Connection, database

Ehmayer, G., Kappel, G., and Reich, S., Connecting databases to the Web a taxonomy of gateways, Database and Expert Systems Applications 8th International Conference Proceedings, 1997. 

Searching for structures or reactions in an external repository is an alternative to entering the structure directly into the scientific document. This is especially helpful if the structure is complex and not easy to author. Another application is the search for structures stored in an external system — for instance, to find already performed identical or similar reactions. The search query is typically entered via commonly used structure editors that provide the required standard file format. The search query can be performed on individual databases or on all connected databases, including the internal one, at the same time. 

The three major reports, as well as key reference reports, will be provided to NASA and DOE and stored in the Office of Scientific and Technical Information (OSTI) Science Research Connection database, administered by the Oak Ridge National Laboratory. 

A substantial amount of work was initiated by the NRPCT to select and develop a concept fora gas-Brayton space reactor for the Prometheus project. The three major technical reports - the feasibility study, the concept selection report, and the close-out report - have been formally issued and stored in the Office of Scientific and Technical Information (OSTI) Science Research Connection database. These reports can inform future developers of space reactors on the work completed during this phase of the Prometheus program. 

A systematic approach for generating optimal process plans for robotic assembly is presented. A CAPP system is proposed which uses a feature database and a connectivity database to generate connectivity graphs and calculate the final position for every part forming a product. It also identifies sub-assemblies, generates feasible assembly sequences and finally performs trajectory planning for the robot arm to carry out the assembly. 

These are databases that provide links to other databases or data sources. In this case, records describe objects that are other databases. The "Gale Directory of Databases" [14] is one of them. The connection between the databases flows through the meta-data of each database. 

Structure databases are databases that contain information on chemical structures and compounds. The compounds or structure diagrams are not stored as graphics but are represented as connection tables (see Section 2.4). The information about the structure includes the topological arrangement of atoms and the connection between these atoms. This strategy of storage is different from text files and allows one to search chemical structures in several ways. 

After return to the Commander window, the reaction retrieval may be executed separately 629 Dicls-Aldcr reactions between aliphatic dienes and cyclic dicno-pliiles are found. This partial result can be narrowed down by restricting tlie reaction conditions by means of the fact editor, The search field codes for the yield and the temperature can be found to be RX.NYD and RX.T, respectively, either by browsing the database structure or by applying the Find option, as described in the first example. To ensure that the retrieved reaction conditions belong to the same experiment, both search terms must be connected by means of the PROXIMITY operator. Before the retrieval is started, the option "Refine results in... 

Compounds are stored in reaction databases as connection tables (CT) in the same manner as in structure databases (see Section 5.11). Additionally, each compound is assigned information on the reaction center and the role of each compound in the specific reaction scheme (educt, product, etc.) (see Chapter 3). In addition to reaction data, the reaction database also includes bibliographic and factual information (solvent, yield, etc.). All these different data types render the integrated databases quite complex. The retrieval software must be able to recall all these different types of information. 

Compounds are stored as connection tables (CT) in structure and reaction databases, e.g., Beilstein, Cmelin, CAS Registry, and CASREACT. 

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. 

In order to verify a retrosynthetic step suggested by WODCA, a direct connection to reaction databases (e.g., Theilheimer [62] has been established in the most recent version of WODCA. 

A somewhat dilferent way to define a molecule is as a simplified molecular input line entry specification (SMILES) structure. It is a way of writing a single text string that defines the atoms and connectivity. It does not define the exact bond lengths, and so forth. Valid SMILES structures for ethane are CC, C2, and H3C-CH3. SMILES is used because it is a very convenient way to describe molecular geometry when large databases of compounds must be maintained. There is also a very minimal version for organic molecules called SSMILES. 

The generation of loops is necessary because disconnected regions are often separated by a section where a few amino acids have been inserted or omitted. These are often extra loops that can be determined by several methods. One method is to perform a database search to find a similar loop and then use its geometric structure. Often, other conformation search methods are used. Manual structure building may be necessary in order to find a conformation that connects the segments. Visual inspection of the result is recommended in any case. 

---