An architecture for electronic field guides

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. This paper discusses our approach to generating an identification tool based on the field guide concept. Our software accepts character lists either expressed as XML (which biologists rarely provide knowingly—although most databases can now export in XML) or via ODBC connections to the data author’s relational database. The software then produces an Electronic Field Guide (EFG) implemented as a collection of Java servlets. The resulting guide answers queries made locally to a backend, or to Internet data sources via http, and returns XML. If, however, the query client requires HTML (e.g., if the EFG is responding to a human-centric browser interface that we or the remote application provides), or if some specialized XML is required, then the EFG forwards the XML to a servlet that applies an XSLT transformation to provide the look and feel that the client application requires. We compare our approach to the architecture of other taxon identification tools. Finally, we discuss how we combine this service with other biodiversity data services on the web to make integrated applications.

[1]  J. Schnoor,et al.  Citizen Science , 2017 .

[2]  Steven J. DeRose,et al.  XML Path Language (XPath) Version 1.0 , 1999 .

[3]  A. S. Harold,et al.  SPECIES CONCEPTS AND PHYLOGENETIC THEORY: A DEBATE , 2002, Copeia.

[4]  Akmal B. Chaudhri,et al.  Object Databases in Practice , 1997 .

[5]  Robert M. May,et al.  How many species , 1990 .

[6]  P. Bryan Heidorn,et al.  A Tool for Multipurpose Use of Online Flora and Fauna: The Biological Information Browsing Environment (BIBE) , 2001, First Monday.

[7]  T. A. Paine,et al.  User's guide to the Delta system: a general system for processing taxonomic descriptions , 1993 .

[8]  J. Edwards,et al.  The Global Biodiversity Information Facility (GBIF) , 2007 .

[9]  S. Boissinot,et al.  Evolutionary Biology , 2000, Evolutionary Biology.

[10]  Matthew B. Jones,et al.  Managing heterogeneous ecological data using Morpho , 2002, Proceedings 14th International Conference on Scientific and Statistical Database Management.

[11]  J. Winston Describing Species: Practical Taxonomic Procedure for Biologists , 1999 .

[12]  K. R. Rao,et al.  JPEG 2000 , 2002, International Symposium on VIPromCom Video/Image Processing and Multimedia Communications.

[13]  James Clark,et al.  XSL Transformations (XSLT) Version 1.0 , 1999 .

[14]  HighWire Press Philosophical Transactions of the Royal Society of London , 1781, The London Medical Journal.

[15]  Hannu Saarenmaa,et al.  Object-oriented taxonomic biodiversity databases on the World Wide Web , 1995 .

[16]  M. J. Dallwitz,et al.  A Flexible Computer Program for Generating Identification Keys , 1974 .

[17]  A. Hallam,et al.  How many species? , 1977, Nature.

[18]  Robert K. Colwell,et al.  Biota: The Biodiversity Database Manager , 1996 .

[19]  M. Lane The Global Biodiversity Information Facility , 2005 .

[20]  John Mylopoulos,et al.  A Semantic Approach to XML-based Data Integration , 2001, ER.

[21]  Michael Stonebraker,et al.  Object-Relational DBMSs: Tracking the Next Great Wave , 1998 .

[22]  Anura Gurugé,et al.  Universal Description, Discovery, and Integration , 2004 .

[23]  Ann Solem Proceedings of the ACM conference on Document processing systems , 2000 .

[24]  Donald V. Osborne,et al.  SOME ASPECTS OF THE THEORY OF DICHOTOMOUS KEYS , 1963 .

[25]  Z. P. Metgalf The Construction of Keys , 1954 .

[26]  C. Macilwain,et al.  Museum research comes off list of endangered species , 1998, Nature.

[27]  T. A. Paine,et al.  Delta user's guide: a general system for processing taxonomic descriptions. , 1993 .

[28]  Don E. Wilson,et al.  Biodiversity at its utmost: tropical forest beetles. , 1997 .

[29]  E. Wilson,et al.  The Tropical Forest Canopy The Heart of Biotic Diversity , 1988 .

[30]  David R. Morse,et al.  Nomencurator: a nomenclatural history model to handle multiple taxonomic views , 2001 .

[31]  Renaud Fortuner,et al.  Advances in Computer Methods for Systematic Biology: Artificial Intelligence, Databases, Computer Vision , 1993 .

[32]  Maryse Condé Tree of Life , 1992 .

[33]  Roger W. Payne COMPUTER CONSTRUCTION AND TYPESETTING OF IDENTIFICATION KEYS , 1984 .

[34]  Vojtech Novotny,et al.  Low host specificity of herbivorous insects in a tropical forest , 2002, Nature.