Bilkent University
Department of Computer Engineering


Libraries and tools for viewing and editing of biological maps in SBGN


Metin Can Siper
MS Student
Computer Engineering Department
Bilkent University

Information about cellular processes and pathways is becoming increasingly available in detailed, computable standard formats including Systems Biology Graphical Notation (SBGN). Effective visualization of this information is a key recurring requirement for biological data analysis, especially for -omic data [1]. Biological data analysis is rapidly migrating to web based platforms; thus there is a substantial need for sophisticated web based pathway viewing and editing tools that support these platforms and other use cases.

We propose to develop a modular software architecture to meet this need. This proposed architecture includes reusable web based libraries and easily customizable and embeddable tools developed using these libraries. Our libraries include SBGNViz.js, a Cytoscape.js based library providing a renderer and an API to develop tools visualizing pathway models represented by SBGN Process Description Notation, and ChiSE.js, an SBGNViz.js based library to visualize and construct pathway models represented in SBGN Process Description Notation, and miscellaneous Cytoscape.js extensions. Our tools are built using these libraries and include SBGNViz and Newt, which are sample applications for SBGNViz.js and ChiSE.js respectively.

A web based visual biocuration workspace, focusing on curating detailed mechanistic pathways, is a good use case indicating reusability of ChiSE.js and embeddability of Newt. It is developed by improving Newt with Share.js and MongoDB supports and was designed as a flexible platform where multiple humans, NLP and AI agents can collaborate in real-time on a common model using an event driven API [2].

Newt is developing to become a first web based SBGN editor with full support for compound structures such as molecular complexes and compartment, static and incremental layout, and complexity management of large maps.

[1] Sari M, Bahceci I, Dogrusoz U, Sumer SO, Aksoy BA, Babur Ö, et al. (2015) SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps. PLoS ONE 10(6): e0128985. doi:10.1371/journal.pone.0128985

[2] Durupinar-Babur F, Siper MC, Dogrusoz U, Bahceci I, Babur O, Demir E. 2016. BT103: Collaborative Workspaces for Pathway Curation. International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016).


DATE: 27 March, 2017, Monday @ 16:30