Natallia Kokash

Researcher at Leiden University

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Projects: ApiNATOMY

Practice, research and training in bio-medicine generate considerable amounts of clinical and scientific resources in the form of electronic data and computational models. A significant proportion of such resources carries information that cross-references to anatomical structures. We target to provide interactive software tools for effective graphical presentation of structured information. We are working on a customizable model for uniform representation of graphs of entities and relationships. Using our modeling languages and GUIs, a user will be able to specify views, templates, and transformations of ontology trees and relationships among their elements. The appropriate layout for the structured information is defined by customized templates and/or using constraint-solving techniques.

My contribution

Anatomy ontology visualization with constraint-based treemaps

In the period from December 2011 to June 2013, I developed a number of prototypes that provide constrained layouts for various anatomical views. These prototypes are implemented as web applications and essentially represent interactive 2d and 3d treemaps. For more details and on-going project samples visit

Open Physiology

A key challenge for the biomedical community is to bridge data from healthcare and experimental biology to computational models of physiology. The core goal for the Open Physiology effort is to develop a knowledge management solution to address this challenge across multiple scales of biological structure. In particular, we are developing open tools to enable the searching, objective comparison and re-use of models and associated data in terms of their physiological meaning.

ApiNATOMY tools
Clinical indices & brain region graphs
Early ApiNATOMY prototypes