Query formulation

Interfacing between reaction retrieval and synthesis planning has so far been used for exchange of database information. But why go fiirther into an integrated system capable of query formulation and query translation ... 

Furthermore, SPARQL queries formulated for the ontology have to be translated into the query language associated with the relational database. An approach applying this architecture is for instance the Apache Jena SDB. It allows the data of the model to be stored in a relational database, like Oracle, PostgreSQL, MySQL, or HSQLDB. A Jena SDB storage can be accessed and managed with the Jena API and can be queried using SPARQL. Sesame also facilitates relational... 

In the interchange standardization approach, the usage of the common model as a mediator (Wiederhold 1992) is a common technique for querying purposes. In this case, a single access point and common conceptualization for querying local data sources is provided by the common concepts. Thus, the query formulation becomes independent of the mediated local data sources. Individual users do not need to have a detailed knowledge on all the concepts used in aU project disciplines, and could focus instead on the common concepts that are relevant for the whole project. 

The first EKB software architecture variant (SWA-A) uses a single ontology component that stores and manages both concepts and individuals (see Fig. 8.3) Engineering tools use the component to insert, update, or delete data, e.g., using the Sesame API, on their local tool data models. Mappings, implemented in SPARQL, describe the relation between two concepts, perform transformations on the provided data, and update the instance set of the targeted model. Queries formulated... 

To support query formulation beyond that of exact match, additional vocabulary terms and syntactic elements have been developed. Extensions to atom vocabulary commonly support limited and unlimited wildcard atom specification, atom inclusion lists (in the sense of a Boolean OR connector), atom exclusion lists (in the sense of a Boolean AND-NOT connector), and variable substituent or hydrogen counts. Extensions to bonding syntax commonly include limited and unlimited bond-type specification, variable bond-types or bond-type lists (linked with Boolean OR connectors), automatic recognition of aromaticity, generalized bond environment ( ring bond or chain bond), and generalized bond topology (cross-link specification). 

Although the majority of CIR systems support this extended specification syntax only for query formulation, more recently developed systems provide the capability to store chemical entities with these specifications intact. Some implementations are useful for representing and retrieving polymer structures other versions were designed to store patent related Maikush structures. 

To support 3D query formulation beyond the spartan specification of relative atomic coordinates in space, a large contingent of 3D features have been devised which encourage the rich description of inter- and intra-molecular geometries and interactions. These additional 3D features and constraints are not simply a minor syntactic extension, but a critical and important capability of any 3D CIR system. 

Fuzzy 2D substructure searching is an extension of substructure searching to the minor extent that it permits the expansion of the query formulation vocabulary to include topological features and substructural wildcards described above. This involves the retrieval of all entities in a CIR system that contain the user-defined partial structure and that satisfy whatever wildcard specification pattern has been specified. The query identifies the partial structure and simple wildcard substitution patterns exactly. As with substructure searching, the use of query features on a partial structure will always identify structures which are equal in size or larger than the query. 

The descriptive power of Markush query formulation is used to greatest effect for chemical patent searching, in part because this syntax reflects that used in chemical structure diagrams embedded in the patent applications or the issued patent. See also Markush Structure Searching in Patents and Structure Representation,... 

Figure 2 Information flow for 3D query formulation. A diagram of a simple 3D query is surrounded by models illustrating several distinct methods by which the 3D spatial information critical to query construction may be derived. The identifying numbers correspond to the section in which each method is described...

The bound conformations of ligands determined by transferred-NOE (nuclear Overhauser effect) can also serve as templates for query formulation, even though this implicit approach cannot identify the spatial arrangement of site residue atoms. With these data, one proceeds with the analysis of the bound conformation as in the case of a co-determined complex (see above) however, the excluded volume constraints cannot be specified. One advantage of this data set is that multiple distance geometry solutions for the NOE-determined bound conformation can be used to define some initial tolerances for the distance, angle, and torsional 3D constraint features. 

CAS Transaction Editor DCRT (NIH) On Line Structure Input System for query formulation (1 ) General processing utilities and a macro processor from Dupont U.S. Army CIDS Substructure Ring Screens and Interactive Search (0) CAS Algorithmic Structure Display (ASD) ( ) and CAS On Line... 

Since the book was conceived new front-ends such as STN Express (26,55), MOLKICK (26,34) and DARC CHEMLINK (26) have appeared on the market. All are IBM PC based graphics packages which allow offline query formulation followed by connection to a host computer and uploading of the query for online searching. Offline query formulation means that an end-user can avoid the so-... 

With in-house data bases, the financial advantages of offline query formulation are less obvious, but there is still a business need for uploading structures from a PC to a corporate data base or downloading from the mainframe to the PC. MDL s CPSS package supplies such a front-end to data bases under MDL s MACCS software. 

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