Next-Generation Organic Chemistry Toolkit from SciTouch LLC
Bingo is a data cartridge for Oracle database that provides the industry’s next-generation, fast, scalable, and efficient storage and searching solution for chemical information.
Bingo seamlessly integrates the chemistry into Oracle databases. Its extensible indexing is designed to enable scientists to store, index, and search chemical moieties alongside numbers and text within one underlying relational database server.
Bingo sets the industry standard in structure and reaction registration and retrieval. You can register entities reliably with the confidence that you can retrieve them rapidly.
Because Bingo implements state-of-the-art indexing algorithms within the underlying Oracle database server, chemical searching is fast and reliable. Users can seamlessly combine chemical substructure, reaction, and exact structure searching with numeric and text SQL or PL/SQL terms.
Bingo has all the necessary features required by modern chemoinformatics applications. It also has features not present in other cartridges, for example, advanced tautomer search, resonance substructure search, and fast updating of the index when adding new structures.
Bingo provides an interface for the Oracle cost-based optimizer where possible, particularly in SMILES queries.
Bingo is reliable. Bingo has no legacy code to maintain, and it has been subjected to extensive testing.
Bingo is fast. We have succeeded in achieving the best performance in the industry for a search cartridge for both screening and matching phases of various types of searches, especially substructure search. Bingo has very effective memory management with no unnecessary reallocations. Communication with Oracle, especially LOB handling, is optimized as well. During substructure searches, molecules and reactions are stored in shared memory to speed up the access.
Searching in a variety of ways:
For molecule structure searching, Bingo supports 2D and 3D exact and substructure searches, as well as similarity, tautomer, Markush, formula, molecular weight, and flexmatch searches. Canonical SMILES, with isomeric information included, are available as well.
For reaction searches, Bingo supports reaction substructure search (RSS) with optional automatic generation of atom-to-atom mapping. All of these techniques are available through extensions to the SQL and PL/SQL syntax.
A chemistry column in a table being searched can be CLOB, BLOB or VARCHAR2 containing Molfile (V2000 or V3000) or SMILES data. Similarly, the query can be CLOB or VARCHAR2 in Molfile or SMILES format. For reactions, Rxnfile or reaction SMILES formats are supported for both target and query structures.
Fragment highlighting is supported for substructure, tautomer, and reaction substructure searches.
Different indexing options are available to optimize storage space requirements versus the speed of registration. For example, switching off the tautomer fingerprints will make the indexing faster. Indexes can be updated or re-built with no downtime for maintenance. The addition of new molecules/reactions does not require the rebuilding of the index.
Flexibility and scalability of an Oracle data cartridge:
Fully compliant with Oracle, Bingo allows structure and reaction tables to be placed anywhere in the schema, and the data can be accessed by any SQL compliant application.
Bingo contains a combined structure and reaction cartridge. 2D and 3D search features are supported by the same index.
Bingo supports a large database operation: It is successfully operating on PubChem database, with up to 40 million structures.
Bingo offers full support for Oracle 9, 10, and 11. It is written in C++ and is thread-safe. Native binaries are built for Windows 32/64 bit, Linux 32/64 bit, Mac OS X, and Solaris.
Bingo has a very simple installation procedure, it is possible to install and use two (or more) versions at the same time.
With Bingo, you can build a fully relational registration system: Insert, delete, and update records in a relational structure or reaction database using Oracle data cartridge technology.
With Bingo, you can develop new applications that manage proprietary structure and reaction information. Since the cartridge is data model independent, it allows great flexibility in the design of applications and the management of proprietary structure and reaction information.
With Bingo, you can use standard tools to integrate the cartridge easily. Open integration enables developers to use standard relational database development tools from Oracle, Microsoft, and other vendors. Developers can also use industry-standard database connection tools including ActiveX Data Objects (ADO), Open Database Connectivity (ODBC), Java Database Connectivity (JDBC), or SQL*Net for reaction and chemical structure searching.
With Bingo, you can speed up application development. You can build cheminformatics applications that manage molecule structures and chemical reactions using industry-standard methods and tools as such any ODBC/JDBC compliant programming language and web-based technologies.
Since Bingo is data-model independent, it allows exceptional flexibility in the design of applications and the management of proprietary molecule and reaction information.
Look at the Downloads page for the installation package suitable for your system.
For Windows, we have no rights to distribute binary packages as the Windows build of Bingo includes OCI libraries copyrighted by Oracle Corporation. See the instructions for building Bingo from source.
See the installation manual for installation instructions.
Read the user manual before using the cartridge.
See also the performance tips and performance measures.
Warning: The user manual and performance measures web pages contain inline SVG and are not displayed properly in Internet Explorer. The options for IE users are:
Copyright © 2009-2010 SciTouch LLC
This program is free software: You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 3 of the License.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If you did not not, please see http://www.gnu.org/licenses/.
Additional permission under GNU GPL version 3 section 7. If you modify this program, or any covered work, by linking or combining it with an Oracle Database, containing parts covered by the terms of the Oracle Technology Network Developer License, the licensors of this program grant you additional permission to convey the resulting work.
If GPL-licensed Bingo does not fit your needs, please contact us at info@scitouch.net to discuss the purchase of a commercial license. You may need the commercial license if you want to:
We provide a public access to PubChem database, conatining over 26 million compounds, imported into Oracle and indexed by Bingo. Please see a topic in our news-group for details. Also, please note that any commercial usage of our public Oracle installation is not allowed.