Linking Florida's Natural Heritage: Science & Citizenry
First Monday


Linking Florida's Natural Heritage: Science & Citizenry

Linking Florida's Natural Heritage: Science & Citizenry is an IMLS-funded project that improves access to diverse information on Florida species and ecology. The project includes the development of a Web-based interface to both library bibliographic files and museum speciman databases; the creation of bibliographic databases with enhanced taxonomic information; the digitization of a core collection of seminal texts; and, the use of a thesaurus and other tools to improve search and access.

Contents

Introduction
Databases of Scientific Literature
Integrating Museum and Library Data
Tools to Enrich the Data and Facilitate Searching
The Future
Conclusion

Introduction

Prior to his death in 1957, Karl Schmidt, renowned herpetologist at the Field Museum of Natural History in Chicago, wrote of the natural history library as a major museum department:

"Not everyone realizes how different the use of books may be in a museum from the familiar pattern of reading and note-taking in a public library. In a museum, a book may be ... tested by reference to a specimen or a series of specimens drawn from the range and laid beside it. Corrections of and additions to the published literature of descriptive natural history are an essential aspect of museum studies." [1]


Figure 1: Many seminal scientific publications are based on data from museum collections.

While the intrinsic relationship between museum collections and scientific literature has always existed, the functionality of the Internet offers rich potential for linking them in innovative ways.

In 1998, the Institute for Museum and Library Studies (IMLS) awarded a National Leadership Grant to five Florida institutions to create a "virtual" library on Florida ecology. The project, Linking Florida's Natural Heritage (LFNH), allows researchers to search both library bibliographic databases and museum specimen databases distributed throughout the state of Florida through the same Web-based interface. Institutional participants include the Florida Museum of Natural History, University of Florida Libraries, Florida International University Library, Florida Atlantic University Library, and the Florida Center for Library Automation (FCLA). Additionally, individual contributors representing twelve additional agencies are acting as collaborators or contributors to this project.

A Web site for Linking Florida's Natural Heritage brings together information about the project, information for contributors, curriculum materials, and descriptive information on museum and bibliographic databases.


Figure 2: The homepage for Linking Florida's Natural Heritage.

The project has three major goals:

  • Developing two new databases of scientific literature: Florida Environments Online and the LFNH Core Collection;
  • Simultaneous access, searching, and retrieval from disparate museum and library data using a Web-based interface; and,
  • Creating tools to enrich the data and facilitate end-user searching including a thesaurus of Florida Environmental Terms and a mechanism for enabling users to search by common name.

Databases of Scientific Literature

While the project was designed to access existing relevant bibliographic databases, two unique databases were created as part of the grant: Florida Environments Online and the LFNH Core Collection.

Florida Environments Online

Florida Environments Online was created by merging eight research bibliographies of Florida scientists: "Florida Ecosystems" compiled by Dr. John Ewel,co-author of Ecosystems of Florida; "Florida Ornithology" compiled by the Florida Ornithological Society; "Fishes of Florida" compiled by George Burgess, Senior Biologist, Ichthyology Department, Florida Museum of Natural History; "Florida Herpetology" compiled by Kevin Enge, Florida Game and Fish Conservation Commission; "Florida Geology" compiled by Dr. Anthony Randazzo, Chair, Geology Department, University of Florida, and author of Geology of Florida; "Bibliography of Literature Useful to the Study of Florida Plants" compiled by Kent Perkins, Collection Manager, University of Florida Herbarium; "Florida Freshwater Bibliography" compiled by Tom Savage and Landon Ross, Florida Department of Environmental Protection; and "Florida Agricultural History" compiled by Dr. Vernon Kisling, Marston Science Library, University of Florida. These personal bibliographies were converted from Microsoft Word, ProCite, and other citation management packages into a modified MARC format.

Because of the unifying taxonomic and geographic components of this project, the MARC records were enhanced accordingly. Taxonomic information was drawn from the Integrated Taxonomic Information System (ITIS) of the Biological Resource Division of the U. S. Geological Survey and placed in the MARC added entry for taxonomic designation (754) field. Geographic names and latitude/longitude coordinates were drawn from the Geographic Names Information System (GNIS) of the U.S. Geologic Survey and placed in the hierarchical place name (752) and coded cartographic mathematical data (034) fields respectively. In addition, hydrologic unit codes (HUCs) and Federal Information Processing System (FIPS) county codes were assigned to the records in geographic subject fields (651).


Figure 3: Enhanced bibliographic data in Florida Environments Online.

Once enhanced, the records were loaded into a single database in the library management system shared by the Florida State University System (SUS) libraries. Currently 8,000 records are in the system. It is expected to grow to 13,000 records before completion of the grant.

To assure that the Florida Environments Online database continues to grow, interested individuals, state agencies, and researchers are being trained to input records into the database using a CATALYST template. CATALYST is a PC client front end to the cataloging module of the library management system that allows users to set up simple data entry templates with appropriate default values. Training for data entry for Florida Environments Online was given for nine contributors in a two-day workshop held in January 2000. Alternatively, contributors can use a simple Web form to e-mail information about a resource to a central agency. The system reformats the information as appropriate, the record is reviewed and enhanced with geospatial and taxonomic information, and then it is added to the file.

LFNH Core Collection

The second database, the LFNH Core Collection, consists of the full texts of more than 200 publications on Florida ecosystems and species. Selected by scientific experts, seminal publications in the fields of entomology, ornithology, marine resources, herpetology, botany, geology, ichthyology, Florida freshwater ecosystems, Florida terrestrial ecosystems, and Florida natural systems were recommended. Copyright clearance was obtained, as needed; the texts were digitized in accord with local best practices; and are now being loaded onto the server at the Florida Center for Library Automation. The texts were digitized as TIFF files and are made available on the Web in JPEG and PDF formats. This collection augments a statewide initiative to digitize materials pertaining to Florida's cultural and natural history known as the "Florida Heritage" project. Analytical records of these publications are being created and added to the Florida Environments Online database.


Figure 4: Page from Mark V. Hoyer and Daniel E. Canfield, A Handbook of Common Freshwater Fish in Florida Lakes, one of the texts digitized for the LFNH project.

Integrating Museum and Library Data

The project developed a single interface using Z39.50, an ANSI/NISO standard client/server protocol for search and retrieval, to search both bibliographic and museum databases. OCLC's WebZ software, part of the SiteSearch software suite, is used as the Z39.50 client. WebZ is configured to allow a user to search a single LFNH database, all databases simultaneously, or any combination of databases.

The WebZ client accesses two Z39.50 servers written by FCLA as part of this project using the Z39.50-1995 toolkit by Index Data. One server is designed to handle the bibliographic data in library files and one handles the SQL data in museum specimen databases. For retrievals from museum files, SQL table columns are mapped to MARC-like fields and returned as MARC records. The Z39.50 client and server use the bib-1 attribute set enhanced with non-conflicting local use attributes for museum data elements. For example, genus is given a use attribute of 8002, species is use attribute 8003, and collector is use attribute 8005.

Clicking on "Search Library and Museum Records" on the LFNH homepage results in a menu of databases that can be searched. The search interface allows you to chose one or more combinations of databases.


Figure 5: A search screen showing a common name search entered against two selected databases.

In this example, the bibliographic file Florida Environments Online and the herpetology specimen database from the Florida Museum of Natural History were selected. A search of a common name American alligator will retrieve 16 museum records and 119 bibliographic records shown below. Complete bibliographic or specimen data can be displayed by clicking on the title; links to images, full text documents, and other online materials are provided when available.


Figure 6: A search results screen showing brief entries retrieved by the search for common name "american alligator."

Tools to Enrich the Data and Facilitate Searching

Thesaurus of Florida Environmental Terms

To facilitate searching across disparate databases, a thesaurus of Florida environmental terms is being developed using MultiTES Thesaurus Development Software. Terms have been imported from ENVOC, Fish and Wildlife Reference Service, Aquatic Sciences and Fisheries Abstracts, Fire Ecology Thesaurus, and the evolving California Resources Agency Environmental Resources (CERES) thesaurus. Where necessary, these international and national vocabularies for natural science and environmental studies have been enhanced and extended to reflect the particular natural features and environmental issues of Florida. Preferred terms for LFNH use will be established and linked to identified synonyms. Variations, Broader Term/Narrower Term, and Related Term relationships will be harmonized. Researchers and catalogers can use this thesaurus to help select terms for use in their bibliographic files. When the thesaurus is complete, terms from this thesaurus will be added to both Florida Environments Online and LFNH Core Collection records. For searchers, these terms will provide a common vocabulary to provide continuity among the various databases, datasets, and bibliographies merged in this project.

Common name searching

A recent NSF grant Species Analyst, awarded to the Museum of Natural History at the University of Kansas, identified key fields in museum specimen records. Designated the "Darwin core," this set of fields includes accession/collection location, taxonomic information, collector, date, and place collected. These fields can be correlated to similar fields in the MARC records, with the critical exception of the taxonomic information. Long ago, the decision was made by the Library of Congress to use common names rather than scientific names in subject cataloging. Obviously, this policy was intended for a much broader audience of library users than the nomenclaturely-literate ranks of the taxonomists and research scientists. In contrast, museum records record only taxonomic information: order, family, genus, and species, but do not contain common names.

The unfortunate implication is that a common name search across museum and library collections would find library data only, unless some method was found to get around this problem. The challenge, then, was to create a crosswalk to connect scientific to common names that would be invisible to the user and be invoked when a search of museum records is initiated.

Under the supervision of Dr. Wayne King, Curator of Herpetology, Florida Museum of Natural History, a student at the University of Florida created a table mapping scientific to common names for approximately 6,800 species of mammals, birds, reptiles, amphibians, fish, and mollusks. Built in MicroSoft Access, this crosswalk is invisible to the searcher but is used by the Z39.50 server to enhance common name searches to include genus species names as well. Future enhancements will include a protocol that will incorporate synonyms as well.

The Future

Completing the subprojects comprising the LFNH project is the first priority. These include:

  • Stabilization of both client and server components of the Z39.50 search system;
  • Completion of the thesaurus of Florida environmental terms and application of terms to records in Florida Environments Online, the LFNH Core Collection, and other databases of descriptive metadata;
  • Expanding the content of Florida Environments Online, both by incorporating additional bibliographies and by expanding the number of trained contributors; and
  • Increasing the number of museum specimen databases available for searching.

Another important subproject is the development of curriculum materials using LFNH as a research resource. Lesson plans for 9th and 10th grade biology and environmental science students are now being created in five areas: identifying, examining and protecting biodiversity; museums, scientists and their role in society; taxonomic basics; studying exotic invasive species in Florida; and "Waging war over water: identifying stakeholders and their needs."

In the longer term, project participants hope to procure additional funding for a LNFH Phase II, which would integrate a GIS component to enhance geospatial access and improve the usefulness of the LFNH databases in species and land use studies.

About the Authors

Stephanie Haas is the Assistant Director at the University of Florida Digital Library Center in Gainesville, Florida. She was formerly the Environmental Sciences Librarian in the Marston Science Library at the University of Florida.
E-mail: haas@mail.uflib.ufl.edu

Priscilla Caplan is the Assistant Director for Digital Library Services at the Florida Center for Library Automation.
E-mail: pcaplan@nersp.nerdc.ufl.edu

Notes

1. K.P. Schmidt, 1958. "The Nature of Natural History Museums," Curator, volume 1, number 1, pp 20-28. http://dx.doi.org/10.1111/j.2151-6952.1958.tb01647.x

2. The metadata standards considered by the CDP included Dublin Core, Encoded Archival Description, VRA, AACR-2/MARC, etc.


Editorial history

Paper received 1 May 2000; accepted 10 May 2000.


Contents Index

Copyright ©2000, First Monday

Linking Florida's Natural Heritage: Science & Citizenry by Stephanie Haas and Priscilla Caplan
First Monday, volume 5, number 6 (June 2000),
URL: http://firstmonday.org/issues/issue5_6/haas/index.html





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