Bingo

Overview

Bingo is a RDBMS data cartridge 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, Microsoft SQL Server and PostgreSQL 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 database server, chemical searching is fast and reliable. Users can seamlessly combine chemical substructure, reaction, and exact structure searching with numeric and text SQL terms.

Why Select Bingo as Your Molecular Search Cartridge?

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 the screening phase and the matching phase of various types of searches, especially substructure search. Bingo has very effective memory management with no unnecessary reallocations. Communication with the underlying database, especially LOB handling, is optimized as well. During substructure searches, molecules and reactions are stored in shared memory to speed up the access.

Features

Searches in a variety of ways: For molecule structure searching, Bingo supports 2D and 3D exact and substructure searches, as well as SMARTS searches. It also supports 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 the optional automatic generation of atom-to-atom mapping. All of these techniques are available through extensions to the SQL syntax.

A chemistry column in a table being searched can contain Molfile (V2000 or V3000) or SMILES data. Similarly, the query can be 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, by switching off the tautomer fingerprints, the indexing will become faster. Indexes can be updated or rebuilt with no downtime for maintenance. The addition of new molecules/reactions does not require the rebuilding of the index.

Flexibility and scalability of a true data cartridge: Fully compliant with the Oracle and MS SQL Server, Bingo allows structure and reaction tables to be placed anywhere in the database, 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 the PubChem database, with up to 27 million structures.

Bingo offers full support for Oracle 9/10/11 and for MS SQL Server 2008. 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.

Integration: With Bingo, you can build a fully relational registration system: Insert, delete, and update records in a relational structure or reaction database using data cartridge technology in Oracle, or automatically generated triggers in MS SQL Server.

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.

Download and Install

Look at the Downloads page for the installation package suitable for your system.

For installation instructions, see the installation manual for Oracle, installation manual for SQL Server or installation manual for PostgreSQL

Read the user manual for Oracle before using the cartridge in Oracle. For SQL Server users, please read the user manual for SQL Server. For PostgreSQL users, please read the user manual for PostgreSQL.

For Oracle users, see also the performance tips.

License

Copyright © 2009-2013 GGA Software Services 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 permissions 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 you modify this program, or any covered work, by linking or combining it with a Microsoft SQL Server Standard Edition or Microsoft SQL Server Express Edition, containing parts covered by the terms of the appropriate Microsoft SQL Server End User License Agreement, the licensors of this program grant you additional permission to convey the resulting work.

Feedback

Do you need assistance using our tools? Do you need a feature? Do you want to send a patch to us? Did you find a bug? Please write to one of the following newsgroups and let us know:

No registration is required: you can write from your ordinary e-mail account to indigo-bugs@googlegroups.com, indigo-dev@googlegroups.com, or indigo-general@googlegroups.com to get your message posted.

Commercial Availability

If the GPL-licensed Bingo does not fit your needs, please contact us at info@ggasoftware.com to discuss the purchase of a commercial license. You may need the commercial license if you want to:

  • Receive ongoing support and maintenance
  • Include Bingo as a component in your proprietary software product
  • Use Bingo with Oracle licensed not with OTN Developer License, or with MS SQL Server Enterprise Edition