Web Technology to Make Taxonomy More Accessible...
Transcript of Web Technology to Make Taxonomy More Accessible...
-
Ken M. Schwab*, Justin E. Lawrence, and Vincent H. Resh Department of Environmental Science, Policy and Management, UC Berkeley *[email protected]
1. Narwani, A., and A. Mazumder (2012). Bottom-
up Effects of Species Diversity on the
Functioning and Stability of Food Webs, J.
Anim. Ecol. 81:701-13.
2. Lawrence, J.E., K.B. Lunde, R.D. Mazor, L.A.
Bêche, Eric P. McElravy, and Vincent H. Resh
(2010). Long-term Macroinvertebrate
Responses to Climate Change: Implications
for Biological Assessment in Mediterranean-
Climate Streams, J. N. Am. Benthol. Soc.
29:1424-1440
3. Merritt, R.W., K. Cummins, and M. Berg.
(2008) An Introduction to the Aquatic Insects
of North America. Stackpole: Dubuque, IA.
4. Fore, L.S., K. Paulsen, and K. O'Laughlin
(2001). Assessing the Performance of
Volunteers in Monitoring Streams, Freshwater
Biology 46:109-23.
5. Thomason, A. Read. (2010). Bugwater: A Fly
Fisher's Look through the Seasons at Bugs in
Their Aquatic Habitat and the Fish That Eat
Them. Stackpole: Mechanicsburg, PA.
Web Technology to Make Taxonomy More Accessible: Enhancing Quantification of Aquatic Biodiversity at the Regional Scale
Thanks to Dr. Chris Lever, Dr. George Roderick, Michael
Peterson, Lisa Hunt, Janet Hsiao, and Pete Oboyski
Figure 4. Example images taken from An Introduction to the Aquatic Insects of North America4.
5
• The order Plecoptera (stoneflies) was chosen for the prototype.
• BMI specimens obtained from the Essig Museum and the Resh Lab at UC Berkeley.
• Images captured from a Leica MZ APO stereomicroscope with montage camera.
• Identification steps in miKey adapted from existing taxonomic keys3 (Figure 4).
• HTML, CSS, PHP, and JavaScript languages used to achieve web functions and
effects (e.g. mouse-over glossary and image zoom functions)
Introduction
miKey is a web-based prototype built to enhance both intuitive comprehension and time efficiency of taxonomic identification by using web technology to improve the way essential
information in taxonomic keys is displayed to users. For example, the mouse-over feature triggers definitions to be populated in the glossary panel (Figure 3A) and the image zoom
highlights distinguishing morphological trait(s) of interest (Figure 3B). The San Francisco Bay region is home to a community of computer-savvy people who can be engaged
through this tool to advance aquatic science4. Future prototypes will include features that display and serve data in geospatial formats (e.g. ArcGIS and Google Earth).
Figure 3. (A) Step three of dichotomous key (to family) for Plecoptera nymphs.
In this step, identifiers compare length and shape of glossae and paraglossae.
(B) Highlighted in this screenshot is the mouse-over image zoom and glossary
panel features. Image zoom provides the user with freedom to explore images
up-close and can provide a view that is more representative of what would be
seen under a dissection scope than is typically available in a printed key.
Monitoring aquatic biodiversity at regional scales to understand the effects of human impacts has emerged as priority
research area in freshwater science1. For example, the biodiversity of benthic macroinvertebrate (BMI) communities in
Mediterranean climate regions has been shown to be responsive to anthropogenic climate change2. A region-specific,
widely accessible tool for identifying BMI communities in the San Francisco Bay Area would facilitate research efforts.
The objective is to design an accessible online macroinvertebrate identification key (miKey) with high quality digital
imagery (Figures 1 & 2) of local specimens to (1) assist professionals, students and citizen scientists of varying levels of
expertise in identifying BMIs with precision and accuracy (Figure 3) and (2) host and disseminate data in formats that
cater to various institutions (e.g. academia, government agencies, and nonprofits) and fields of research (see flow chart).
Flow Chart: Process from Data Collection through Data Dissemination
Web
Access
• miKey website
• Gov't agency websites
• Non-profit websites
Quality
Control
Identification
Keys
• miKey
• Printed keys
(e.g. Figure 3)
miKey
Web
Server
Analyze
Data
• Calculate
metrics
• Geo-spatial
formats
Data
Collectors
• Professionals
• Students
• Citizen scientists
Methods
Discussion
Screenshots
References
Acknowledgements
A
Quantifying Aquatic Macroinvertebrates
Figures 1 & 2. Images of the order Plecoptera with distinguishing morphological traits highlighted. Families represented include (1A) Pteronarcyidae, (1B) Chloroperlidae, (2A),
Nemouridae, and (2B) Chloroperlidae. Images captured by Ken Schwab.
1A
Analysis and Dissemination of Data
= prototype near completion = in development
1B 2A 2B
B
B A