Genedata Phylosopher

Architecture

Built on a scalable, industry-standard Oracle® relational database, Genedata Phylosopher stores and interconnects biomolecules, annotations, sequences, pathways, regulatory elements, and expression profiles. A flexible web interface offers powerful query capabilities, as well as interactive visualizers and tools for data drill downs. Data are managed with a rich toolkit, and well-documented public APIs enable integration into existing research IT environments. With minimal effort, the unique Xtend API lets users build custom extensions and query forms to integrate external databases and sources into the user interface.

User Interface
Interactive query and analysis interface

A web portal provides access to different system data. Intuitive query forms and data, displayed in a tabular format for full data manipulation, enable users to focus on data of interest. Data are also available in summary displays with details on specific data entry in a reader-friendly fashion and fully-configurable groups of information via a tab-oriented interface. The web portal and query forms can be customized on a per-user or system-wide basis. Beyond the Genedata Phylosopher portal, users can investigate with more sophisticated, interactive graphical tools using Java™-based analyzers and WebStart technology, which simplify application administration particularly for large corporations.

Phylosopher Database
Integrated and structured data storage

Genedata Phylosopher is based on an Oracle® relational database management system, which provides scheme modeling state-of-the-art data in a minimally redundant fashion. The data model hosts custom data and scales for large data quantities. The careful use of traditional B-tree and modern full-text indexing provides excellent data retrieval times for very complex queries.  Genedata Phylosopher’s modular structure simplifies work with the Phylosopher data model.

Managed by standard Oracle tools, the database system is easily administered. The Oracle Grid Control and Enterprise Manager Console monitor capacity, session load and system integrity, backup scheduling, and user administration.

Data Management Tools
Facilitating data maintenance and data updates

Genedata Phylosopher comes with a rich toolkit for automatically administering content. Data management tools handle massive parallel execution. System architecture accommodates multiple host environments, and allows integration into cluster computing farms for data mining. The key concepts of data integration and a description of the management tools including program manuals are available in comprehensive software documentation.

The tools provided by Genedata Phylosopher offer a number of benefits:

  • Integrates arbitrary genomes, both eukaryotic and prokaryotic, as well as sequence databases from popular public and commercial data providers

  • Scales to thousands of genomes
  • Loads, maps and exports proprietary sequences such as clones, reagents and primers
  • Generates genome-wide electronic Northerns
  • Calculates orthology for arbitrary genomes
  • Transcription factor binding site prediction for arbitrary genomes
  • Signaling for biological network management, including:

    • Consolidates pathway data from multiple data providers into a single super-pathway
    • Automates portioning of pathway data into annotated and human-manageable sub-networks

  • Automates annotation pipeline for sequence feature calculations
  • Programs framework for creation of robust custom data management software
  • Synchronizes and optimizes the Oracle® database performance when working with very large data volumes

Programming Interfaces
Flexible integration with IT and system infrastructure

The Genedata Phylosopher system offers various levels of programmatic access. These provide flexible and structured ways to load, read, and manipulate data and integrate Genedata Phylosopher with other systems.

The Xtend API is a portal extension with custom components for search forms and data displays, it offers a tight integration of data from other systems and comprehensive visualizations. The connectivity is on the schema level through dedicated interfaces. In addition to this high level interface, a number of other APIs are part of Genedata Phylosopher:

  • Portal API – accessibility for web services, connectivity to other systems; public APIs and interfaces for external system integration
  • Genedata Phylosopher Data Exchange Facility – data loading facility available for non-programmers used for the entry of data in tabular upload file format
  • Standard APIs – via the comprehensive Perl application framework, enterprise data model or PL/SQL data processing interfaces, programmers can easily create powerful analysis and data manipulating applications.