Category Cross-Omics>Pathway Knowledge Bases/Databases/Tools

Abstract PATIKAweb (PATIKA - Pathway Analysis Tools for Integration and Knowledge Acquisition) is a Web-based service with a user-friendly interface that does Not require any registrations or installations.

It focuses on providing a simple yet advanced interface for querying and visualizing the PATIKA Database.

The PATIKA database currently contains human pathway data integrated from popular public pathway databases such as Reactome (see G6G Abstract Number 20267), and interfaces with certain other major databases and ontologies such as UniProt, Entrez Gene, and GO.

It features a user-friendly interface, dynamic visualization, graph- theoretic queries for extracting biologically important phenomena and import/export facilities from and to various exchange formats such as BioPAX.

PATIKAweb fully supports the PATIKA Ontology, including a multiple- view schema for bioentity and mechanistic levels, compartments and compound graphs for visualizing molecular complexes, pathways and black-box reactions.

Its ability to import pathway models in BioPAX (level 2) format makes analysis of one's private data possible.

The advanced querying mechanisms of PATIKAweb are presented through user-friendly graphical interfaces. This facility enables access to data in both biological entity and mechanistic levels.

The querying component supports SQL-like queries and an array of graph-theoretic queries such as common targets and regulators, shortest paths, feedback loops, and “interesting sub-graphs” based on the user’s genes of interest.

Once retrieved from the database, the query results may be merged to the user's current model and highlighted to provide an incremental, user-friendly retrieval and analysis interface.

Constructed models can be saved in a native XML-based format (". pmdl"), exported to standard formats such as BioPAX level 1 and SBML, or converted to static images.

The query interface of PATIKAweb has been implemented as an applet. The layout component uses a specialized layout algorithm (see below), which can handle both compound graphs and compartments, to automatically layout pathways.

Graph editing functionalities such as scrolling and zooming, do/undo and delete as well as advanced features such as expand/collapse nested abstractions are available to manage the current pathway model.

Pathway Layout -- a previous version of PATIKAweb featured a new algorithm for layout of biological signaling pathways.

This algorithm uses a force-directed layout scheme, taking into account directional and regional constraints enforced by different molecular interaction types and sub-cellular locations in a cell.

Compound Pathway Layout -- Pathway drawings in the new generation of PATIKA tools (e.g., PATIKAweb) are even more complicated with nesting / grouping support as PATIKAweb supports advanced features of the 'PATIKA ontology' including molecular complexes and various types of abstractions to represent relational data at varying levels of detail.

The manufacturer has developed a new algorithm for automatically laying out pathway drawings in PATIKAweb.

PATIKAweb supports the automatic layout of nested pathway drawings. PATIKAweb also has a comprehensive 'microarray data analysis' component named PATIKAmad (see G6G Abstract Number 20269), integrated into its advanced visualization environment. The tool enables users to visualize microarray data mapped onto pathway models. It also provides mechanisms for clustering microarray data using popular methods.

System Requirements

PATIKAweb version 2.1 is publicly available for non-profit use, and the implementation uses the JSP (JavaServer Pages technology) edition of the 'Tom Sawyer Visualization' technology to handle this highly-dynamic and advanced visual content.


Manufacturer Web Site PATIKAweb

Price Contact manufacturer.

G6G Abstract Number 20268

G6G Manufacturer Number 100408