BioRS Integration and Retrieval System

Category Genomics>Genetic Data Analysis/Tools

Abstract The BioRS™ Integration and Retrieval System quickly and efficiently retrieves biological data from public and proprietary databases. Multiple databases can be searched simultaneously using convenient Web interfaces. Flat-file and relational databases (Oracle, MySQL and DB2) are easily integrated using Web or command-line interfaces and standardized data formats based on Extensible Markup Language (XML).

It allows the integration of heterogeneous databases (flat-file as well as relational) to be integrated into a homogenous environment. Multiple databases can be accessed simultaneously by a single query, although the locations of the integrated databases are distributed.

Note: Combined text and sequence search -- As the amount and complexity of data continues to grow, efficient information retrieval is critical for research and development. Extracting information from multiple heterogeneous sources - including your own data as well as data from public and commercial databases - is an essential part of nearly every biological research project in the areas of biotechnology, medicine, pharmacology and agriculture.

Products features/capabilities include:

1) The BioRS query form allows text fields to be searched while simultaneously using Basic Local Alignment Search Tool (BLAST) similarity and pattern searches with sequence fields. The integrated text and BLAST search allows fast and specific results focusing on areas of interest. Search results provide a choice of views for sequence, including graphical and FASTA formats. Sequence alignments can be performed.

2) Proprietary data - even when stored at different locations - can be combined with public and commercial databases and integrated into a unified environment. Scientists can locate related information from multiple sources using the extensive cross-linking between databases and combined reports.

3) The database search environment is convenient for all users - occasional, every-day and expert. Multiple flat-file and relational databases are searched simultaneously with a single query. Convenient tools allow retrieved information to be viewed and exported.

The BioRS system can be run as a stand-alone data integration and retrieval system or, alternatively, can be used as an information backbone supporting other software, such as the Pedant-Pro (see G6G Abstract Number 20094) and BioXM (see G6G Abstract Number 20179) systems.

4) Find the information you want -- Whether you want to perform a quick search on several databases simultaneously or a detailed search that takes advantage of database-specific features, the BioRS system provides easy-to-use tools for building queries and viewing search results.

The integrated search allows a single query to combine a text search with a sequence similarity search (BLAST) for highly specific results. Retrieved sequences can be used to perform pair-wise and multiple alignments.

5) Comfortable work environment -- Both queries and search results can be saved in an individual archive for subsequent reuse or modification. Researchers can define their individual work environment with pre-selected sets of databases and user-specific views. Queries and environment customization can be made available to all users.

6) Efficient use of retrieved data -- Query results can be downloaded in various formats (e.g., Excel) for use with other applications.

7) Create an information backbone for your company -- The BioRS system provides a search environment that is perfectly tailored to your company, combining public and proprietary databases from local and remote instances. Both flat-file and relational databases of different formats can be integrated into a unified environment.

New databases can be easily added and indexed ‘parser development’ support is available for making new database formats available. The Biomax Database Update Tool guarantees that all data is always up-to- date.

8) Integrate the BioRS system into your IT infrastructure -- The BioRS system can be easily integrated into different computing environments. Parallel processing on multiprocessor computers or computer clusters provides optimal scalability for the growing amount of data and large user groups. Different interfaces are available for integration into the software environment: a command-line interface, Hypertext Transfer Protocol (HTTP) and Web services.

9) Technical description -- Using client-server architecture, the BioRS system provides individual modules for searching and indexing as services within a distributed computing environment. While the server runs on a UNIX® system, users can access the BioRS system with commonly used Web browsers. As the BioRS system does Not require Internet access, maximal confidentiality is ensured. Individual users and user groups can be assigned privileges for controlling access to sensitive information.

External applications can be seamlessly integrated. The modular structure of the system together with the distributed programming approach allows parallel processing.

Extensible Markup Language (XML) is used for internal representation of heterogeneous biological, medical or literature databases, allowing semantic inter-operability and normalization regardless of differences between source data formats.

System Requirements

The following platforms and operating systems are supported:

Also see Technical Profile

Manufacturer

Manufacturer Web Site BioRS Integration and Retrieval System

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G6G Abstract Number 20180

G6G Manufacturer Number 100421