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II. Invasive Species: The Role of Lucid Identification Keys
Geoff Norton
Centre for Biological Information Technology
The University of Queensland
Brisbane, Australia, 2005-11-01

Abstract

This paper discusses the Lucid identification systems, which are computer-based identification tools aimed at contributing to taxonomic capacity building by enabling identification keys to be easily developed and by increasing the availability and usefulness of these keys by making them available on CD or via the Internet. This paper focuses on the Lucid identification software, particularly in the areas of: software development, particularly the new Lucid3 matrix key system; Lucid key development - a number of new keys released which provide identification aids for specific groups of invasive/quarantine species; Lucid training which is part of the AusAID ASEAN-APEC technical support program; and future developments aimed at new and faster ways of producing digital keys.

Introduction

Different computer-based identification tools, particularly two Lucid identification systems - the Lucid Professional (matrix key) and Lucid Phoenix (dichotomous key) systems, have been discussed by the author in 2003. Both of these identification systems, like other systems such as Delta and Linnaeus II, include two components: a key development tool or builder (that allows taxonomists or others to clone their knowledge base into a form that is readily accessible by other people); and a key interface or player (through which end-users interact with the Lucid key that has been developed and distributed either as a CD-ROM or via the Internet). For further information, visit www.lucidcentral.org.

The main purpose in developing these Lucid identification systems has been to contribute to taxonomic capacity building in two ways: by enabling identification keys to be easily developed and by increasing the availability and usefulness of these keys by making them available on CD or via the Internet.

This paper focuses on the Lucid identification software and provides an update on progress in four areas:

  • Software development - the new Lucid3 matrix key system;
  • Lucid key development - a number of new keys released that aim to provide identification aids for specific groups of invasive/quarantine species;
  • Lucid training - a two-week regional workshop held in Kuala Lumpur as part of the AusAID ASEAN-APEC technical support program; and
  • Future developments - a number of plans and ideas for the future, aimed at new and faster ways of producing digital keys.

Software Development

A new Lucid matrix key system was released in 2004. Lucid3 is the result of a major redevelopment of Lucid Professional (Lucid2) that involved complete rewriting of the code, using the Java program. This allows the Lucid3 builder to run on any operating system that supports the Java Runtime Environment (JRE), which can be downloaded free of charge. These operating systems include Microsoft Windows, Mac OSX, Linux and Sun Solaris. For a brief summary of how a Lucid3 key operates, see Fig. 1(1260).

The complete rewrite of Lucid3 has provided the opportunity to redesign the architecture of Lucid. While retaining the basic key building techniques of Lucid 2, a number of new features have been added to Lucid3. One significant difference is that Lucid3 now features an applet player. An applet is a program written in the Java programming language that can be included in an HTML page, much in the same way as an image is included in a web page. This means that key developers can compile their keys with the applet and deploy them on a web site. When a Java-enabled browser is used to access a key in an HTML page, clicking on the URL automatically transfers the applet's code to the user's computer and opens up the selected key.

Subsequent versions of Lucid3 will include an application version of the player - to be installed on the user's computer and which has additional features to the applet version, and a server-side player that can be browsed within a web page - a form of the player likely to be more appealing to casual key users.

Other new features in the Lucid3 player include the ability to switch from a list view of "taxa remaining" to a gallery view of images, allowing the user to switch from a list of names to a "gestalt", image-based method of identification when the taxa remaining list is relatively short.

Lucid Key Development

A number of the many Lucid keys developed over the past few years have focussed on agricultural and quarantine pests and invasive organisms. Table 1(1246) lists some of these keys, which are published on CD or available across the Internet. The right-hand column indicates where more information about them can be found or where to access them.

Lucid Training

In September 2004, a 10-day Lucid training workshop for participants from ASEAN countries was held in Kuala Lumpur, Malaysia. Focusing on quarantine and biodiversity issues, the main purpose of the course was to build taxonomic capacity in the region associated with the development of computer-based keys.

The main workshop sessions introduced participants to Lucid identification systems and provided hands-on experience in the development and use of Lucid and Phoenix keys. The 29 participants from 11 countries (Thailand, Vietnam, Lao PDR, Singapore, China, Myanmar, Indonesia, Brunei Darussalam, Philippines, Cambodia, and Malaysia) then worked on developing their own keys, having brought data and images with them to the training course.

The course was organized by ASEANET (the South East Asian loop of BioNET-International) and was funded by AusAID (as part of the ASEAN-APEC support program), by the ASEAN Regional Centre for Biodiversity Conservation (ARCBC) and the Gordon and Betty Moore Foundation. Further workshops are being planned in ASEAN and other countries, to provide continuing support for local key development.

Future Issues

Recent experience suggests that computer based identification keys will become an increasingly important part of the move towards providing taxonomic information on-line. By making identification keys for invasive species available to a wide range of users, the chances of detecting new invasions earlier are likely to increase. However, to develop a set of keys that cover the main taxa of concern, a number of issues need to be addressed, all relating in one way or another to resource issues.

The first issue concerns the resources available to key developers. Although there are various technical ways in which the efficiency of key development might be improved, sharing of content offers the best option. Being in a digital form, the content of computer-based keys can be easily transferred and added to by other key developers, allowing content to be shared to achieve greater cost effectiveness in producing identification keys.

To achieve this in practice often requires advance planning, as illustrated by the strategy adopted by a group of Australian dipterists who have obtained funding to develop a key to the families of Australian flies. Although this initial key has an Australian focus, it is being developed as the first stage of a world key. Colleagues in other continents have already been involved or are being consulted about future developments, to expand the scope of the key to include all fly families. A similar development occurred at the Kuala Lumpur workshop where several participants have decided to collaborate on key development.

CBIT is also exploring ways of making the process of key development more efficient. The most time consuming activity for many key developers is the time they spend developing html taxon fact sheets, including images and hyperlinks. To make this process a lot easier, CBIT has developed a fact sheet builder (Fact Sheet Fusion) that allows users to input their text and images into a fact sheet in a simple form that is then converted to a style sheet according to the template chosen. Fact sheet fusion automatically incorporates images, generates an index and glossary, and produces hyperlinks.

These and other software developments will undoubtedly increase the efficiency of developing individual Lucid and Phoenix keys, such as those listed in Table 1(1246). But even so, we are still likely to be some way off achieving the range of keys required to cover the main taxa of concern to those involved in monitoring and managing invasive species. Therefore, a more radical key development strategy is also required.

CBIT, together with a number of collaborators, is proposing an ambitious plan to dramatically increase the number and range of keys available by developing a federated or distributed database of morphological characters for quarantine and invasive taxa that will form the basis for developing customized keys. The databases will be populated in various ways, including the use of the Phoenix builder to convert existing (printed) dichotomous keys into Phoenix keys and then deconstructing these keys where necessary to provide "character state-taxon" data for the database.

When a complete set of data for a specific taxonomic group has been incorporated in the database, customized keys can then be developed on the fly. To create a key of relevance to Taiwan, for example, the first step would be to list those taxa of interest. This list would then form the basis for automatically constructing a Lucid3 key for Taiwan, in a similar way to that performed by the existing "filter" facility in the Lucid Phoenix system.

References

  • Moritz, G., L.A. Mound, D.C. Morris and A. Goldarazena. 2004. Pest Thrips of the World. http://www.cbit.uq.edu.au/software/pestthrips/default.htm.
  • Norton, G.A. 2003. Identification software for tackling biological invasions. Proceedings of International Seminar on Biological Invasions. NIAES and FFTC. pp. 139-153.

Index of Images

Figure 1 The Lucid (Matrix) Key System

Figure 1 The Lucid (Matrix) Key System

Table 1 List of Keys of Relevance to Quarantine/Invasive Species

Table 1 List of Keys of Relevance to Quarantine/Invasive Species

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