Presentation Abstracts October 19-20, 2002
Indaiatuba, SP, Brasil


The INRAM Biodiversity Database Project

Christopher K Frazier
INRAM Biodiversity Program Manager
Dept of Biology
University of New Mexico
Albuquerque, NM, USA 87123

cfrazie AT unm.edu

The Institute of Natural Resource Analysis and Management (INRAM) is charged with producing new understanding of the natural resources of New Mexico, USA, and making this understanding accessible to the scientific community and to the general public. INRAM is funded by the National Science Foundation and the state of New Mexico as part of the New Mexico EPSCoR Infrastructure Program. The Biodiversity section of INRAM is currently providing support to database and georeference the major biological museum collections in NM and to provide these data through web and programatic access. Another division of INRAM, the Laboratory for Environmental Spatial Analysis, intends to provide the biodiversity data from museum collections and other sources in a web-based interface that supports more advanced analysis of these and other natural resource geospatial data. Over the three years of our funding period, we expect to greatly increase access to biodiversity and other natural resource data from NM and provide it in a context that supports more advanced scientific study.


Unicode Processing for BioCASE

Anton Güntsch & Wolfgang Lipp
Botanic Garden and Botanical Museum Berlin-Dahlem
Königin-Luise-Str.6-8
14191 Berlin
Germany

a.guentsch AT bgbm.org

The "Biological Access Service for Europe" (http://www.biocase.org) will implement a transnational network for biological specimens and observation collections at both meta and unit level for Europe and Israel. The project decided in its first general meeting that the network should be unicode enabled to make sure that eastern European and Hebrew language character sets provided by national nodes or collection databases can be processed in their original form. Therefore, the software technology to be used for the various system components has to be considered carefully regarding their multibyte ability.

The presentation summarizes the ongoing discussion on the choice of software. A special focus is on the programming language to be used to implement a unit level database wrapper module, that is software which implements the data access protocol for collection information providers.


Search Features over Semi-Structured Taxonomic Documents.

P. Bryan Heidorn
Graduate School of Library and Information Science
University of Illinois at Urbana-Champaign MC-493
Rm. 221, 501 East Daniel St., Champaign, IL 61820-6212
pheidorn AT uiuc.edu

One of the reasons to mark up documents in XML is to enable improved information services. Given improved markup, people should be able to find and use the information in the flora more effectively. The biodiversity informatics team at the University of Illinois developed automatic techniques to mark up and index flora in XML. People can search individual sections of a floristic description including the nomenclature, morphological description, distribution, discussion and references. We trained one group of botanists and two groups of high school science teachers on the use of the system. We followed these sessions with focus groups. These groups suggested changes to the system design and confirmed the basic usefulness of the markup and search system. In November, sixty plant taxonomy students are participating in a controlled experiment evaluating the effectiveness of search features over a semi-structured Flora of North America collection. In a two by two design, one condition is full document versus semi-structured search. The other condition tests the effectiveness of automatic query expansion through the thesaurus published with the Flora of North America. The treatment group will have the option of having their queries automatically expanded though a database of synonyms, broader and narrower terms. This study is funded by the National Science Foundation, Biological Databases and Informatics Program.


Data Access: challenges and opportunities

Charles Hussey
Science Data Co-ordinator,
Department of Information and Library Systems,
The Natural History Museum,
Cromwell Road,
London SW7 5BD
United Kingdom

c.hussey AT nhm.ac.uk

Drawing upon work done by the NHM for the ENHSIN, SPICE for Species 2000 and VIADOCS projects, as well as internal experience on integrated data access and data migration, this talk presents pragmatic approaches to delivering access to real-world specimen and taxa data.


International and Special Characters in Scientific Data

Adrian Rissone
Information Systems Manager
Department of Palaeontology
The Natural History Museum,
Cromwell Road,
LONDON SW7 5BD

A.Rissone AT nhm.ac.uk

The Universal Character Set (UCS) and Unicode have, for the past 10 years, promised the means to display text in a wide variety of language characters. The practical reality has been somewhat different and it is only in recent times that software vendors have started to introduce genuine "international" text data. Even now, display of Unicode and UTF-8 characters is often system-dependent and even major players having severe limitations and inconsistencies in their products. I will give a brief history of developments, summarise the problems and give results of a recent survey (September 2002) of well-known scientific data management system vendors.


Intelligent Components for Systematics

Guillaume Rousse
Laboratoire Informatique et Systématique
Université Pierre et Marie Curie
12 rue Cuvier
75005 Paris

rousse AT ccr.jussieu.fr

Components are an answer of software engineering to the ever-growing need to share and reuse code. They can be defined as independent pieces of software
which can be plugged together for rapid development of larger and more complex applications. Whereas mainly used for generic purposes as graphical
interfaces, database access, etc., they are more and more used for domain-specific tasks, such as sequence parsing and analysis in molecular
biology.

This talk shows how an object-oriented language can be used to capture data and logic specific to systematics into a set of software components. Those components constitute an operational ontology of the domain, and provide basic blocks for easily building applications sharing a common semantics. The interests of this approach, especially in context of large collaborative projects, are discussed. Finally, a generic web database interface is presented as a practical use case.


Bioinformatics at the New York Botanical Garden:  an update

Melissa Tulig1, Emily Ashley2 and Barbara M. Thiers3

Herbarium
New York Botanical Garden
Bronx, NY 10458

  1. Mtulig@nybg.org
  2. Eashley@nybg.org
  3. bthiers@nybg.org

In the past two years the New York Botanical Garden Herbarium has not only moved into a new collections facility, but also has achieved some informatics milestones as well, namely the completion of the Vascular Plant Type Specimen Catalog and our first library digitization project.  We have recently decided to abandon our in-house specimen cataloging software development in favor of using a commercial product that will be configured for our needs.  Adoption of this product will provide us with the tools for integration of our electronic specimen catalog, GIS, transaction management, and electronic publication, into a richer information resource in a much shorter time frame than originally envisioned. The shorter time line for completion of the full range of features for this information system is most welcome, but also presents certain challenges in project standards and management, and in the integration of activities of several departments that have heretofore worked independently. The effects of additional specimen tracking responsibilities, project updates on day to day operations of herbarium are yet to be fully determined.  Issues of archiving and storage are compounded by the increased quantity of data that will be maintained electronically.


TaxoNote: a platform independent personal notebook for nomenclatural research

Nozomi Ytow1 , Hiroshi Kajihara2 , David R. Morse3 and David McL Roberts4

  1. University of Tsukuba, Japan.
    nozomi AT biol.tsukuba.ac.jp
  2. JSPS Domestic Research Fellow, Japan
  3. the Open University, UK
  4. the Natural History Museum London

TaxoNote is intended to capture and retain nomenclatural information to be used in a stand-alone manner or as an interface to other applications. In order to do its job, TaxoNote handles the information as a large number of linked fields. The user interface, described here, is designed to guide the user through this process of de-constructing a taxonomic publication into its component parts. The objective is to allow the software to make logical inferences based on the information present in the taxonomic statements. For those interested in the design and philosophy of this data model, please refer to: Ytow, N., Morse, D. R. & Roberts, D. M. (2001). Nomencurator: a nomenclatural history model to handle multiple taxonomic views. Biological Journal of the Linnean Society 73, 81-98. http://www.nomencurator.org/

This work is partially supported by MEXT, Japan (Grant-in-Aid for Exploratory Research, 13878069, 2001-2003, and Special Coordination Fund for Promoting Science and Technology to a project organised by Junko Shimura at NIES, Japan) and Ebbe Nielsen Prize.