Matt Calder, Robert A. Morris, Francesco Peri. Revised Sep 2009; to
We describe a semantic data validation tool that is
capable of observing incoming real-time sensor data and performing reasoning against a set
of rules specific to the scientific domain to which the data belongs. Our software solution
can produce a variety of different outcomes when a data anomaly or unexpected event
is detected, ranging from simple flagging of data points, to data augmentation, to
validation of proposed hypotheses that could explain the phenomenon. Hosted on the
Jena Semantic Web Framework, the tool is completely domain-agnostic and is made
domain-aware by reference to an ontology and Knowledge Base (KB) that together
describe the key resources of the system being observed. The KB comprises ontologies
for the sensor packages and for the domain; historical data from the network;
concepts designed to guide discovery of internet resources unavailable in the local KB but
relevant to reasoning about the anomaly; and a set of rules that represent domain
expert knowledge of constraints on data from different kinds of instruments as well as
rules that relate types of ecosystem events to properties of the ecosystem. We describe an
instance of such a system that includes a sensor ontology, some rules describing coastal
storm events and their consequences, and how we relate local data to external
resources. We describe in some detail how a specific actual event---an
unusually high chlorophyll reading---can be
deduced by machine reasoning to be consistent with a hypothesis of
benthic diatom re-suspension and inconsistent with a hypothesis of an algal bloom, both
of which might otherwise have been potential explanations.
Rule based Security Policy management forWeb Service
Hui Dong, Zhimin Wang, Robert A, Morris. PDF
With the prevalence of loosely coupled web service composition
in the service oriented infrastructure, distributed
security management has become important to offer flexible
web security. In our project affiliated with NatureServe
we developed a XACML policy oriented security
system to provide trust data service to 75 network partners
in the Natural Heritage Program. A Horn Logic based
rule inference engine extension to XACML model is used to
solve the possible policy conflicts over context and semantics
in the key decision making step. Approaches to facilitate
such decision making process in various ways by using the
extension are illustrated.
A. Morris, Mathew Passell, Jun Wan, Robert D. Stevenson and William
], in Towards a global biological information infrastructure
Challenges, opportunities, synergies, and the role of entomology
H. Saarenmaa and E. S. Nielsen, eds.
European Environment Agency,
Technical report 70
, pp. 49-59, Copenhagen, 2001.
UMASS-Boston Electronic Field Guide Project , UMB-EFG
provides a web-accessible distributed object-oriented database for the
identification of biological specimens from field observations. The
data, including both taxonomic and environmental or ecological data,
will aid in identification by building a context for each
observation. As observation data accumulates, larger-scale ecological
studies can be carried out using the data. UMB-EFG is being
constructed and populated under The EFG project has recently been
expanded to encompass investigation of a number of issues and solutions
under discussion in the eco-informatics community, including the use of
XML for federation of data from disparate distributed database, as well
as for more common tasks such as data exchange and system
This paper describes our engineering approach to the building of these
systems and reports on their current status.
and solutions in distributed
The paper is derived from a
presentation at the 2000 International Congress of Entomologists (ICE2000).
field guides and user communities in the eco-informatics
Abstract: The recognition that taxonomy is central to the
biodiversity has reestablished the critical role of taxonomy in
biology. However, many of the tools taxonomists produce for the
identification and characterization of species, e.g., dichotomous keys,
have been difficult to use and largely ignored by the general public in
favor of field guides, which are essentially browsable picture guides.
We review the role of field guides in species identification and
discuss the application of a host of digital technologies to produce
user-friendly tools for identification that are likely to greatly
enhance species identification in the field by nonspecialists. We
suggest that wider adoption of the citizen science model and the use of
electronic field guides will enhance public understanding and
participation in biodiversity monitoring.
bioinformatics, birding, citizen
science, ecoinformatics, field biology, field guides, species
identification, taxonomic keys, taxonomy.
2003 Stevenson, R. D., W. A.
Haber, and R. A. Morris. 2003.
Electronic field guides and user communities in the eco-informatics
revolution. Conservation Ecology 7(1):
3. [online] URL:
http://www.consecol.org/vol7/iss1/art3 Copyright © 2003 by the
decision trees with application to biological informatics. 2005,
SaintOurs, Robert D. Stevenson and Hua Tang.
To appear, J. Intelligent Information Systems.[PDF
describe a mechanism for the identification of biological organisms
the use of enhanced taxonomic keys–decision trees with nodes
property lists that can serve as arguments to web or local services
databases or other resources about species, specimens, and ecosystems.
of these identification schemes can use simple spreadsheet tools to
the identification abstractions, and middleware renders the resulting
into many different forms, with the databases possibly discovered and
at the time an identification is proposed.
An Architecture For
Electronic Field Guides
Robert D. Stevenson and
William Haber. To
appear, J. Intelligent Information Systems. [PDF
People who classify and identify things based on their
observable or deducible properties (called
“characters” by biologists) can
benefit from databases and keys that assist them in naming a specimen.
paper discusses our approach to generating an identification tool based
field guide concept. Our software accepts character lists either
expressed as XML (which biologists rarely provide
databases can now export in XML) or via ODBC connections to the data
relational database. The software then produces an Electronic Field
implemented as a collection of Java servlets. The resulting guide
queries made locally to a backend, or to Internet data sources via
returns XML. If, however, the query client requires HTML (e.g., if the
responding to a human-centric browser interface that we or the remote
application provides), or if some specialized XML is required, then the
forwards the XML to a servlet that applies an XSLT transformation to
the look and feel that the client application requires. We compare our
to the architecture of other taxon identification tools. Finally, we
how we combine this service with other biodiversity data services on
the web to
make integrated applications.
Morris. To appear, Proceedings of
the Conference on Biodiversity Informatics, Ashoka Trust for Research
in Ecology and the Environment (ATREE), Bangalore, June 2003. [Word
Abstract. We present a survey of some of the issues
biodiversity data that arise when the data is scattered and in many
focus is on XML-based standards and technologies that are being
applied by the biodiversity communities worldwide
discusses the underpinnings of the JSP- and XSLT-directed
of XML species pages generated by the EFG to browser-independent HTML,
as this generation stood in May 2001.
Processing of Invasive
2003 summit on invasive species, Invasive Plant
New England IPANE poster materials.
2003 ESA Meeting, Fort Laurderdale, November 2003,
workshop on data sharing . PowerPoint
2002 ACM Joint Conference on Digital Libraries. PowerPoint
Recent biology papers by
members of the project