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Extended LineSets: a visualization technique for the interactive inspection of biological pathways.

Paduano F, Forbes AG - BMC Proc (2015)

Bottom Line: We introduce a technique inspired by LineSets that enables biologists to fulfill these tasks more effectively.Our technique incorporates intuitive graphical representations of different levels of information and includes a well-designed set of user interactions for selecting, filtering, and organizing biological pathway data gathered from multiple databases.Based on interviews with domain experts and an analysis of two use cases, we show that our technique provides functionality not currently enabled by current techniques, and moreover that it helps biologists to better understand both inter-pathway connectivity and the hierarchical structure of biological elements within the pathways.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science M/C 152, University of Illinois at Chicago, 851 S. Morgan, Room 1120, Chicago 60607-7053, IL, USA.

ABSTRACT

Background: Biologists make use of pathway visualization tools for a range of tasks, including investigating inter-pathway connectivity and retrieving details about biological entities and interactions. Some of these tasks require an understanding of the hierarchical nature of elements within the pathway or the ability to make comparisons between multiple pathways. We introduce a technique inspired by LineSets that enables biologists to fulfill these tasks more effectively.

Results: We introduce a novel technique, Extended LineSets, to facilitate new explorations of biological pathways. Our technique incorporates intuitive graphical representations of different levels of information and includes a well-designed set of user interactions for selecting, filtering, and organizing biological pathway data gathered from multiple databases.

Conclusions: Based on interviews with domain experts and an analysis of two use cases, we show that our technique provides functionality not currently enabled by current techniques, and moreover that it helps biologists to better understand both inter-pathway connectivity and the hierarchical structure of biological elements within the pathways.

No MeSH data available.


The figure demonstrates hierarchical inspection using the symbolic overview and the the pruned tree. In (a), the user selects protein G from the expanded node within the node-link diagram; this protein is highlighted within the pruned tree visualization, which also provides more information about its siblings (the proteins D, E, and F) and its parent and grandparent nodes (the complexes C, B, and A). In (b), the user selects a complex B in the expanded node, which is displayed in a similar manner in the pruned tree.
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Figure 4: The figure demonstrates hierarchical inspection using the symbolic overview and the the pruned tree. In (a), the user selects protein G from the expanded node within the node-link diagram; this protein is highlighted within the pruned tree visualization, which also provides more information about its siblings (the proteins D, E, and F) and its parent and grandparent nodes (the complexes C, B, and A). In (b), the user selects a complex B in the expanded node, which is displayed in a similar manner in the pruned tree.

Mentions: Figure 4 illustrates how the symbolic overview and the pruned tree are coordinated in order to enable the inspection of a hierarchical structure. In Figure 4(a), the user selects protein G, which brings up a pruned tree that indicates the hierarchy of parent complexes that contain G, fist A, then B, and then the direct parent C. The right side of the pruned tree shows protein G and its siblings D, E and F. Figure 4(b) illustrates a similar case for complex B and its corresponding pruned tree.


Extended LineSets: a visualization technique for the interactive inspection of biological pathways.

Paduano F, Forbes AG - BMC Proc (2015)

The figure demonstrates hierarchical inspection using the symbolic overview and the the pruned tree. In (a), the user selects protein G from the expanded node within the node-link diagram; this protein is highlighted within the pruned tree visualization, which also provides more information about its siblings (the proteins D, E, and F) and its parent and grandparent nodes (the complexes C, B, and A). In (b), the user selects a complex B in the expanded node, which is displayed in a similar manner in the pruned tree.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4547339&req=5

Figure 4: The figure demonstrates hierarchical inspection using the symbolic overview and the the pruned tree. In (a), the user selects protein G from the expanded node within the node-link diagram; this protein is highlighted within the pruned tree visualization, which also provides more information about its siblings (the proteins D, E, and F) and its parent and grandparent nodes (the complexes C, B, and A). In (b), the user selects a complex B in the expanded node, which is displayed in a similar manner in the pruned tree.
Mentions: Figure 4 illustrates how the symbolic overview and the pruned tree are coordinated in order to enable the inspection of a hierarchical structure. In Figure 4(a), the user selects protein G, which brings up a pruned tree that indicates the hierarchy of parent complexes that contain G, fist A, then B, and then the direct parent C. The right side of the pruned tree shows protein G and its siblings D, E and F. Figure 4(b) illustrates a similar case for complex B and its corresponding pruned tree.

Bottom Line: We introduce a technique inspired by LineSets that enables biologists to fulfill these tasks more effectively.Our technique incorporates intuitive graphical representations of different levels of information and includes a well-designed set of user interactions for selecting, filtering, and organizing biological pathway data gathered from multiple databases.Based on interviews with domain experts and an analysis of two use cases, we show that our technique provides functionality not currently enabled by current techniques, and moreover that it helps biologists to better understand both inter-pathway connectivity and the hierarchical structure of biological elements within the pathways.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science M/C 152, University of Illinois at Chicago, 851 S. Morgan, Room 1120, Chicago 60607-7053, IL, USA.

ABSTRACT

Background: Biologists make use of pathway visualization tools for a range of tasks, including investigating inter-pathway connectivity and retrieving details about biological entities and interactions. Some of these tasks require an understanding of the hierarchical nature of elements within the pathway or the ability to make comparisons between multiple pathways. We introduce a technique inspired by LineSets that enables biologists to fulfill these tasks more effectively.

Results: We introduce a novel technique, Extended LineSets, to facilitate new explorations of biological pathways. Our technique incorporates intuitive graphical representations of different levels of information and includes a well-designed set of user interactions for selecting, filtering, and organizing biological pathway data gathered from multiple databases.

Conclusions: Based on interviews with domain experts and an analysis of two use cases, we show that our technique provides functionality not currently enabled by current techniques, and moreover that it helps biologists to better understand both inter-pathway connectivity and the hierarchical structure of biological elements within the pathways.

No MeSH data available.