Query object

The user either enters, or copies, a query object at search time, using the graphical user interface. 

The connection table of the query object (similarity probe) is processed to obtain the set of atom pairs, and then the database file is scanned to evaluate the similarity between the query and each of the database structures. The maximum number of structures that the program will select is specified, as well as the minimum similarity score that a database compoimd must show to be selected. Within these limits, the program will select from the database the structures that are most similar (with the highest similarity value) to the query and will create an output file of compoimd numbers and similarity values, sorted by decreasing similarity, for the selected compounds. 

Notice two things in the load() method. First, it performs a registry lookup one more time. The reason is that the load() method might be called by other finder methods, for example, findBySubtructure, which do not perform a lookup. Second, the load() method puts the newly queried object into the registry. 

Text-mining methods employ algorithms that rrse similarity-based functions in order to obtain k nearest neighbors for novel query objects [32], Term weighting is performed to measrrre the importance of a term in representing the information contained in the docirment [33], For mining literature, the two most common approaches are ML-based and the rule-based approaches, though in practice a combination of approaches works best [34],... 

Library searching techniques are of two kinds identity searches and similarity searches. Identity searches (i.e., searches requiring an exact match between the query and the reference) are successful only if the sought spectrum or structures are already in the reference library. If not, the search fails completely. In contrast, similarity searches depend on the metrics introduced into the representation of the spectra or structures. The metrics and consequently the distance or the similarity measure between the query object and the reference depend on the problem being studied hence, the results obtained on the basis of similarity are not directly comparable when the problems are from different fields. 

The hypothetical enantiophore queries are constructed from the CSP receptor interaction sites as listed above. They are defined in terms of geometric objects (points, lines, planes, centroids, normal vectors) and constraints (distances, angles, dihedral angles, exclusion sphere) which are directly inferred from projected CSP receptor-site points. For instance, the enantiophore in Fig. 4-7 contains three point attachments obtained by ... 

Object behaviors have no clear counterpart in this world of relational databases, which are concerned primarily with storing the attributes and links between objects. The database can be driven with something such as SQL, but the queries and commands are not encapsulated with specific relations. 

Do not use language primitive casts to access other interfaces of a component, because they would understand only language-level objects. Instead, there is a prescribed explicit query protocol for getting to other interfaces. 

Every interface supports Query Interface, a common function that queries for other interfaces based on unique identifiers assigned to interfaces. Each interface is immutable once published a new version is a new interface. Because references to an object via different interfaces are physically different pointers, determining whether two references refer to the same object is not direct. Instead, COM prescribes that each component possess a single distinguished interface called IUnknown, which reliably serves as the identity. 

We hope that the next generation of component-aware languages can make an assembly of objects appear as one, with intelligent query of object identity and interfaces. 

In OCL the built-in objects are immutable and have fixed relations with other objects. In Catalysis we model all these relations as attributes or parameterized attributes. Thus, a < b is syntactical sugar for a.<(b), or a.isLessThan(b). Because Catalysis also offers package scope, this could also be described as a top-level query within a package isLessThan (a, b). 

The main objective in gene module analysis of reverse chemical genomics is to find new functional relationships between different chemicals. Once a set of gene modules annotated by GO and KEGG is obtained, check the common function names for every combination of query chemicals with a significant p value threshold. 

At the beginning of the EntityDictionaryDao, it defines a series of constants the size and the name of each entity dictionary. Using these constants, the code allocates the Java Collection objects so that the sizes of these Collection objects do not need to expand at runtime, which causes extra CPU cycles to be wasted. Following the sizes are String constants names that are used to look up each entity dictionary. The class also defines SQL statements that are used to query the entity dictionary as static variables and initialize them in a static block ... 

The code does not rerun the query for each lookup. It accesses the data only once from the data source and adds the Person object from each row to all lookups in each iteration of the while loop. This approach offers good performance for building the entity dictionary. 

The Data Persistence Layer performs four types of operations in the database on behalf of the Business Layer query, insert, update, and delete. These operations are invoked by the service objects in the Business Layer. In Chapter 12, we presented one type of service—the Registration Service. There are other types of services such as Query Service and Update Service, each of which leverages the Data Persistence Layer to perform database operations. 

All entity objects should be able to be queried by their primary keys. The way it works has little difference between the entity objects except in the SQL statement. The method abstractFind() abstracts out common behaviors of find by primary key operation of all entity objects ... 

The registry object, defined as an instance variable of the AbstractMapper class, caches the entity objects in a map, the primary key of the object as the key and the object as the value. The abstractFind() method performs a lookup in the registry and returns the object being searched if it is already in the cache. Otherwise it performs a database query, calls the load() method to build tlie entity object, and returns it. 

The CompoundMapper defines specific data access logic for the Compound object. Its findStatementPrimaryO method defines how to query the compound table using its primary key. The findByCorpIdPrimary() defines how to query the compound table using its corporate id and so on. 

Readers who are familiar with the MDL database should not be surprised to see MDL s structure query operators such as sss, molsim, and flexmatch. The CompoundMapper s StatementSource objects use ChemDBQueryBuilder to append these structure search operators to the structure search SQL statements. Take the substructure search as an example. In CompoundMapper, we have an inner class FindBySubstructure whose getSql() method is as follows ... 

Third, the validation is often adapted to the final objective in the search for a pharmacophore. Whether its is to be used as a query for virtual screening, to predict accurately the activity of a series of molecule or to serve as a guide for drug design, some validation approaches can be emphasized over others. So, if the title of this chapter were to be rephrased, we could have asked Are you sure you have the right model... for the envisaged application ... 

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. 

The Microsoft Access database (http //www.microsoft.com/) is a collection of data and objects related to a particular topic (Hutchinson and Giddeon, 2000). The data represent the information stored in the database, and the objects help users define the structure of that information and automate the data manipulating tasks. Access supports SQL (Structured Query Language) to create, modify, and manipulate records in the table to facilitate the process. It is a table-oriented processing. The user is referred to the Microsoft Access User s Guide or online Help for information. 

Figure 1 Drug query labeled multiple objects used to find in vivo inhibitors of CYP2B6. Display from the Metabolism and Transport Dmg Interaction Database (http // www.druginteractioninfo.org, accessed October 2006).

The query used is labeled multiple objects and is available under the section Dmg Queries (Fig. 1). The objects used for the search are bupropion and efavirenz. 

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