Genedata Phylosopher®

Category Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools, Genomics>Gene Expression Analysis/Profiling/Tools, Cross-Omics>Biomarker Discovery/Analysis/Tools and Cross-Omics>Sequence Analysis/Tools

Abstract Genedata Phylosopher is an enterprise data management and analysis system supporting pharmaceutical research processes for the discovery and validation of novel and existing therapeutic targets.

A comprehensive system, Phylosopher includes built-in innovative systems biology tools that enable integrated registration, analysis, and validation of targets. The platform supports all related processes spanning compound efficacy assessment, drug safety evaluation, biomarker discovery, and translational medicine.

Modular, scalable, and extensible, Genedata Phylosopher is an open system, which easily integrates into an existing research IT environment. It works out-of-the-box in its default configuration, without additional customization.

Phylosopher key benefits are:

1) Integrated system to capture, structure, manage, and visualize all target-related information in a pharmaceutical R&D organization.

2) Elucidates disease mechanisms to identify underlying pathways.

3) Evaluates model organisms through comprehensive annotation and comparison of all medically relevant model organisms.

4) Identifies, prioritizes, and validates drug targets according to disease-relationship and structural features and other criteria.

5) Supports assay development for both enzymatic as well as reporter assay development.

6) Prioritizes drug candidates with integrated tools for compound mode-of-action (MOA) studies.

7) Advances pharmacogenomics and translational medicine with integrated analysis of genotypes and disease phenotypes.

Genedata Phylosopher Modules -- Genedata Phylosopher® is a fully integrated enterprise system composed of modules focusing on specific application areas. The modules integrate out-of-the-box, without any development or configuration effort. In addition, APIs and connectors enable easy integration of Genedata Phylosopher with existing in-house infrastructures.

Genome Explorer - Genome Explorer (Genome Analysis), the core of Genedata Phylosopher, power-queries the human genome for proprietary or public data. Additionally, Genedata Phylosopher includes tools to evaluate the suitability of a wide range of species as a test system for a given disease pathway, including mouse, rat, worm, fly, or zebra fish.

The automated comparison of a large number of higher eukaryotes, together with an in-depth comparison of disease loci and encoded pathways, helps to define a suitable model system for the therapeutic indication of interest.

Sequence Data Center (Sequence management) - Sequence Data Center is tightly integrated with SequenceExplorer. Dedicated to the secure behind-the-firewall management of stand-alone proprietary and public sequence databases, Sequence Data Center can be referenced against genomic sequences.

A comprehensive suite of agents for all major public and proprietary data repositories automatically updates relevant content.

Sequence Explorer (Sequence analysis toolbox) - Sequence Explorer provides a comprehensive integration platform including all major sequence analysis programs such as BLAST, ClustalW, Pfam, and the EMBOSS suite.

Sequence Explorer is easily extended with other sequence analysis tools and specifically with proprietary algorithms. All results are saved permanently and can be analyzed interactively with advanced graphical programs.

Expression Explorer (Expression analysis) - Expression Explorer connects expression measurements to gene annotation and is compatible with all standard microarray technologies (e.g., Affymetrix, Agilent) and real-time PCR data (e.g., TaqMan).

It allows users to view and analyze genes corresponding to a list of co-regulated probe sets such as those derived from molecular profiling studies, generate gene-centric views of key profiling data across multiple samples (‘electronic Northern’), and quality-check and assess reagents.

Pathway Explorer (Metabolic pathway analysis) - Pathway Explorer enables the storage and analysis of public and proprietary pathways data. Its tools for pathway activation pattern investigations allow analyses of transcriptomic, proteomic, and metabolomic profiling data in a pathway context.

Moreover, Pathway Explorer enables cross-organism pathway analyses to identify the most suitable model organisms for experimentally testing disease hypotheses and performing compound MOA studies.

Signaling Explorer (Signaling pathway analysis) - Signaling Explorer focuses on the storage and analysis of signaling pathway data. By integrating data from different public and commercial providers, it enables the generation of super-pathways based on different data sources.

It models arbitrary molecules and events such as compounds, promoters, co-factors, enzymatic reactions, or post-translational modifications in different cellular compartments, overlays molecular profiling data on signaling pathways, and extends pathways to capture the latest knowledge in the field.

Promoter Explorer (Regulatory network analysis) - Promoter Explorer enables the integrated storage and analysis of promoter and regulatory network data. It facilitates the genome-wide analysis of human transcription control mechanisms and specifically helps to predict target genes of specific transcription factors.

It includes tools that integrate experimental data (e.g., ChIP-chip, validated miRNA targets), compare data with computational predictions (generated e.g., from PWM-based approaches), and investigate promoter architectures.

These capabilities help to answer critical questions in drug discovery such as which transcription factors account for co-regulation of a group of genes, or if transcriptional control is conserved in a group of orthologs.

Mutation Explorer (Integrated genotype analysis) - Mutation Explorer enables the integrated storage and analysis of mutation information, including SNPs and more complex polymorphisms. It facilitates the genome-wide analysis of genotypes and correlates specific mutations as well as complex mutation patterns with disease phenotypes.

Developed specifically for managing and interpreting genetic studies, it enables genetic profiling and provides tools to identify biomarkers and genetic markers for predicting disease risk, progression and prognosis, and to support pharmacogenomics-driven drug development programs. It processes data derived from both classical as well as next-generation sequencing (NGS) technologies.

Literature Explorer (Scientific literature analysis) - Literature Explorer facilitates the storage and querying of scientific literature and other document-based findings.

Scientific articles (e.g. PubMed) link to relevant biological entities including genes, proteins, transcription factors, pathways, and more. This tight data integration allows effortless retrieval of, for example, all genes with diabetes associations in all available literature.

Patent Explorer (Intellectual property analysis) - Patent Explorer stores and analyzes bio-molecule patent information. It enables interdisciplinary collaboration among scientists, patent lawyers, and project and business managers so that targets are evaluated from both intellectual property and biological standpoints.

Advancing decision-making based on competitive data in specific research areas and filing and priority dates, Patent Explorer drives scientifically sound early-stage target identification, which is free of competing intellectual property claims.

Project Manager (Framework for structuring R&D projects) - Project Manager provides a framework to store, structure, and publish results in the form of reports, presentations, or spreadsheets on targets, assays, compounds, or projects.

Results link to any relevant target project or other biological entities, such as genes, sequences, signaling pathways, or promoter regions. Users and project managers can define a project hierarchy based on factors such as project status, IP landscape, experimental results, or functional analysis and share results and reports.

Xtend API (System integration interfaces) - In addition to a comprehensive API framework, Genedata Phylosopher provides a specialized high-level API. The Xtend API enables easy integration of Genedata Phylosopher with other database and IT systems, from which it dynamically pulls and appropriately displays relevant data.

It facilitates target-centric organization of all discovery-related information including screening and pharmacology data, molecular profiling data, or portfolio and project databases. Xtend API also allows customization of the Phylosopher User Interface according to customer requirements.

Phylosopher offers more than 2,000 pages of HyperText Markup Language (HTML) Documentation include FAQs and HowTo's as well as pages for the Explorers, system administration, agent documentation and Perl API.

System Requirements

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Manufacturer Web Site Genedata Phylosopher

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G6G Abstract Number 20130R

G6G Manufacturer Number 101107