title: User-centered evaluation of Arizona BioPathway: an information extraction, integration, and visualization system.
abstract: 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.
authors.affiliation: Department of Management Information Systems, University of Arizona, Tucson, AZ 85721, USA. karin@alumni.rice.edu
authors.forename: Karin D
authors.initials: KD
authors.lastname: Quiñones
authors.forename: Hua
authors.initials: H
authors.lastname: Su
authors.forename: Byron
authors.initials: B
authors.lastname: Marshall
authors.forename: Shauna
authors.initials: S
authors.lastname: Eggers
authors.forename: Hsinchun
authors.initials: H
authors.lastname: Chen
mesh_terms: D003628:Database Management Systems; D016208:Databases, Factual; D016247:Information Storage and Retrieval / Q000379:methods*; D008954:Models, Biological; D009323:Natural Language Processing; D010506:Periodicals as Topic; D020543:Proteome / Q000145:classification / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D020543:Proteome