TY - JOUR
T1 - User-centered evaluation of Arizona BioPathway
T2 - An information extraction, integration, and visualization system
AU - Quiñones, Karin D.
AU - Su, Hua
AU - Marshall, Byron
AU - Eggers, Shauna
AU - Chen, Hsinchun
N1 - Funding Information:
Manuscript received April 27, 2006; revised August 13, 2006. This work was supported by the NIH/NLM under Grant 1 R33 LM07299-01, 2002–2006, “GeneScene: A Toolkit for Gene Pathway Analysis.” K. D. Quiñones, H. Su, and H. Chen are with the Department of Management Information Systems, University of Arizona, Tucson, AZ 85721, USA (e-mail: [email protected]; [email protected]; [email protected]).
PY - 2007/9
Y1 - 2007/9
N2 - Explosive growth in biomedical research has made automated information extraction, knowledge integration, and visualization increasingly important and critically needed. The Arizona BioPathway (ABP) system extracts and displays biological regulatory pathway information from the abstracts of journal articles. This study uses relations extracted from more than 200 PubMed abstracts presented in a tabular and graphical user interface with built-in search and aggregation functionality. This paper presents a task-centered assessment of the usefulness and usability of the ABP system focusing on its relation aggregation and visualization functionalities. Results suggest that our graph-based visualization is more efficient in supporting pathway analysis tasks and is perceived as more useful and easier to use as compared to a text-based literature-viewing method. Relation aggregation significantly contributes to knowledge-acquisition efficiency. Together, the graphic and tabular views in the ABP Visualizer provide a flexible and effective interface for pathway relation browsing and analysis. Our study contributes to pathway-related research and biological information extraction by assessing the value of a multiview, relation-based interface that supports user-controlled exploration of pathway information across multiple granularities.
AB - Explosive growth in biomedical research has made automated information extraction, knowledge integration, and visualization increasingly important and critically needed. The Arizona BioPathway (ABP) system extracts and displays biological regulatory pathway information from the abstracts of journal articles. This study uses relations extracted from more than 200 PubMed abstracts presented in a tabular and graphical user interface with built-in search and aggregation functionality. This paper presents a task-centered assessment of the usefulness and usability of the ABP system focusing on its relation aggregation and visualization functionalities. Results suggest that our graph-based visualization is more efficient in supporting pathway analysis tasks and is perceived as more useful and easier to use as compared to a text-based literature-viewing method. Relation aggregation significantly contributes to knowledge-acquisition efficiency. Together, the graphic and tabular views in the ABP Visualizer provide a flexible and effective interface for pathway relation browsing and analysis. Our study contributes to pathway-related research and biological information extraction by assessing the value of a multiview, relation-based interface that supports user-controlled exploration of pathway information across multiple granularities.
KW - Biomedical information extraction
KW - Pathway analysis
KW - System evaluation
KW - Visualization
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UR - http://www.scopus.com/inward/citedby.url?scp=34548680543&partnerID=8YFLogxK
U2 - 10.1109/TITB.2006.889706
DO - 10.1109/TITB.2006.889706
M3 - Article
C2 - 17912969
AN - SCOPUS:34548680543
SN - 1089-7771
VL - 11
SP - 527
EP - 536
JO - IEEE Transactions on Information Technology in Biomedicine
JF - IEEE Transactions on Information Technology in Biomedicine
IS - 5
ER -