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Lucid digital identification keys:

their role in on-line taxonomy

[ This article appeared in the “Embiopteran tools” section of Antenna 29 (January 2005) pp 64-70. Antenna is the Bulletin of the Royal Entomological Society of the UK.]

Introduction

With developments arising from the Global Biodiversity Information Facility, Species 2000 and other initiatives to create on-line taxonomic databases, computer-based identification keys will have several, increasingly important roles to play. Foremost among them is the capture of taxonomists’ expertise, particularly of those about to retire, and making this expertise readily accessible for non-experts to make identifications themselves. For many potential users of taxonomic information - such as ecologists, conservation managers, quarantine inspectors, plant health officers and students - computer-based identification keys, that enable them to identify and name specific taxa, are likely to be the only effective portals by which they will be able to access the wealth of taxonomic data that is rapidly being made available on the Internet.

As with many other break-throughs in biology, when we look at the main computer-based identification systems currently available, entomologists appear to have played a central role in their development. The DELTA system, one of the earliest matrix key systems, emerged from CSIRO Entomology in Australia, CABI-KEY emerged from the International Institute of Entomology in the UK and Lucid, the system that I will focus on in this issue of Embiopteran tools, also emerged from an entomologically focussed organisation - the Cooperative Research Centre for Tropical Pest Management.

In this short article on Lucid computer-based identification systems I will provide a brief summary of what these software tools can do and illustrate how the software is being used to develop Lucid keys for a range of end-users, particularly associated with quarantine and biodiversity related activities. I will conclude with a discussion of future issues, including plans and ideas for the future as well as the vexed question of sustainability, an issue that confronts all those involved in biological software development.

What is Lucid identification software?

The Centre for Biological Information Technology (CBIT) (at The University of Queensland, Brisbane, Australia) currently produces two identification software systems – Lucid3 – the latest release of the Lucid matrix key system - and Lucid Phoenix – a new identification tool that enables printed dichotomous keys to be easily converted into interactive, web-based dichotomous keys. Both of these identification systems, like other systems such as Delta and Linnaeus II, include two components –

Therefore, both Lucid systems have two important features. First, they are generic, in the sense that they can be used to develop identification or diagnostic keys to just about anything. Second, since Lucid development tools are relatively simple to use, they can be used by a wide range of key developers – from specialist taxonomists through to students learning the basics of key development. In developing these Lucid systems, a major objective 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.

Let’s look at these two Lucid systems in more detail.

The Lucid3 (Matrix) key system

The Lucid3 system is the latest version of the Lucid matrix key system. In a matrix key, the process of making an identification involves selecting those states from a list of character states that best describe the specimen to be identified. These character states can be selected (or de-selected) in any order, resulting in a shortening (or lengthening) of the list of remaining taxa that best match the described specimen. Key developers can include line drawings and images to help the user to correctly differentiate between different character states and can attach information sheets on each taxon – to help users confirm their identification and to provide additional information and links for that taxon.

Fig.1. Screen shot from the recent Lucid key - “Pest Thrips of the World” – showing images for the states associated with the character “Head, pronotal and metanotal sculpture”. For more information – go to http://www.cbit.uq.edu.au/software/pestthrips/default.htm.

The earliest version of Lucid, designed for PC/Windows, was released in 1998. The second version, which was also for PC and released in February 2000, enabled keys placed on a web site to be accessed across the Internet. However, in order to access the key, users need to have an application version of the player installed on their hard drive – a model analogous to the Acrobat Reader.

The latest version - Lucid3 (Build 1) - which was released earlier this year, is Java-based, allowing the Builder to run on any operating system that supports Java Runtime Environment (JRE), including Microsoft Windows, Mac OSX, Linux and Sun Solaris. The Player in this initial release of Lucid3 is in the form of an applet. This means that key developers can compile their key with the applet and deploy it on a web site. When a Java-enabled browser is used to access a key in an HTML page, by clicking on the URL the applet’s code is automatically transferred to the user’s computer and opens up the selected key.

Lucid3 (Build 2) – due later this year – will have all the main features of the “Lucid2” builder but also include a number of new features. This next release will also include a full featured Player in the form of an application - to be installed on the user’s computer. One of the new features included in the Lucid3 player is the ability to switch from a view of taxa remaining as a list of names to a gallery of images, allowing the user to switch to a “gestalt” method of identification when the taxa remaining list is relatively short. Finally, a server-side player is being developed that can be browsed directly on a web site – a form of the player likely to be more appealing to casual key users.

Lucid Phoenix (Dichotomous) key system

This second Lucid identification system, released earlier this year, is also Java-based and is accessed via an applet player. However, while new dichotomous keys can be built using this tool, the main reason for developing Lucid Phoenix has been to take advantage of the thousands of dichotomous keys that already exist. Published dichotomous keys can be converted into interactive, web-based or CD-based keys by first scanning the published key, using optical character recognition (OCR) software to convert it into a text file, and then importing it into the builder. A single key stroke will then deploy the key in the applet player, producing a key which is interactive, can be enhanced with multimedia, and delivered seamlessly across the Internet.

In using the Lucid Phoenix player, users are presented with one couplet at a time. As users select one of the options in the couplet, the key automatically follows the lead and presents the next relevant couplet. As the identification process proceeds, the history of these selections is shown in another window, while a third window displays the current list of taxa remaining.

Using a Lucid Phoenix key to make an identification has a number of advantages over traditional paper-based dichotomous keys. For instance, Phoenix keys can better deal with the “unanswerable couplet problem” – a well known short coming of dichotomous keys. If users of a traditional paper based key come to a couplet that they cannot answer – for instance, flower colour, where the plant specimen is not in flower - then it is difficult for the user to proceed. However, Lucid Phoenix keys can help overcome this problem by allowing the user to skip one or more problem couplets and be automatically guided through the remaining branches of the key that can be answered.

Fig. 2 A screen shot of a Lucid Phoenix key to Insect Orders – showing the four windows structure

Another enhancement in Lucid Phoenix keys, not possible with traditional dichotomous keys, is the opportunity to use filters. Lucid Phoenix allows users to identify those taxa of relevance for a particular situation (based on a regional species list, for example) and to filter out those taxa not of relevance. The Lucid Phoenix player then automatically prunes the original key to generate a customised key for the chosen set of taxa.

For further information about Lucid3 and Lucid Phoenix, to download demonstration versions of the software, and to obtain information and access to existing Lucid keys, please visit www.lucidcentral.org.

 

How are Lucid identification tools being used?

Since hundreds of Lucid builders have been distributed over the past 6 years or so, many different types of keys have been developed, for a range of taxa and for a range of purposes. Two areas where identification is of critical importance – quarantine and biodiversity – are discussed below. However, for an indication of the full range of Lucid keys developed, visit www.lucidcentral.org and click on the Search for a Key button. You can search by taxon type, key words, Internet keys, etc. for details of those keys that have been entered on the site by their authors.

Quarantine/Plant Health

Correct identification of insect pests, diseases, weeds and beneficial species is a critical requirement for implementing management plans for quarantine and plant health. However, the world-wide decline in taxonomic expertise has made many identification services either unavailable or prohibitively expensive, especially for developing countries. Computer-based keys provide one solution to this problem. For instance, Lucid keys are being developed and deployed as:

Biodiversity

Many Lucid keys have been developed for biodiversity monitoring, providing ecologists or conservation groups with a valuable identification and information tool. One of the earliest Lucid keys developed in Australia was on fresh water aquatic invertebrates, providing a resource for water quality assessment. More recently, the Australian Museum in Sydney has “published” a series of “Faunakeys” on their web site, including Heteroptera and stink bugs of Australia and flower chafers, Christmas beetles, dung beetles, Criocerinae, Spilopyrinae, Sagrinae and Chrysomelinae of New South Wales - see http://faunanet.gov.au/faunakeys/

Education

Another important role for Lucid software is in the education field. Apart from the use of existing Lucid keys in schools and universities as part of their course work – for instance, the use of the Orders of Insects key in systematics courses – there is increasing interest is students developing their own keys, as a valuable and active learning experience. Earlier this year a special educational version of Lucid was released – Lucid-ID – that includes a series of project material for students to develop keys using supplied content and ideas on how to develop keys on their own chosen topic.

Future issues

Recent experience suggests that computer-based identification keys will become an increasingly important part of the move towards making taxonomy on-line. However, to fully realise this potential a number of issues need to be addressed, all relating in one way or another to resource issues.

First, we need to address the issue of the resources required to develop keys.  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 and achieving greater cost effectiveness in producing identification keys.  However, to achieve this in practice often requires advance planning.  For instance, a group of taxonomists in Australia 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.

CBIT is seeking to address these resource issues in various ways, all of them aimed at making the process of key development more efficient. One of the main time consuming activities in key development is the development and incorporation of html taxon fact sheets. CBIT has recently developed a fact sheet builder that allows users to input their text and images in simple form that is then converted to a style sheet according to the template chosen. Other initiatives involve combining and converting Lucid Phoenix keys into Lucid3 keys and exploring the feasibility of producing a Lucid score matrix by parsing natural language descriptions. A more ambitious aim, involving a number of collaborators, is to develop a means of accessing distributed databases of morphological characters to allow Lucid keys to be developed on the fly for a specific list of taxa.

The other set of issues that need to be addressed concern the resources required to sustain the software tools for developing and deploying computer-based keys. A number of key systems have been developed in the past and many of them are no longer supported or maintained. The CBIT/Lucid strategy aims to obtain funding to continue development and support of Lucid software by combining a commercial approach with project grants, contracts and donor funding. With increasing calls for taxonomic information and keys to be “free-to-air” across the Internet, the issue of who pays to sustain software development and support remains. As with other biological software, with a limited, niche market, this issue will continue to be a challenge.

Acknowledgements

I wish to acknowledge colleagues in the Centre for Biological Information for their role in making Lucid happen – in particular, Kevin Thiele, Matt Taylor, Damien Barnier, Dan Marzano, Paul Holmes and Robert Smith. We are grateful to many key authors, colleagues and organisations in Australia and overseas, too numerous to mention by name, for providing ideas and support for the Lucid strategy.

 

 

 
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