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An architecture for electronic field guides

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Abstract

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.

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References

  • ACM (1988). Proceedings of the ACM conference on document processing systems. New York: Association for Computing Machinery.

  • Apache (2005a). Apache axis. http://ws.apache.org/axis/ [accessed 2005].

  • Apache (2005b). Xalan-Java version 2.5.0. http://xml.apache.org/xalan-j/ [accessed 2005].

  • Aspinall, R. J., Burton, G., & Landenburger L. (1998). Mapping and modeling wildlife species distribution for biodiversity management. http://gis.esri.com/library/userconf/proc98/PROCEED/TO800/PAP783/P783.HTM [accessed 2005].

  • Beach, J. (2005). Specify biodiversity collections management. http://www.specifysoftware.org [accessed 2005].

  • Brach, A. R., Lampinen, R., Liu, S., & McCree, K. (2000). Internet directory for botany. http://www.botany.net/IDB/ [accessed 2005].

  • Colwell, R. K. (1996). Biota: The biodiversity database manager. Sunderland, Massachusetts: Sinauer Associates.

    Google Scholar 

  • Cornell Lab of Ornithology (2003). Citizen science. http://www.birds.cornell.edu/LabPrograms/CitSci/ [accessed 2005].

  • Dallwitz, M. J. (1974). A flexible computer program for generating identification keys. Systematic Zoology, 23, 50–57.

    Article  Google Scholar 

  • Dallwitz (1993). DELTA and INTKEY. In R. Fortuner (Ed.), Advances in computer methods for systematic biology (pp. 287–296). Baltimore: The Johns Hopkins University Press.

    Google Scholar 

  • Dallwitz, M. J. (1999). Desirable attributes for interactive identification programs.

  • Dallwitz, M. J., Paine, T. A., & Zurcher, E. J. (1993). User’s guide to the DELTA System: A general system for processing taxonomic descriptions (4th edn.). http://biodiversity.uno.edu/delta/ [accessed 2005].

  • Diederich & Milton (1993). NEMISYS: A computer perspective. In R. Fortuner (Ed.), Advances in computer methods for systematic biology (pp. 165–179). Baltimore: The Johns Hopkins University Press.

    Google Scholar 

  • discoverlife.org (2004). Discover life web site. http://www.discoverlife.org/ [accessed 2005].

  • Erwin, T. L. (1988). The tropical forest canopy: the heart of biotic diversity. In E. O. Wilson (Ed.), Biodiversity (pp. 123–129). National Academy Press, Washington, D. C.

    Google Scholar 

  • Erwin, T. L. (1997). Biodiversity at its utmost: tropical forest beetles. In M. L. Reaka-Kudla, D. E. Wilson & E. O. Wilson (Eds.), Biodiversity II (pp. 27–40). Joseph Henry Press, Washington, D. C.

    Google Scholar 

  • Exolab (2005). The Castor project. http://castor.exolab.org/ [accessed 2005].

  • Fortuner, R. (1993). Advances in computer methods for systematic biology artificial intelligence, databases, computer vision. Baltimore: The Johns Hopkins University Press.

    MATH  Google Scholar 

  • Futuyma, D. J. (1998). Evolutionary biology. MA: Sinauer Associates.

    Google Scholar 

  • Gautier, Pave, & Rechenmann (1993). Object-centered representation and fish identification in Antartica. In R. Fortuner (Ed.), Advances in computer methods for systematic biology (pp. 181–195). Baltimore: The Johns Hopkins University Press.

    Google Scholar 

  • GBIF (2005). The global biodiversity information facility. http://www.gbif.org [accessed 2005].

  • Geocities (2004). Digital taxonomy software. http://www.geocities.com/RainForest/Vines/8695/ [accessed 2005].

  • Hagedorn, G. (2005). Delta access. http://www.diversitycampus.net/Workbench/Descriptions/index.html [accessed 2005].

  • Heidorn, P. B. (2001). A tool for multipurpose use of online Flora and Fauna. First Monday (Online), 6.

  • Higgins, D., Berkley, C., & Jones, M. B. (2002). Managing heterogeneous ecological data using morpho. In: 14th International Conference on Scientific and Statistical Database Management (SSDBM’02) (pp. 69–77). IEEE Computer Society.

  • ITIS (2005). Integrated taxonomic information system. http://www.itis.usda.gov/ [accessed 2005].

  • JDOM (2005). JDOM. http://www.jdom.org/ [accessed 2005].

  • JPEG2000 (2004). JPEG 2000. http://www.jpeg.org/jpeg2000/ [accessed 2005].

  • Lampinen, R. (2005). Cartographic links for botanists. http://www.helsinki.fi/~rlampine/cartogr.html [accessed 2000].

  • Loomis, M. E. S., & Chaudhri, A. B. (1998). Object databases in practice. Upper Saddle River, N.J.: Prentice Hall PTR.

    Google Scholar 

  • LTER (2005). The U.S. long term ecological research network. http://www.lternet.edu/ [accessed 2005].

  • Marcus (1993). The goals and methods of systematic biology. In R. Fortuner (Ed.), Advances in computer methods for systematic biology (pp. 31–53). Baltimore: The Johns Hopkins University Press.

    Google Scholar 

  • May, R. M. (1990). How many species? Philosophical Transactions of the Royal Society of London. B, 330, 293–304.

    Article  Google Scholar 

  • Meier, W. M. (2005). Open source XML database. http://exist-db.org/ [accessed 2005].

  • Metcalf, Z. P. (1954). The construction of keys. Systematic Zoology, 3, 38–45.

    Article  Google Scholar 

  • Microsoft (2005). Basics of .NET. http://www.microsoft.com/Net/Basics.aspx [accessed 2005].

  • Morris, R. A., Passell, M., Wan, J., Stevenson, R. D., & Haber, W. (2001). Engineering considerations for biodiversity software. European Environmental Agency Technical Reports.

  • MySQL (2005). MySQL developer zone. http://dev.mysql.com/ [accessed 2005].

  • National Wildlife Federation (2005). eNature online field guides. http://enature.com/guides/select_group.asp [accessed 2005].

  • Nature (1998). News briefing: Museum research comes off list of endangered species. Nature, 394, 115.

    Article  Google Scholar 

  • NBII (2003). Biocomplexity thesaurus. http://thesaurus.nbii.gov/about.html [accessed.

  • Novotny, V., Basset, Y., Miller, S. E., Weiblen, G. D., Bremer, B., Cizek, L., et al. (2002). Low host specificity of herbivorous insects in a tropical forest. Nature, 416, 841–844.

    Article  Google Scholar 

  • Osborne, D. V. (1963). Some aspects of the theory of dichotomous keys. New Phytologist, 62, 144–160.

    Article  Google Scholar 

  • Pankhurst (1993). Principles and problems in identification. In R. Fortuner (Ed.), Advances in computer methods for systematic biology (pp. 125–136). Baltimore: The Johns Hopkins University Press.

    Google Scholar 

  • Payne, R. W. (1984). Computer construction and typesetting of identification keys. New Phytologist, 96, 631–634.

    Article  Google Scholar 

  • Rodríguez-Gianolli, P., & Mylopoulos, J. (2001). A semantic approach to XML-based data integration. In H. S. Kunii, A. Solvberg, & S. Jajodia (Eds.), Conceptual modeling—ER 2001 In: 20th International Conference on Conceptual Modeling. 117 ff. Springer Lecture Notes in Computer Science.

  • Saarenmaa, H., Leppäjärvi, S., Perttunen, J., & Saarikko, J. (1995). Object-oriented taxonomic biodiversity databases on the World Wide Web. In A. Kempf & H. Saarenmaa (Eds.), Internet applications and electronic information resources in forestry and environmental sciences. In: Workshop at the European Forest Institute (pp. 121–129). EFI Proceedings.

  • Santos-Mello (2000). A mediation layer for integration of XML data sources with ontology support.

  • SDD (2005). Taxonomic database working group, Subgroup on the Structure of Descriptive Data (SDD). http://www.tdwg.org/sddhome.html [accessed 2005].

  • Shattuck, S., & Fitzimmons, N. J. (2000). BioLink® the biodiversity information management system (p. 3066). Collingwood Victoria: CSIRO Publishing.

    Google Scholar 

  • Stonebraker, M., Brown, P., & Moore, D. (1999). Object relational dbms: Tracking the next great wave. (2nd edn.). Morgan Kaufmann.

  • Sun Microsystems (2005) JDBC technology. http://java.sun.com/products/jdbc/ [accessed 2005].

  • TDWG (2005). IUBS taxonomic database working group. http://www.tdwg.org/ [accessed 2005].

  • Thiele, K. (2005). Lucid 3. http://www.lucidcentral.com/ [accessed 2005].

  • Tree of Life (2005). Tree of life web project home page. http://tolweb.org/tree/phylogeny.html [accessed 2004].

  • uBio (2004). uBio home page. http://www.ubio.org/ [accessed 2005].

  • UDDI (2005). Universal description, discovery and integration of web services. http://www.uddi.org [accessed 2005].

  • Vanel, J. M. (2005). Worldwide botanical knowledge base search and identification engine with 8467 species of the Flora of China. http://jmvanel.free.fr/protea.html [accessed 2005].

  • W3C (1999a). XML Path language (XPath) version 1.0 W3C recommendation 16 November 1999. http://www.w3.org/TR/xpath [accessed 2005].

  • W3C (1999b). XSL Transformations (XSLT) version 1.0; W3C recommendation 16 November 1999. http://www.w3.org/TR/xslt [accessed 2005].

  • W3C (2001). Web Services Description Language (WSDL) 1.1 W3C Note 15 March 2001 http://www.w3.org/TR/2001/NOTE-wsdl-20010315. http://www.w3.org/TR/2001/NOTE-wsdl-20010315 [accessed 2005].

  • W3C (2003). SOAP version 1.2 part 1: Messaging framework. http://www.w3.org/TR/2003/REC-soap12-part1-20030624/ [accessed 2005].

  • Wheeler, Q., & Meier, R. (2000). Species concepts and phylogenetic theory: A debate. New York: Columbia University Press.

    Google Scholar 

  • Wilson, E. O., & Peter, F. M. (1988). National forum on BioDiversity: Biodiversity. Washington, D.C.: National Academy Press.

    Google Scholar 

  • Winston, J. E. (1999). Describing species: Practical taxonomic procedure for biologists. New York: Columbia University Press.

    Google Scholar 

  • Ytow, N. (2002). Managing species names. http://www.gbif.org/GBIF_org/prize/lecture2002.htm [accessed 2002].

  • Ytow, N., Morse, D. R., & Roberts, D. M. D. (2001). Nomencurator: A nomenclatural history model to handle multiple taxonomic views. Biological Journal of the Linnean Society, 73, 81–98.

    Article  Google Scholar 

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Authors and Affiliations

  1. Department of Computer Science, University of Massachusetts, Boston, MA, USA

    Robert A. Morris

  2. Department of Biology, University of Massachusetts, Boston, MA, USA

    Robert D. Stevenson

  3. Missouri Botanical Garden, St. Louis, MI, USA

    William Haber

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  1. Robert A. Morris
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  2. Robert D. Stevenson
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  3. William Haber
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Correspondence to Robert A. Morris.

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Morris, R.A., Stevenson, R.D. & Haber, W. An architecture for electronic field guides. J Intell Inf Syst 29, 97–110 (2007). https://doi.org/10.1007/s10844-006-0033-9

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