Query definition

Even with the advent of interactive menu-driven query construction (see Section 3.5.8 below), it is still advisable to draw the required fragment carefully on paper and to consider the query definition under the following four subheadings. 

The investigations reported in this paper are only preliminary. They are driven by the obvious importance of similarity analyses in large databases and by a perceived need for a very flexible approach to the problem for both 2-D and 3-D molecular structures. The results obtained so far indicate that similarity searches can be effective at various levels of query definition chemical, 2-D bonding pattern and 3-D distance distribution, and that these levels can be combined or integrated depending upon the information coded in the query. What is important are (a) the selection of suitable attribute sets for each level of discrimination, (b) the compact storage of attributes for each database entry and (c) the selection of effective metrics for assessment of similarity at the various levels. 

Mixed selections for Query Definition (attributes to be changed on multiple selected nodes/bonds). 

Query Definition. The definition of a question is a two step procedure. Once the question has been defined by the user in his own mind in terms of information available In the system, component parts of the query such as the keys, any individual structures needed for Iterative search, and a list of output data items are input interactively from a terminal, with edit progr2ims validating each command. Once a component is input and stored under a user name in a file called the INQDFTN file, the components are assembled, using whatever logical relationship that is required, into a full query which is Itself stored by name. This query can then be searched on-line using the terminal or run later, using a batch version of Inquiry. 

Output. Based on what is requested in Query Definition, and on what a user commands during Inquiry Execution, the output of a search can be directed to an alphanumeric terminal, to a Tektronix graphics terminal if structures are needed, to CAS system printers, to a transaction file (PTFC) for the Communications Processor to produce standard chemistry cards at CAS, or to two types of disk files a temporary browsing file (RESULTS) or a permanent SAVE file which can be accessed either sequentially through GET or as a search key in SSS. 

The definitions of MDL s 166 MACCS search keys can be found in the ISIS/ Base help file, section 49.2.4 Specifying searchable keys as a query. 

Current chemical information systems offer three principal types of search facility. Structure search involves the search of a file of compounds for the presence or absence of a specified query compound, for example, to retrieve physicochemical data associated with a particular substance. Substructure search involves the search of a file of compounds for all molecules containing some specified query substructure of interest. Finally, similarity search involves the search of a file of compounds for those molecules that are most similar to an input query molecule, using some quantitative definition of structural similarity. 

Block composition, (2), and IF-THEN composition, (3), do not affect cycle domination so we need consider part (B) of the definition of line-like only for WHILE composition, (4). But the query node q cycle dominates all of B and these are the only cycle dominations added in so if (B) is line-like then is line-like. ... 

We will begin by assuming that, for a particular query point 09, an algorithm exists (discussed below) for finding the nearest point in composition space 0q]. It then remains to determine if 0j lies >n the EOA of 1. The definition of the EOA requires aparameter toi... 

In practice, the definition of the initial EOA, (6.264), is often overly conservative such that 50o does not satisfy (6.264) even though (6.265) is satisfied. In the ISAT algorithm, if 0Q does not satisfy (6.264), then (6.251) must be integrated numerically to find Since 0 can be computed by linear interpolation, the interpolation error slI can then be computed and compared to toi. Thus, for a given query point 0j, one of three possible outcomes will occur as follows. 

Dotz reaction is proposed. According to our calculations the addition of the alkyne molecule to the carbene complex takes place before CO loss in the initial steps of the reaction. Further, our study shows that a novel proposal involving a chromahexatriene intermediate entails lower energy barriers and more stable intermediates than the previous reaction mechanisms postulated by Dotz and Casey. The novel findings query revision of the classically assumed paths and put forward that additional experimental and theoretical studies are necessary to definitely unravel the reaction mechanism of this intringuing reaction. 

Given a set of molecules known to be inside PGVL as query molecules, what is the success rate for returning the expected molecules identical to the query molecules (100% similarity threshold) This is by definition a baseline test that a validated search strategy must pass. 

The inactive ingredients are updated quarterly, by the fifth working day of April, July, October, and January. To search for the excipient, one can enter any portion of the name of an excipient, of at least three characters. Search results are displayed alphabetically, sorted first by ingredient, then by the route of administration and dosage form. Routes of administration and dosage forms are derived from current approved labeling. Refer to the IIG query search results column headers for data field definitions. 

Perhaps the earliest attempt to give to this force of chemical affinity a more precise definition was by Isaac Newton in his Opticks.2 His consideration of the subject is in No. 31, the last of a series of queries propounded to the reader at the close of the last book of his Opticks in order, as he says, to a farther search to be made by others. ... 

One of the most widely used chemical structure-encoding schemas in the pharmaceutical industry is the MDL Connection Table (CT) File Format. Both Molfile and SD File are based on MDL CT File Format to represent chemical structures. A Molfile represents a single chemical structure. An SD File contains one to many records, each of which has a chemical structure and other data that are associated with the structure. MDL Connection Table File Format also supports RG File to describe a single Rgroup query, rxnfile, which contains structural information of a single reaction, RD File, which has one to many records, each of which has a reaction and data associated with the reaction, and lastly, MDL s newly developed XML representation of the above—XD File. The CT File Format definition can be downloaded from the MDL website http //www.mdl.com/downloads/public/ctfile/ctfile.jsp. 

The definition of pharmacophores is done manually by applying so-called schemes using a Pharmacophore Query Editor. A template molecule is generally used for this purpose. In the MOE environment, a scheme is a collection of functions that define how each ligand is annotated. This is accessed via an SVL function. The default scheme is called PCH (Polarity-Charged-Hydrophobicity). New schemes can be created to represent certain molecules better, e.g. Planar-Polar-Charged- Hydrophobiaty [91]. 

In other words, the samples have to reflect, without distortion, the piece of information required from the population. Otherwise, the conclusions from the analytical data - the output of the analytical laboratory - about the state of the investigated object are definitely arbitrary and may cause momentous errors in the interpretation of results. Samples of a population must, therefore, be representative according to the specific query. This means that they must be both accurate and reproducible. This implies that the sampling process is affected by errors in each case. The question of representativeness is a question which has to be answered for each individual case in relation to the heterogeneity of the population to be sampled, the accuracy required, and the reproducibility of results. The extent of representativeness is, therefore, highly dependent on the expenditure on sampling and analysis and the time needed for the investigation. 

There is no definitive answer possible, but no candidate more suitable than Wasson s has yet appeared. A recent Ph.D. thesis at the University of California, Berkeley, entitled "Huoma, renews this query, suggesting on the basis of linguistic factors that the plant contained a harmaline compound (which in botanical terms does not fit with Soma s identification). 

An example of where field definition can improve the database integrity is simply date format, which is especially critical for data shared between organizations in the United States and other parts of the world. If a database query is entered for records between 1/4/02 and 7/4/02, should the database interpret this as January 4 to July 4 or April 1 to April 7 If the field is defined to display dates in a dd-mm-yy format, 04-Jul-02 will be unambiguously interpreted. 

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