Judith Bayard Cushing
Scientific Inquiry (Computer Science)
The Evergreen State College
2700 Evergreen Parkway
Olympia WA
98505-0002
(360) 867-6652
(360) 867-5430
judyc@evergreen.edu
http://academic.evergreen.edu/j/judyc
Biodiversity and Ecosystem Informatics
Semantics (Ontologies and Glossaries)
Database Schema Evolution and Spatial Data Support
Sensing Technologies
Modeling, Visualization and Analysis Infrastructure
In February, 2003,
Principal Investigators of Biodiversity and Ecosystem Informatics (BDEI
CISE-EIA) planning and incubation grants came together with agency
representatives (NSF, USGS and NASA) and others to report research results and
refine the BDEI research agenda.
Participants emphasized that biodiversity and ecosystem connections to
climate, agriculture, resource management, recreation, and public health make
ecosystem informatics a high priority for society. There was unanimous recommendation that funding agencies focus
research in the following areas:
• Semantics, metadata and data provenance
support, including terminology management with ontologies and glossaries,
attaching metadata to data, and other data annotation.
• Adaptive, flexible database schemas, domain-specific data types and schema management, including specialized support for spatio-temporal data and support for different data models.
• Data
acquisition, documentation and cleaning, including retroactive data capture
to speed up digitization of data from static media, in situ and remote sensing
technologies, all with automated or semi-automated metadata acquisition and
management.
• Modeling
and analysis infrastructure, including better mathematical and statistical
models of organisims and ecological and biological systems, better
visualization, integration of data models with models, and uncertainty and
missing data management.
Workshop participants
further emphasized that the social context of technology is critical. Research in the above areas must be
considered in terms of a variety of researchers, students, resource and
information managers (including the US Forest Service, Bureau of Land
Management and National Parks), and policy makers. Furthermore, research products must coalesce into the cyber infrastructure needed
for tomorrow’s ecologists.
The
BDEI research agenda overlaps with that developed at a National Library of
Medicine (NLM) sponsored Workshop on Data Management for Molecular and Cell
Biology. Considerable synergy could be
generated by capitalizing on this overlap.
The 15 current BDEI
research projects are categorized into four areas:
Spatio-temporal Data &
Sensing Technologies. New sensors – aloft, among,
and in situ – yield more and more data.
A recent confluence of technologies – orbital sensors complemented by
mobile citizen-scientists teams and specialists equipped with geo-referential
proximal sensors and robust wireless networks of reactive sensing agents –
result in data streams rich in dimensionality and across a wide range of
spatial, temporal, spectral, radiometric, thematic, and taxonomic scales. Robust representations capturing the
complexities of environmental patterns and processes, are required. Flexible database schema and sophisticated
queries, algorithms for spatio-temporal analysis, wireless reactive agent
networks and tools for metadata acquisition, management and interpretation are
the most critical research areas.
Enhanced sensory presentation of environmental data encompassing visual,
sonic, and haptic feedback systems are needed to explore high-dimensional data
spaces.
Modeling and Forecasting. Advanced frameworks, including hardware for adaptive and
intelligent systems and high performance computing are needed. Memory and speed continue as important
bottlenecks, so modular models, model coupling, and hardware grid /distributed
computing are required. Model-Data
interaction is key since many problems could be informed by existing large data
sets, but inference methods for high dimensional problems are lacking. Data are indirect, massively unbalanced with
missing observations, and subject to stochasticity. Processes interact at a range of scales and hidden ‘parameters’
are often more like variables. Data exhibit variability, uncertainty, and
complexity. Meaningful visualization
must be part of working models on which measurements may be made and change
simulated. Biodiversity science
requires more efficient algorithms, ways to deal with incomplete knowledge,
better understanding of spanning spatio-temporal scales, and techniques for
high dimensional problems. Derived
data products and provisioning data at multiple places are also critical.
Putting it into Practice. Advancement hinges on closing various “digital divides”, shaping
an ecoinformatics culture and developing socio-technological partnerships. We must solve social and ethical conundrums
among various players: industry and science; bioinformatics and ecosystem
informatics; ecologists conducting “big science” and traditional individual ecologists working in relative isolation;
scientists and information managers; professional and citizen scientists; and
the tripartite scientists, resource managers and policy makers. Telecommunications
and consumer electronics industry R&D budgets, as well as those in defense, health services and even
bioinformatics, dwarf ecosystem informatics budgets; BDEI should look there for
technologies, keeping in mind some unique requirements. Stakeholders should
adapt open source models, in particular for specialized robots to digitize
museum collections. Even with appropriate technology, extensive user training
will be required. Finally, technology
is not enough: who should contribute information,
who should have access, and how should research resources be allocated for
information management?
BDEI Workshop Co-Organizers and Report
Co-Authors: Kate
Beard-Tisdale (U. Maine), Kathleen Bergen (U. Michigan), Jim Clark (Duke), Geof
Henebry (U. Nebraska), Eric Landis (Natural Resources
Information Management), David Maier (Oregon Graduate Institute), John
Schnase (NASA), Rob Stevenson, (U. Mass. Boston).
We
aim to inform funding directions in NSF, USGS and NASA by identifying key areas
where informatics research will significantly benefit biodiversity and ecology
research, resource management and policy. The report will inform computer
science researchers of research opportunities and potential applications, and
software and hardware vendors who seek opportunities for new products for researchers
and citizen ecologists.
To organize and conduct the February 2003 workshop, write a report identifying the research agenda for biodiversity and ecosystem informatics, and disseminate these results to funding agencies and the research community. Identifying research needs = to the computer science community in technical detail is of high priority.
Ecologists and biologists have articulated a need for better technology for biodiversity and ecology research. As a result, in June 2000, an NSF-NASA-USGS sponsored workshop brought biologists, ecologists and resource managers together with computer scientists to identify the CS/IT research issues that impede biodiversity and ecosystem research and ecosystem information infrastructure. Their report sparked the National Science Foundation to issue a call for proposals and 15 awards were made in late 2001. This project coordinates results of that research into a cohesive report.
·
Workshop
on Data Management for Molecular,Cell Biology http://www.lbl.gov/~olken/wdmbio
canopy.evergreen.edu/bdeipi
BDEI Workshop Web Site, including
agenda, presentations, descriptions of BDEI Projects.
www.evergreen.edu/bdei/2003
BDEI 2003 Workshop Report.