The PATIKA Project
by E. Demir, U. Dogrusoz, O. Babur, A. Ayaz, E. Giral, Z. Erson,
G. Nisanci and G. Gulesir

Lately, there has been an enormous amount of effort for creating ontologies,
standards and tools to facilitate modeling and analysis of biological
pathways. Still, current bioinformatics infrastructure is far from coping
with inherent complexity of data produced by state-of-the-art biology
techniques. 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.

PATIKA 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.

In this talk, we will give an overview of PATIKA project and discuss latest
improvements to its ontology, including bioentity level interactions and
attributes and a better structured cell model. We will also present
features of our new editor, PATIKApro, such as ability to represent
varying levels of abstractions through nested pathway drawings, multiple
pathway views, facilities for analysis of gene expression data including
a new method for inference of pathway activity using gene expression data.
Finally we will talk about our efforts for populating the PATIKA database
by automated pathway inference.

http://www.patika.org