Standard query

Another important feature of a LIMS DBMS is the abiUty to perform ad hoc database queries. It is impossible to predict all the forms in which LIMS users will want to display their data while the LIMS is being designed. As a result, it is desirable to select a LIMS which allows users to define their own reports. Most commercial DBMS have a standard query language (SQL) interface. SQL is a simple database query tool which is based on... 

Standard query Select the databanks and click Standard button under Query forms. This opens the standard query form where the user is given choices of data fields to search, operator to use, wild card to append, entry type, and result views. 

Traditionally data, properties, information etc has been stored in files on computer disks. More recently, it has become common practice on Macintosh computers, when using Microsoft software or some UNIX applications, to use either extensions to the file name or the first few bytes in the file (or another file) to indicate some aspects of the data, for example that it is suitable for Microsoft Excel. While this approach is practical to indicate something about files containing columns of data, it is not appropriate to store information about the values in cells in spreadsheet or how it relates to data in other columns. This requires a relational database such as ORACLE, and for performance reasons the values in the cells may only be accessed via the ORACLE API (Application Programming Interface) or SQL (Standard Query Language), in other words, it is suggested that relational databases such as ORACLE should be viewed as sophisticated file systems which allow the values to be organised, efficiently stored, rapidly retrieved etc. 

SRS provides an extremely powerful, but relatively simple, web interface to the databases mentioned above. It is possible to select a database that one wants to search and then retrieve the whole database, or search one or more fields within the database. Figure 1.12 shows the standard query page for the SWISSPROTdatabases. Users can either search for their search term in the ID, keyword, or other fields of the database, or search all text fields for their search term. 

The bottom line question that summarizes aU of these is, How does one design a data model and data description language to enable efficient and effective data acquisition, storage, and use There are many related questions one concerns the design of what are called standard query languages (SQLs) such that it is possible to design a specific DBMS for a given application. 

ORACLE is available in our company also on the VAX computer cluster. Figure 1 presents the major relevant functions. The kernel comprises all software for the management of the database and other parts of the system. Data are stored in a collection of tables described by a dictionary. A table consists of columns and rows. SQL (Structured Query Language), a standard query language, forms a shell round the kernel. Instructions for the kernel are passed down via SQL. 

Simultaneous display of all the relevant product data on a single screen is a convenient feature of the current Version 4.1 (Fig. 11.13). As one scrolls through the product listing in the top left window, data for the product corresponding to the cursor location is instantaneously displayed in the other three windows. The program has advanced search features to help find one or more material that can meet the criteria set by the user. Besides the ability to conduct standard queries by specify-... 

Direct property prediction is a standard technique in drug discovery. "Reverse property prediction can be exemplified with chromatography application databases that contain separations, including method details and assigned chemical structures for each chromatogram. Retrieving compounds present in the database that are similar to the query allows the retrieval of suitable separation conditions for use with the query (method selection). 

The plastics properties catalogue includes single-point data, multi-point data, processing data, product description texts and customer service information. You can select plastic products for your specific application by using the query options. The main feature of the CAMPUS philosophy is comparable data. The properties are based on the international standards ISO 10350 for Single-Point data and ISO 11403-1, -2 for Multi-Point data. CAMPUS is available in English, German, Spanish, French and Japanese. 

The E-state indices may define chemical spaces that are relevant in similarity/ diversity search in chemical databases. This similarity search is based on atom-type E-state indices computed for the query molecule [55]. Each E-state index is converted to a z score, Z =(% -p )/0 , where is the ith E-state atomic index, p is its mean and O is its standard deviation in the entire database. The similarity was computed with the EucHdean distance and with the cosine index and the database used was the Pomona MedChem database, which contains 21000 chemicals. Tests performed for the antiinflamatory drug prednisone and the antimalarial dmg mefloquine as query molecules demonstrated that the chemicals space defined by E-state indices is efficient in identifying similar compounds from drug and drug-tike databases. 

OODBs traditionally have not supported declarative query access, choosing explicit navigation instead. This situation is starting to change, with standards such as the ODMG... 

If one s purpose is to determine only the presence or absence in a data base of a specific structure, this can be accomplished with the search option IDENT , as is shown in Figure 11. This program hash-encodes the query structure connection table and searches through a file of hash-encoded connection table for an exact match. The search, which is very fast by substructure search standards, has been designed specifically for those users who, to comply with the Toxic Substances Control Act [26l have to determine the presence or absence of specific compounds in Environmental Protection Agency files. 

The period required from receipt to approval of the application is treated as that for handling of the standard clerical service, except for replying to PAFSC inquiries and that for correcting incomplete applications. The period for handling the standard clerical service is 12 months. The applicant also has another 12 months to respond to queries and requests from the agency. 

At the level of individual hits, the database can be queried to retrieve either marketed BioPrint drugs that have that same activity, or the ADR associations discussed in the previous section can be queried to identify potential ADRs and their relative risks. At the profile level, compounds with similar profiles can be identified using standard statistical methods such as similarity metrics and hierarchical clustering. This similarity can be assessed using the whole panel of assays or by using selected subsets of those assays as determined by the user. Once compounds with similar profiles have been identified, in vivo data for the similar compoimds can be accessed and examined for information that may permit the user to anticipate in vivo effects. 

As an alternative, we have made extensive use of the data retrieval and manipulation functions within Pipeline Pilot to provide more powerful querying capabilities without sacrificing ease of use. Figure 4 shows the user interface for the standard ad hoc assay protocol used by most chemists and... 

Like the similarity protocol, the user interface for the Pipeline Pilot SSS protocol supports multiple databases and multiple probes in a single query. The input of the probe molecule(s) is accomplished using a SD file, which can be generated in most standard chemical drawing programs. This file is supplied as one of the inputs in the SSS interface. The use of identification numbers is not as applicable here as it is in the case of the similarity protocol since we are most likely not using existing molecules as substructures. Consequently, textbox input is not an option nor is the upload of a list of numbers in CSV or Excel format. 

M D Lmolfile Standardized file format for chemical structures including substructure query features (initially defined by Molecular Design Ltd)... 

As stated before, PGVL is too large to be fully enumerated practically. Therefore our strategy is to find a way to focus in a just-in-time manner on much smaller sub-regions ( 104) of PGVL for subsequent on-the-fly enumeration followed by standard similarity search against the same query molecule. It is intuitively evident that a virtual compound space built from parallel synthesis reaction protocols has inherent array structures in the form of implicit arrays of related just-in-time enumerated compounds, even if those compounds do not have their molecular structures yet enumerated at the time this inherent array structure is exploited. 

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