The PATIKA Project aims to provide scientific community with an integrated environment composed of a central database and a visual editor, built around an extensive ontology and an integration framework. It also features tools for analyzing microarray data and inference of pathways.

PATIKApro has been designed mainly for distributed research communities, who wish to build large-scale integrated pathway models in a collaborative manner. Users may retrieve desired parts of the model stored in the database via a querying interface for standard and graph based queries. Pathways constructed from query results or built from scratch by the user can be modified and submitted to the server. These changes are then integrated back into the central model, after resolving potential conflicts including those due to concurrent modifications of others.

PATIKApro is designed onto an intuitive, comprehensive and uncomplicated ontology for representation of cellular events. It enables integration of fragmented or incomplete pathway information via collaboration, and supports manipulation of the stored data. In addition, it facilitates concurrent modifications to the data while maintaining its validity and consistency. Furthermore, novel structures for representation of multiple levels of abstraction for pathways and homologies is provided. Lastly, PATIKA ontology supports efficient querying of large amounts of data.

The microarray data analysis component of PATIKA helps to relate the expression data to the pathways. An activity inference algorithm is implemented for finding possible paths that construct dependencies between differentially expressed genes. PATIKApro editor also facilitates easy inspection of the data and inference by visual tools.

The PATIKApro editor uses state-of-the-art graph visualization tools of Tom Sawyer Software and also features a new, elegant automated layout component to visualize complex pathways with nestings and groupings.

See our ISMB 2004 Poster on the PATIKA Project.