University of Michigan Ann Arbor:
In-kind Support; Collaborative Research
Some equipment (e.g. PC printer) owned by University of Michigan was
used by C. Parr in pursuit of work relevant to both this project and
BioKIDS (Interagency Education Research Initiative REC-0089283).
Personnel on both projects advised the efforts of the other,
programmers communicate to ensure compatibility across projects.
In order to collaborate on user studies of Graph Visualization
software, personnel from the SAGE project at RPI provided and
installed an eyetracking system in our facilities and will assist in
designing data collection and analyzing results.
Jeffrey Jenson, University of Maryland College of Life Sciences,
instructor of the college course for which we designed software and
conducted user testing. He provided content, advice, and logistical
support, and administered user surveys.
William Fagan, University of Maryland College of Life Sciences is
providing content and advice related to food web visualizations.
Wayne Gray, Rensselaer Polytechnic Inst. and other members of the SAGE
project are collaborating on cognitive aspects of the graph
visualization user study.
We are collaborating with Tim Finin, University of Maryland Baltimore
County, and other members of the SPIRE project on semantic web
representations of ecological interaction data and natural history
Kevin Omland, University of Maryland Baltimore County. We have begun
investigating the role of visualizations in 'tree-thinking' for
Activities and findings:
Research and Education Activities:
We continued our studies of tree visualization techniques through
further development and testing of our software applications TaxonTree
and DoubleTree. TaxonTree allows users to browse and search a very
large tree of almost 200,000 animal names that we constructed by
integrating data from a number of public and private sources. Names
link to external web pages on three different, publicly available
TaxonTree uses zooming interactivity, integrated searching and
browsing, and dynamic queries. In particular, search results are
presented in a larger biological context. We used zoomable user
interface toolkits, Jazz and Piccolo, developed by our project
personnel, as well as Java, Microsoft Access, and MySQL.
We published results from a qualitative user study of TaxonTree
conducted near the end of our first year. Through interviews and
specific tasks we characterized information-seeking behavior and
interaction preferences in the biodiversity domain.
We developed DoubleTree, an extension of TaxonTree that allows
comparison of two trees using coupled interaction. We implemented our
prototype with various datasets. First, we compared the original
TaxonTree dataset of 200,000 names with a widely used classification
from ITIS. Then, we constructed a 'folk biology' tree using a small
set of animal names from the BioKIDS project in southeastern Michigan,
manually coupled this to the original large TaxonTree scientific tree,
and demonstrated how a 'folk' tree could help non-expert users
navigate a scientific tree. In our third year we began collaborating
with Kevin Omland at UMBC to further investigate the role of tree
visualizations in 'tree-thinking' for evolutionary biology.
We ported TaxonTree to MySQL and Java Web Start so that it could be
deployed on the web, and compared its querying and browsing
performance to stand-alone versions and DoubleTree. We presented our
results at two conferences: Advanced Visual Interfaces and the
Ecological Society of America.
We have completed integrating TaxonTree with the existing high-traffic
website, University of Michigan's Animal Diversity Web (ADW)
(http://www.animaldiversity.org); it is functional now for Windows
users and will soon be available for Mac OSX users. This fall we will
conduct two quantitative studies comparing effectiveness of our
interface with the more traditional interface already available on
ADW. One study will involve volunteers in a controlled laboratory
setting, and one will involve surveys and site log analysis of usage
by the worldwide general public. When complete this Fall, these
studies will fulfill our original project objectives.
We have engaged in three activities beyond our original goals.
First, we are extending our exploration beyond simple hierarchical
data. We have compiled ecological interaction datasets and have
implemented a new tool, TreePlus (Figures 1 and 2, attached pdf), that
employ similar and new techniques to allow users to interact with
graph data. We have also adapted an existing tool, PaperLens, to
serve as a database visualization platform, EcoLens, for the over 250
food web datasets. Qualitative assessment of EcoLens will be conducted
by asking food web researchers to evaluate it using their own data.
We will soon conduct a quantitative user study to determine for which
tasks and graph densities TreePlus, which uses an incremental
tree-layout approach, outperforms a more traditioal spring-embedded
Second, we have begun exploring ontologies, in terms of applying
visual interactive tools for them and in building them in
collaboration with the Animal Diversity Web. A preview of this work
was presented at the CODATA 2005 conference in Berlin. We are
exploring using ontologies in collaboration with the Semantic
Prototypes in Research Ecoinformatics project (SPIRE) at UMBC,
providing data and expertise towards developing a semantically-rich
predictive modeling framework. EcoLens and TreePlus will probably be
used by SPIRE personnel. Animal Diversity Web will be one of the
first large databases available on the semantic web as a case study
and data source for biologists.
Third, we organized a full-day workshop entitled 'HCI in Biodiversity
Largely supported by the National Biological Information
Infrastructure, it was held on June 2, 2005 in association with the
University of Maryland Human-Computer Interaction Laboratory's 22nd
Annual Symposium and Open House. Twenty-five participants from
academia, industry, and government gathered to hear 8 invited
speakers, join 3 invited panelists for discussion, and engage in
hands-on software demonstrations. Participants decided to prepare a
white paper covering the state of the field and suggestions for future
work to be submitted to a journal.
Our qualitative user study of TaxonTree in an undergraduate course is
the first to describe usage patterns in the biodiversity domain. We
found that interaction with an animated, zoomable node-link diagram
aided users' understanding of the data. Most users approached
biodiversity data by browsing, using common names and general
knowledge rather than the scientific keyword expertise necessary to
search using traditional interfaces. Users with different levels of
interest in the domain had different interaction preferences --
results suggest that users with higher interest levels (usually
female) prefer greater control over node opening.
Performance of TaxonTree and DoubleTree on large datasets was quite
good, with basic browsing and querying tasks requiring from 62 ms to
2547 ms. This is because our approach is to show only the subset of
data of immediate interest to the user, while retaining the ability
for users to browse to obtain nearby detail.
Our work demonstrates trade-offs inherent in displaying phylogenetic
vs. classification trees and shows that a combined approach is not
only feasible but usable. Coupling a folk tree with a large
scientific tree shows promise but a more effective way to illustrate
one to many mappings is needed. Preliminary, unpublished results
suggest that TaxonTree's tree-drawing style does not result in
significantly more misconceptions when compared to more traditional
cladogram styles. In fact, subjects naive to evolutionary biology
often misinterpret both kinds of trees and further research will be
necessary to explore the role of visualizations in fostering
Training and Development:
In addition to teams of undergraduate design partners we worked with
in our early years, we continued to work with a computer science
undergraduate, Svetlana Yarosh. She gained database implementation
skills as well as experience implementing zoomable interfaces, and
designed a user study.
Our graduate student, Bongshin Lee, developed and defended her
doctoral dissertation proposal last year and gained expertise in graph
visualization implementation this year.
Our project biologist, Cynthia Parr, continued to learn semantic web
technologies and community ecology theory. Together with Bill Fagan,
she led a seminar course for ten biology graduate students on
Students participated in discussing recent literature and technology
concepts, tested software, and conducted independent research projects
By collaborating with a college course for two years we exposed nearly
200 undergraduates to a novel use of technology in the classroom. Our
technology is freely available to the general public on our website,
and is now available on the high-traffic outreach and education site,
Animal Diversity Web. We demonstrated the technology to visitors at
several Human-Computer Interaction Laboratory open houses. The CIPRes
project evaluated our software with high school teachers to determine
its suitability for future outreach related to the tree of life.
Other Specific Products:
Two XML formatted biological classification trees to be used for
benchmark testing of information visualization tools
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:
TaxonTree version 1.3 is now available to Windows OS users by choosing
"Find in TaxonTree" from most Animal Diversity Web pages. Names now
link to different kinds of resources available at that website. A new
feature, "Load List", makes it possible to see how any given list of
taxonomic names is grouped taxonomically.
Version 1.2 is still available from our project web page.
Originally designed for teaching of college-level animal diversity
courses this is an interactive, searchable tree of almost 200,000
scientific names. Many names link to web pages created by others
outside our project and some names have synapomorphies diagnosing
groups. Users can choose to work online, using any web browser and
Java Web Start, or can work offline using a stand-alone version.
Version 1.2 Available free to all users at
Version 1.3 available from most pages at
DoubleTree is an application for comparing two trees using coupled
interaction. Download include several datasets, including two large
scientific trees of animal names, and one smaller "folk" tree of
animals in southeastern Michigan.
Available at http:www.cs.umd.edu/hcil/biodiversity
TreePlus: a tree-layout approach to graph visualization using
animation, zooming, and incremental exploration.
Will be downloadable from website
http://www.cs.umd.edu/hcil/biodiversity. Video demonstrations are
EcoLens: a database visualization tool for ecological interactions
Will be made available on http://www.cs.umd.edu/hcil/biodiversity
ADW Ontology: an ontology for animal natural history
Freely available at Open Biological Ontologies,
EcoLens data: a collection of ecological interaction datasets taken
from public or private sources and modified for use in ecological
Selected data available upon request of the researcher. Some data is
not publicly available and/or should not be redistributed by us.
This page provides a synopsis of the project and offers online usage
or free downloads of all of our products for non-commercial use.
Contributions within Discipline:
Our work in the third year consisted of extensive programming to
implement graph and database visualization tools drawing upon our
previous results, and integration of our previously developed tool
with a widely used online database.
Generally, our findings extend the understanding of zooming and
integrated searching and browsing and incremental exploration. Our
emphasis on content understanding, and not just ease of use, shows
promise for contributing to efforts to innovate in this arena. We are
adding to knowledge about the behavior of non-content experts and how
they can be supported in exploring complex biological databases. We
have also begun to better characterize changes in user preferences as
they gain content expertise. We have illustrated the value of coupled
interaction in comparing two large trees or in allowing one folk tree
to foster exploration of a large scientific tree. We have developed
new ways to implement incremental exploration of graphs using a tree
layout, adjacent node previews, and path previews. Our work on
EcoLens has identified directions for generalizing coupled views to
robustly support two-element schema.
Most current work in biodiversity informatics emphasizes back-end
issues such as metadata standards and interoperability and distributed
computing. Our work provides some of the first findings focused on
front-end systems, and in particular in targeting an expanded user
community of non-experts. It could be argued that directing energy
towards user needs and experiences will drive further innovation in
back-end systems, as new users provide feedback on the kinds and
sources of biodiversity information resources available to them.
Our biologist collaborators at the Animal Diversity Web already have
begun using TaxonTree to proofread their taxonomic database. Other
projects such as CIPRes and SEEK are evaluating our tools so that they
may modify them for taxonomic concept displays for experts and for the
general public. A future Assembling the Tree of Life project will use
a TaxonTree-like interface for data sharing .
We have provided an innovative application for education.
Finally, we provide further evidence of lay user cognition,
contributing to the field of cognitive anthropology, or
We have previously exposed undergraduate design partners to research,
particularly in an exciting new field, thus modeling potential career
paths. All of these design partners were women. This project provides
research opportunities for our project biologist in a way that
substantially expands her technical skillsets. Finally, computer
science students (undergraduate and graduate) are further developing
their skills in working in multidisciplinary teams.
In addition to producing TaxonTree as a resource for teaching, we have
provided content resources for three other projects.
First, our integrated taxonomic content is now being used by the
University of Michigan's Animal Diversity Web
Second, we also developed sample datasets for an Information
Visualization Contest (http://www.cs.umd.edu/hcil/iv03contest/),
expected to generate innovative solutions to the problem of comparing
Third, the ADW natural history ontology and augmented composite
ecological interaction database are being used by the SPIRE project at
University of Maryland Baltimore County.