20,000 references, which were critically selected and evaluated by means of keywords. Included is work done by MRR-spectroscopy, electron diffraction of gases, and molecular radio astronomy the documentation refers to more than 6000 compounds. As an additional feature, MOGADOC contains explicit numerical data on the structure of approximately 2000 compounds. A detailed description can be found in ref. [20],... 

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