iOpener Workbench: Tools for Rapid
Understanding of Scientific Literature
Cody Dunne, Ben Shneiderman, Bonnie Dorr & Judith Klavans
{cdunne, ben, bonnie}@cs.umd.edu, jklavans@umd.edu
27th Annual Human-Computer Interaction Lab Symposium
May 27-28, 2010
College Park, MD
iOpener Workbench
Contribution
• Infrastructure for rapidly summarizing
scientific endeavor
– Integrate statistics, visualization, reference
management, and automatic summarization
– Multiple coordinated views
Use Cases
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Learn about new fields
Understand how communities form
Analyze citation patterns within communities
Easily explore & export all papers in a
community
What we integrate
• Potent network analysis tool – SocialAction
– Citation network statistics & visualization
– Automatic community detection & visualization
• Reference & document management – JabRef
– Powerful reference manager with extensive features
for search, grouping, review, annotation, and export
• Document view with citation linking & highlight
• Automatically generated summaries
– Citation text, keywords, abstracts
What can you do with a graph?
• Statistics, lists, and text is helpful, but
• Visualizations show unexpected trends,
clusters, gaps, outliers
• Data cleaning & verification
• “Information visualization answers questions
you didn't know you had” – Ben S.
Importance of Survey Articles
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Rapidly expanding disciplines
Large volume of scientific publications
Increasing cross-disciplinary research
Need for accurate surveys of previous work
– Short summaries
– In-depth historical notes
• Multiple users
– Scientists
– Students & Educators
– Government decision makers
iOPENER
• NSF Info Integration & Informatics program
• Information Organization for PENning
Expositions on Research
Components
• Bibliometric lexical link mining
• Automatic summarization techniques
• Visualization tools for structure and content
Ongoing Work
• Increase preprocessing of citation texts to
vastly improve trimmer summary
comprehension
• Preliminary case studies with UMD student
domain experts
– Dependency parsing subset of the ACL Anthology
Network (AAN)
Coming Soon
• Multi-dimensional in-depth long-term case
studies
– longitudinal case studies with domain experts
using their data
– close participant observation
• Software & generated surveys publicly
available and presented to academia and
wider audiences
iOpener Workbench
• Infrastructure to aid rapid summarization of
scientific literature
• Integrates
– Statistics
– Visualization
– Reference management
– Automatic summarization
iOpener Workbench: Tools for Rapid
Understanding of Scientific Literature
Cody Dunne, Ben Shneiderman, Bonnie Dorr & Judith Klavans
{cdunne, ben, bonnie}@cs.umd.edu, jklavans@umd.edu
tangra.si.umich.edu/clair/iopener
This work has been partially supported by NSF grant "iOPENER: A
Flexible Framework to Support Rapid Learning in Unfamiliar Research
Domains", jointly awarded to UMD and UMich as IIS 0705832.
Network Analysis
Reference Manager
Document &
Citation View
Summarization
Features – Network analysis
• SocialAction (Perer, Shneiderman)
• Citation network visualization
– Force-directed placement (by linkages)
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Scatterplots of paper attributes & statistics
Statistics rank tables
Categorial and numerical range coloring
Automatic community detection
– Newman '04 fast heuristic
Features – Reference Manager
• Search by field with simple regex
– abstract|keywords=nonprojective and year = 2008
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Grouping -- automatic, search results, manual
DOI/URL, fulltext (annotated PDF, plain text)
Metadata, abstracts
User generated reviews
BibTeX, Word, OpenOffice integration
HTML, EndNote export
Document view - features
• Citation links
• Highlighting
Summarization - Features
• Automatically generated summaries
Citation text, keywords, abstracts
• Working to substantially improve coherence &
relevance