Visualizing aggregated biological pathway relations

ABSTRACT

The Genescene development team has constructed an aggregation interface for automatically-extracted biomedical pathway relations that is intended to help researchers identify and process relevant information from the vast digital library of abstracts found in the National Library of Medicine's PubMed collection. Users view extracted relations at various levels of relational granularity in an interactive and visual node-link interface. Anecdotal feedback reported here suggests that this multi-granular visual paradigm aligns well with various research tasks, helping users find relevant articles and discover new information.

REFERENCES

• 1: Andrey Rzhetsky , Ivan Iossifov , Tomohiro Koike , Michael Krauthammer , Pauline Kra , Mitzi Morris , Hong Yu , Pablo Ariel Duboué , Wubin Weng , W. John Wilbur , Vasileios Hatzivassiloglou , Carol Friedman, GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data, Journal of Biomedical Informatics, v.37 n.1, p.43-53, February 2004 [doi>10.1016/j.jbi.2003.10.001]
• 2: Daniel M. Mcdonald , Hsinchun Chen , Hua Su , Byron B. Marshall, Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parser, Bioinformatics, v.20 n.18, p.3370-3378, December 2004 [doi>10.1093/bioinformatics/bth409]
• 3: B. Marshall, H. Su, D. McDonald, and H. Chen, "Linking ontological resources using aggregatable substance identifiers to organize extracted relations," presented at Pac. Symp. Biocomput., Big Island, Hawaii, 2005.

INDEX TERMS

Primary Classification:
  H. Information Systems
  H.5 INFORMATION INTERFACES AND PRESENTATION (I.7)
      H.5.2 User Interfaces (D.2.2, H.1.2, I.3.6)
          Subjects: Graphical user interfaces (GUI)

General Terms:
Algorithms, Human Factors

Keywords:
biological pathway relations, knowledge aggregation, visualization