Improvements on pathwaymapper: a collaborative pathway curation tool
Author(s)
Advisor
Date
2018-07Publisher
Bilkent University
Language
English
Type
ThesisItem Usage Stats
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Abstract
Information visualization focuses on visually representing abstract data to amplify
human cognition. Graph visualization is one of the most common types in
the eld of information visualization because of its capabilities to present huge
amount of data in a clear and meaningful manner. A graph is a suitable data
structure for representing relational information and for this reason graph visualization
has a wide usage in biological pathway visualization as well. In this
thesis, we focus on collaborative construction of cancer pathways and visualization
of cancer genomics data overlaid over such networks. Several biological
pathway visualization tools have been developed to help biologists analyze cancer
genomics data, using various formats, including standard formats like SBGN,
in the past. Nevertheless, most biologists prefer curated pathway diagrams like
the ones featured in The Cancer Genome Atlas (TCGA) manuscripts, using a
simpler notation. These pathway diagrams outline the alterations occurring in
pathways for di erent cancer types. To address this need, a web-based tool called
PathwayMapper was previously developed. PathwayMapper can be used to view
pre-curated cancer pathways or to create new pathways from scratch. It has
many features including overlay of genomic alteration data from the cBioPortal.
It also includes a collaborative mode so that the users can interactively create
and modify the cancer pathways.
With this thesis, we improve PathwayMapper in several ways to make it a
more complete and powerful editor with a better user interface. New features
include complexity management operations, edge bend support, interactive node
resize, and various highlighting capabilities. Furthermore, the user interface has
been improved to be more user friendly with the addition of a toolbar.
Keywords
Graph VisualizationPathway Editor
Systems Biology
Biological Pathways
Cancer Genomics
Pathway Curation Tool
Web-Based Ssoftware