Fragment coded search system

A key phase of the project involved the creation of the structure database, a gradually enlarging collection of approximately 60,000 chemical structures which over the years had either been synthesized in-house for testing purposes or obtained from outside organizations. The fragment-coded search system also operated on this collection of compounds however, since fragment codes represent structural attributes, the codes could not be used to regenerate complete connection tables. 

With the variety of chemical substance representations, i.e., fragment codes, systematic nomenclature, linear notations, and connection tables, a diversity of approaches and techniques are used for substructure searching. Whereas unique, unambiguous representations are essential for some registration processes, it is important to note that this often cannot be used to advantage in substructure searching. With connection tables, there is no assurance that the atoms cited in the substructure will be cited in the same order as the corresponding atoms in the structure. With nomenclature or notation representation systems, a substructural unit may be described by different terms or... 

As with the numeric data, the content of stmctural information in the secondary literature is fimited, and we therefore have a situation in which many specicdised systems have been developed to deal with stractural data. Files of chemical stractures, and means of accessing them, have been with us for a number of years, certainly from before computers. Traditionally, these have used notations, fragment codes, etc., as the means of recording structural information, and have allowed searches to be made for complete compounds or for all compounds containing certain specified substractures. More recently, topographical systems have been developed. In these the complete stractures are recorded in the form of "connection tables", which store full details of all the atoms and bonds in a molecule, and the precise arrangement in which they are connected. 

Traditional substructure search systems work in two stages the first stage is a preliminary filter using fragment codes the second stage applies atom-by-atom search to check the isomorphism of the subgraphs. 

Whatever the search software offered, however, the database was of utmost importance. The DARC system not only offered a means to search generic structures in the short term, it also offered a way to record all of the information about structures found in patents, through a new and flexible input system. This capability was of incredible import to Derwent we could build a database that would not only serve the users today, but in future could be of more utility as search software was further developed. As opposed to the fragmentation code, there should never be a question of time-ranging. Moreover, though we assume that Markush DARC is a system not only of today but of tomorrow, we are building a database that can be converted and adapted to other search systems that may be offered by other organisations. 

At this juncture, Markush search systems for patents are fairly mature. The fragment code and graphical systems in... 

The problem of poor retrieval precision, and the development of search systems based on unambiguous (complete) representations of the structure has led to the general demise of fragment codes as a primary representation of chemical structures, at least for specific compounds. However, hidden from the user they remain an important component of structure search systems, and a few user-visible fragment-code systems continue to be used in the handling of Markush structures from chenaical patents these are discussed in more detail in Markush Structure Searching in Patents. 

No numerical codes are used by the system. A search for a specific subject can be carried out by entering the subject word itself. If the word mass is entered, searches for 7 terms (all those containing the fragment mas i.e. mass spectra, mass discrimination, mass measurement, etc.) are conducted and the user is asked to select the one of interest. In this way knowledge of the correct subject words or of their correct spelling is not necessary. 

TOXMAP is a Web resource that uses maps of the United States to show the amount and location of toxic chemicals released into the environment. Data are derived from the TRI database (described above), which provides information on toxic releases into the environment as reported by US industry. TOXMAP helps users create nationwide or local area maps showing where chemicals are released into the air, water, and ground. It also identifies the releasing facilities, color-codes release amounts for a single year, and provides multi-year chemical release trends, starting with 1987. Users can search the system by chemical name, chemical name fragment, and/or location (such as city, state, or zip code). TOXMAP also overlays map data such as US Census population data. 

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