Search Interfaces for Biodiversity Informatics

ITR/IDM 0219492

Principal Investigator

Keywords

Project Summary

This project explores technologies for visualizing complex datasets to assist information retrieval and understanding.   Our particular interest is in biodiversity information, which underlies most pressing environmental and conservation debates but is needed by users without significant content expertise.  This project combines information visualization techniques and rapid feedback dynamic query interfaces coupled with an aggressive approach of working with representative users from design through evaluation. Zoomable interfaces will allow users to navigate multiple hierarchies, in order to visually accommodate and understand highly interconnected data.

Publications and Products

1. Parr, C.S., B. Lee, D. Campbell, and B. Bederson. "Tree browsing: Visualizing biodiversity information" , Biosciences Day poster presentation, University of Maryland, (2002). Poster available at http://www.cs.umd.edu/hcil/taxontree.
2. Parr, C.S., B. Lee, D. Campbell, and B. Bederson.  “Classification Datasets,” Datasets made available for the IEEE Symposium on InformationVisualization InfoVis Contest 2003: Visualization and pairwise comparisons of trees.  (2003) Available at: http://www.cs.umd.edu/hcil/iv03contest/.

Project Impact

Discoveries at and across the frontier of science and engineering
Our findings extend our understanding of zooming and integrated searching and browsing as tools for information retrieval. We are adding to knowledge about the behavior of non-content experts and how they can be supported in exploring complex biological databases, even as they gain content-expertise.. Our first application. TaxonTree scales up to very large trees (about 200,000 nodes) through use of a database backend. We contributed sample datasets for an Information Visualization Contest expected to generate other innovative solutions to the problem of comparing large trees. We are exploring and evaluating different ways to display node-link diagrams and node attributes.

This interdisciplinary work provides some of the first findings focused on front-end systems in biodiversity informatics. In particular it targets an expanded user community of non-experts. At the same time, expert biologists will benefit from the ability to visualize and interact with taxonomic and phylogenetic databases.

Connections between discoveries and their use in service to society
Supporting users across content-expertise levels is of vital importance to the global information economy. People in governments and schools and private industry rely on internet resources for decision-making and learning. Specifically, this project represents a new approach for visualizing and reducing biodiversity data complexity so that it can be successfully used across society.

A diverse, globally oriented workforce of scientists and engineers
Other than the PI, all project personnel including one Ph.D. student, two part-time research scientists, and five undergraduate design partners have been women.

Improved achievement in mathematics and science skills needed by all Americans
Our tools are expected to support increased understanding of scientific databases and biodiversity data. In addition to its use in a core biology course at University of Maryland, TaxonTree may be adapted for use by the BioKIDS project (NSF REC 0089283). BioKIDS’ inquiry-based biodiversity curriculum targets 5th and 6th graders in the Detroit Public School System.

Goals, Objectives and Targeted Activities

Our project goals are to:
1) Develop a searching interface for biodiversity databases targeting domain-novice adults.
2) Build interfaces combining "folk" and "scientific" understanding.
3) Evaluate the developed interfaces and compare them to existing interface models in the biodiversity domain.

Specific objectives for the first year were to take existing technology and adapt it for the biodiversity domain as a first step towards understanding the domain and its users. Since initiating the project in September 2002 we created one application and two prototypes towards the first two goals and have conducted one qualitative user study towards the third goal.

We developed a new software application, TaxonTree by modifying an existing application, SpaceTree. TaxonTree allows users to browse and search a very large node-link diagram of animal names that we constructed by integrating data from a number of public and private sources. Names link to external web pages. TaxonTree uses zooming interactivity, integrated searching and browsing, and dynamic queries. Search results are presented in the larger biological context of their classification tree. TaxonTree was made available to an undergraduate biology class with 100 students. Towards the second goal, we developed a prototype called DoubleTree which couples navigation in the scientific biological classification in TaxonTree with a simpler, folk tree; another prototype supported multi-dimensional natural history data exploration. These experiences will guide further development in visualizing complex networked datasets involving biodiversity ontologies. A qualitative user study of TaxonTree provided evidence of usability and user preference for browsing in this domain. We can now refine the tasks and metrics to allow comparative studies to accomplish goal 3 for TaxonTree and future applications.

Area Background

This research addresses the general problem of diverse users and complex information sources via visualization.  In the same way that bioinformatics has revolutionized the fields of molecular biology and biophysics, biodiversity informatics is at the threshold of providing data and tools to allow the next generation to discover and understand global patterns and processes governing the diversity of life.  Much biodiversity information is already available on the Internet (Bisby, 2000), where keyword searches remain the predominant method of access (Cockburn & McKenzie, 2000). In the biodiversity domain, the efficiency of single word searches is constrained because inherently complex biological data are stored in a controlled language that is not necessarily understood by domain novices.  Users may be professionals such as taxonomists and conservation biologists, or they may be domain novices, such as students or educated professionals of other fields such as land-use planners or lawyers (Maier et al., 2000).

Area References

1. Bisby, F.A. (2000). The quiet revolution: biodiversity informatics and the Internet. Science 289:2309-2312.
2. Cockburn, A., & McKenzie, B. (2000). What Do Web Users Do? An Empirical Analysis of Web Use. International Journal of Human-Computer Studies, 54(6), pp. 903-922, Academic Press.
3. Maier, D., E. Landis, J. Cushing, A. Frondorf, A. Silberschatz, M. Frame, and J.L. Schnase, eds. (2000). Research directions in biodiversity and ecosystem informatics. Report of an NSF, USGS, NASA Goddard Space Flight Center, June 22-23, 2000. Available http://bio.gsfc.nasa.gov/ (accessed 30 January 2002).

Potential Related Projects

Project Websites

Illustrations

Online Software

TaxonTree is built on SpaceTree, one of the HCIL Products. If you need information on licensing SpaceTree or TaxonTree source code please contact Jim Poulos at University of Maryland's Office of Technology Commercialization (301)-403-2711 or jp227@umail.umd.edu.   TaxonTree may be downloaded and used without charge for educational fair use.

Taxontree 1.1 was released May 29, 2003 (12 MB). Requires Java 1.4.1. Not currently compatible with Macintosh. The download includes the customized database of almost 200,000 names in MS Access tables.

Online Data