Refining, search queries

Refine a Search Query. The process of adding or modifying constraints of a search query to reduce or increase the number of hits. Constraints may be added, removed, relaxed, or tightened to achieve the desired search results. 

Non-structural parameters such as molecular formula, accession numbers (L-number), registrant s name, and date of registration can all be used to refine the search query. These data are included in the CSIS record. Ancillary data contained in separate databases can also be used to restrict or supplement CSIS output. Examples of such data are sample availability, references to compound sources, and audit trails of sample distribution for biological evaluation. 

If the query provides thousands of hits, the analyze features are particularly advantageous. One method is to analyze the results by any of the criteria that arc listed, c.g., by language (default), author names, journals, puhlication year, and so on. If one specification is selected and the choice is modified, the hit list will be updated. A more specific analysis is available with the Refine" option. where the user has the opportunity to choose one of eight criteria (including the search topics above) with further individual input. Several refinements of the hit list can reduce the result to a concise list of literature. To read the abstract of an article, the microscope button (to the right of the citation) has to be pressed (Figure 5-15). 

Today, the use of CHIRBASE as a tool in aiding the chemist in the identification of appropriate CSPs has produced impressive and valuable results. Although recent developments diminish the need for domain expertise, today the user must possess a certain level of knowledge of analytical chemistry and chiral chromatography. Nevertheless, further refinements will notably reduce this required level of expertise. Part of this effort will include the design of an expert system which will provide rule sets for each CSP in a given sample search context. The expert system will also be able to query the user about the specific requisites for each sample (scale, solubility, etc.) and generate rules which will indicate a ranked list of CSPs as well their most suitable experimental conditions (mobile phase, temperature, pH, etc.). 

A training database is recommended to be constructed for the purposes of optimizing the query hypotheses to improve the hit accuracy in database search. Such a training database usually contains a thousand compounds typically, consisting of 980 random molecules and 20 known active ligands. For example, users can examine and refine the hypothetic pharmacophore (or query) against the test database in terms of hit precision rate, false-negative rate, and false-positive rate. The process is very... 

Entrez is basically a multi-database search engine. Under the surface are a vast number of details on which fields are available fo be searched, what the many types of links mean, how the core Entrez controls function, and so on. All of this may be a bit daunting to the casual user, but understanding these details unlocks the true power of Entrez. This section serves as a guide to PubChem s Entrez databases, including what indices, links, and filters are available, and how these combine together to create an advanced query refinement system. 

While the input query and search type are all that are necessary to perform a sfmcfure search in PubChem, there are numerous choices by which one may narrow the search to smaller subsets of PubChem. For example, one may search only within a previous Entrez search result, or even a previous stmcture search result, or upload a file of ClDs againsf which fhe search is fo be performed. One may filter based on a wide variety of properties, such as molecular weight, heavy atom count, presence or absence of stereochemistry, assay activity, elemental composition, depositor name or category, etc. Most of these subset operations could be accomplished through appropriate Entrez index queries followed by Boolean operations on structure search results however, the structure search tool provides a convenient one-step interface for chemical search refinement. 

Two recently added GDB tools are GDB BLAST and e-PCR. These are available from the Other Search Options page and enable users to employ GDB s many data resources in their analysis of the emerging human genome sequence. GDB BLAST returns GDB objects associated with BLAST hits against the public human sequence. GDB s e-PCR finds which of its many amplimers are contained within queried DNA sequences and is thereby a quick means to determine or refine gene or marker localization. In addition, the GDB has many useful genome resoince Web links on its Resources page. 

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