Multimedia Tools to Aid Identification and Diagnosis for Plant Health

Transcription

1 Multimedia Tools to Aid Identification and Diagnosis for Plant Health Geoff Norton, Kevin Thiele, Matt Taylor, Dan Marzano, Damien Barnier & Robert Smith Centre for Biological Information Technology, The University of Queensland, Brisbane 4072, Australia. April Summary 2. Introduction 3. Plant Health Diagnostic Resources 4. Software Identification Tools 4.1 Lucid identification software The Lucid Professional/Lucid3 Toolkit The Lucid Phoenix toolkit 5. The Future Role of Software Identification Keys in Crop Protection 1. Summary Correct identification of pests, diseases, weeds and beneficial species is a critical requirement for implementing management plans for plant health. The world-wide decline in taxonomic expertise and services has meant that many identification services have either become unavailable or prohibitively expensive, especially in developing countries. The development of computer-based, multi-media keys provides one means of addressing this critical identification and diagnostic function. This paper describes two specific software identification tools developed by the Centre for Biological Information Technology at The University of Queensland, Australia. Lucid3 is a generic software toolkit for developing and publishing matrix keys on CD or the Internet. It consists of a builder, a player and a suite of complementary software tools. A number of Lucid3 keys have been developed for use by quarantine agencies in the USA, Australia and China. Lucid Phoenix is a new software toolkit for developing and deploying pathway or dichotomous keys on the World Wide Web. The main role that Lucid Phoenix can play, at least initially, is to enable existing, published dichotomous keys to be rapidly converted to Internet keys. Keys developed for plant health and quarantine agencies using these generic software systems are described and the potential role they can play in plant health diagnosis is discussed.

2 2. Introduction A critical issue in dealing with invasive species is the timely and accurate detection and identification of introduced organisms. The world-wide decline in taxonomic expertise and the increasing difficulty, cost and time taken to access identification and diagnostic expertise has resulted in a taxonomic crisis. This is particularly felt in many developing countries, which traditionally relied on accessing expertise and services from more developed countries in Europe, North America and Australasia. One solution to this problem is increased training of taxonomists and the development of a molecular diagnostic capability. However, while these developments will provide assistance in identifying and diagnosing some introduced organisms, it is a solution that will take many years to achieve. In the shorter term, alternative solutions need to be explored. This paper describes the role that computer based identification and diagnostic (key) systems can play in addressing that aspect of the taxonomic crisis associated with the difficulties of obtaining access to identification and diagnostic services for plant health and for the detection of quarantine pests in particular. Following a brief review of software identification tools, we describe the way in which Lucid identification systems can be used to create and deliver multi-media keys via CD or the Internet. Examples are provided of keys that have been developed to assist plant health and quarantine agencies, and the future role these keys have to play in plant health diagnosis is discussed. 3. Plant Health Diagnostic Resources Quarantine agencies and others concerned with preventing the introduction and spread of invasive species currently use a range of expert, technical and other resources to identify and diagnose organisms suspected of being new introductions. These resources are indicated on the left-hand side of Figure 1.

3 Figure 1. The role that Lucid identification systems can play in complementing plant health diagnostic resources. Since many developing countries do not have these resources themselves, there is an urgent need to increase their diagnostic capability, for instance, by improving their insect, plant disease and weed collections. However, this will take considerable time and funds. In the meantime, computer based identification systems have an important role to play in increasing local identification capability. These key systems, which can also link to other on-line databases and other resources providing further diagnostic information (Figure 1), can be developed at comparatively little cost, especially where keys are shared with other quarantine agencies. 4. Software Identification Tools In the past few years, a number of dichotomous keys served as web pages and usually constructed by hand, using HTML editors, have become available on the Internet. While many of these keys do an excellent job, they have a number of disadvantages: It takes considerable time to construct an HTML dichotomous key, since each key developed is a one-off. It is difficult to update HTML keys when additional information becomes available or a key is to be modified for other locations or purposes. HTML dichotomous keys are unable to provide users with increased functionality in making an identification or diagnosis.

4 It is in this context that generic key systems, and particularly matrix key systems, come into their own, as they provide a much more powerful identification system and enable key developers to input their key data and multi-media easily, using a specialised key-building programme. A search of taxonomic and identification web sites reveals a number of such generic key systems, although a number of these systems are either no longer being supported or developed or they do not have a track record of being used to develop and distribute a broad range of keys. The following key systems are the main ones currently in use: Delta/Intkey - Linnaeus/IdentifyIt - Lucid - XID - TAXIS To illustrate the features of generic identification software systems, we will describe the Lucid identification software. Details about the other four systems can be readily accessed from their respective web sites. 4.1 Lucid identification software For the past 7 years, a team at The University of Queensland, Australia has been designing, developing and distributing a series of identification products. Lucid Professional, and more recently Lucid3, is the main tool that has been developed over this period, providing a comprehensive, high quality identification toolkit. Lucid Phoenix is a new development, aimed at providing a rapid means of converting existing published (dichotomous) keys into interactive web-based identification tools The Lucid Professional/Lucid3 Toolkit Lucid Professional/Lucid3 consists of a suite of software tools that allow taxonomists to clone their knowledge base into a form that is readily accessible as an identification tool. Taxonomists or other key developers use the Lucid Builder to create electronic random-access identification keys. These are matrix-based data structures that, when deployed in the Lucid Player, can be used to accurately and efficiently name an unknown specimen, with images, other multi-media and various functions being provided to assist the identification process. Lucid keys can be published on CD-ROM or via the Internet. Lucid Professional is a Windows-based system that has been available for over 3 years. Lucid3, which was released in April 2004, is a third-generation cross-platform system that operates on Macintosh, Unix and Linux systems, as well as Windows. For more information about Lucid Professional, Lucid3 and Lucid keys, go to Figure 2 provides a screen shot of the Lucid3 builder. Key developers create a list of the entities or taxa they wish to include, and of the features or character states that are to be used to identify the taxa. Once the entity and feature lists have been

5 created, the key developer scores each entity by ticking those features that describe it. Figure 2. The Lucid3 builder interface showing the hierarchical structure and scoring mode for a simple demonstration key. Users access the key using the Lucid Player. The following two examples of Lucid matrix keys illustrate how these keys guide users through the identification process for invasive weed species and the Bactrocera dorsalis group of fruit flies, respectively. Declared Plants of Australia This key to the Declared Plants (or noxious weeds) of Australia, which is due to be released mid-2004, is intended for use by government officers, advisors, farmers, students and others with an interest in declared plants. Note that you can access a similar weed key from the Compendium go to Identification Keys from the main menu. Figure 3 shows the front screen of the key, the equivalent of a home page. From this screen users can view a tutorial about the key, look up information about weed

6 species keys directly (from an alphabetical listing) or go to the Lucid key to identify a weed. Figure 3. The "Declared Plants" opening screen. A user of Declared Plants of Australia, with a specimen of an unknown weed, describes the specimen to the Lucid Player by choosing features that are observable in the specimen; the Player responds by progressively eliminating species until only one or a few weed species remain. Figure 4 shows how the user can access images to help distinguish specific character states in this case, the type of leaf. The series of images illustrate the different forms of leaf type possible. The user can select one of these character states either by clicking on the appropriate image or double clicking on the character state in the Characters available window.

7 Figure 4. The Lucid player showing line drawings to illustrate leaf type characters. Along the way, Lucid provides many additional functions to make the identification process easier and more efficient. Figure 5 shows a typical interrogation of the key. Four character states have been selected by the user as matching the specimen to be identified. This has resulted in the shortening of the list of weed species from 791 to seven the seven weed species shown in the weeds remaining window fit the four character states chosen.

8 Figure 5. Screen shot part way through an identification, showing the short list of weeds that match the characters selected. Once the number of likely weed species has been reduced to a few possibilities, the user can access high-quality photographs, descriptions, notes, etc., to help to decide whether the identification is correct, and to provide more information on the identified species such as its range, its impact on conservation or agriculture, possible confusion with similar species, etc. An example of the summary screen for a particular weed species is shown in Figure 6. This summary displays the main distinguishing features of the weed. Further information can be accessed via hyperlinks - to sections on distribution, similar species, ecology, etc.

9 Figure 6. Fact sheet for a specific weed species. Fruit Flies Fruit flies are an important group of organisms, of wide interest to many people both professional and non-professional. Some species of fruit flies cause major losses to a wide range of fruit and vegetable crops and are of great concern to quarantine agencies. However, identifying fruit flies is a difficult task, with only a handful of taxonomists worldwide able to consistently identify fruit flies to species level. A user wishing to know the name of a fruit fly specimen has often had few options other than sending a specimen to an expert for determination of its identity, with concomitant delays and expense. A key to the Bactrocera dorsalis complex of fruit flies has recently been developed for use by plant health officers in the Californian Department of Food and Agriculture. Using copious multi-media aids and advisory sections on the process of making an identification, Dorsalis provides a tool that allows non-fruit fly experts to identify fruit flies themselves.

10 Figure 7. Screen shot from the key to fruit flies, showing how images can be used to help in the identification process. Version 1.0 of the Lucid Professional toolkit was released in 1997 after approximately 3 years of development. Since then, upgrades have been released regularly, and subsidiary tools have been developed to make the task of developing Lucid keys much easier. Lucid Professional is currently being used to develop keys in over 40 countries and Lucid players are now available in a number of languages, including Chinese (Mandarin), Thai, Vietnamese, Bahasa Indonesia, German and Spanish. The most recent version of Lucid, Lucid3, which was released in April 2004, is platformindependent and fully web-enabled. Lucid3 incorporates many new features gained from user workshops and the experience of producing and using earlier versions. The number of keys either already developed or in the process of being developed for plant health and quarantine purposes has increased dramatically in the past few years details of some of these keys are shown in Table 1. Table 1. Some of the keys already developed or being developed for plant health and quarantine [For more information about Lucid keys, visit KEY CLIENT AGENCY

11 Mites, thrips, molluscs and weed seeds Mites, Elaterid beetles, scales and whiteflies (Aleyrodidae) of quarantine significance for North America Stone fruit Lepidoptera larvae pests in USA Seeds of federal noxious weeds of USA Conversion of Intkeys: World Fabaceae (Legumes), Fruit fly adults/larvae Insects found in rice Cotton insects Fruit Flies Bactrocera dorsalis complex Declared Plants of Australia Australian Quarantine and Inspection Service (AQIS) Animal and Plant Health Inspection Service (APHIS), USA APHIS APHIS APHIS AusAID, International Rice Research Institute Aventis California Department of Food and Agriculture Council of Australian Weed Science Societies In addition to these identification keys, two crop diagnostic keys have been developed using Lucid software. In this case, the user is faced with a sick crop a sick rice crop or a sick sweet potato crop. The user selects those character states that best describe the symptoms and appearance of the sick crop and so shorten the list of possible causes of the sick crop. Linked fact sheets on these causes then provide further information to confirm the diagnosis and provide advice on management. Visit for further information about these diagnostic keys The Lucid Phoenix toolkit While key systems like Lucid3 provide powerful, yet easy to use, identification tools, they do require the construction of a matrix key, which is not a trivial task. On the other hand, there already exist many thousands of published (hard copy) dichotomous keys which, if converted to an electronic format, have the potential to make this accumulated data vastly more accessible for identification purposes. With this objective, the team at The University of Queensland has recently developed a generic dichotomous key system - Lucid Phoenix. Lucid Phoenix is a cross-platform, computer based dichotomous or pathway key system that enables traditional paper based identification keys to be converted into interactive Phoenix keys and published on the Internet or on CD. Although they are dichotomous keys, Lucid Phoenix keys are more like Lucid3 keys in look and

12 operation. Figure 8 shows the Lucid Phoenix four windows interface, the multi-media capability and the history of a specific identification scenario. Figure 8. A screen shot of a Lucid Phoenix key to Insect Orders showing the four windows structure. Apart from providing a means of making dichotomous keys available across the Internet, Lucid Phoenix has a number of other advantages over traditional, paperbased identification keys: The traditional shortcoming of dichotomous keys is the "unanswerable couplet problem", in which a user is unable to answer one question in the key. For example, a traditional paper-based key may have a couplet relating to flower colour but the user has a specimen without flowers. Lucid Phoenix keys can help overcome this problem by "book marking" unanswerable couplets, allowing the user to skip the problem couplet and to follow both branches from that couplet to end up with a shortlist of two taxa, or more if other couplets are unanswerable and have to be skipped. Lucid Phoenix allows additional enhancements, not possible with traditional keys, to be added, such as filters. This utility allows a simple matrix of character states (such as geographical data) to be attached to the Phoenix key. Using filters, the user of the key is able to discard certain taxa, such as those not present in a certain locality, and produce an automatically generated, cut-down version of the Phoenix key for that specific taxa list. As users work their way through the Phoenix key, they are able to observe the dynamic changes occurring in the lists of taxa remaining and taxa discarded.

13 Lucid Phoenix provides multimedia capabilities to support users in the process of making an identification and supports Internet standards such as URLs, GIFs, JPEGs, PNGs. Keys can be distributed easily over the Internet by embedding them directly into a web page. Paper based keys once scanned can be imported into the Phoenix Builder within minutes and there they can be edited, restructured and additional taxa can be added. To convert a published key into a Phoenix key, the hard-copy key first needs to be converted into a digitized form, using a scanner and OCR (Optical Character Recognition) program. Once the key is scanned to a text file, it can be opened in the Phoenix Importer. The Importer automatically scans the key, identifies any logical errors which need to be edited before the key can be opened in the player, and rewrites the key as an XML file that can be read by the Phoenix Player. Once these edits have been made, a single mouse click starts up the Phoenix player and opens the converted key. 5. The Future Role of Software Identification Keys in Crop Protection Having described how software identification keys can be developed and used, what practical role can they play in crop protection, particularly in dealing with quarantine pests and invasive species? Existing Lucid keys that address these issues have been designed to address the identification needs of the three main groups involved in managing pest species. Specialist keys for plant health/quarantine identifiers - World experts have been involved in the development of Lucid keys for such difficult groups as thrips, mites and fruit flies, thus making their expertise readily available to support specialist plant health scientists and quarantine identifiers. Training and operational keys for quarantine officers and advisors These middle level keys provide quarantine officers and crop protection advisors with a tool to key out the easier groups and make quarantine and crop protection decisions. Where difficult taxonomic groups are encountered, the key would advise that these specimens should be passed on to specialist identifiers. Keys for farmers and the general public Valuable information about the incidence and spread of quarantine or invasive species is often obtained from farmers, their advisors or the general public. By making keys such as the Australian Declared Plants key generally available either on CD or via the Internet, a much better informed public with an improved capability to make sound identifications will result. Thus, when a farmer detects an unusual

14 organism, he/she will be in a much better position to determine whether it is likely to be an invasive species or not. In the future, Lucid keys are likely to play a much more significant role in plant health. A number of quarantine agencies have already developed databases of quarantine pests and other invasive species. Since the user needs to know the name of an organism in order to access information about it, there is a clear role for linking Lucid identification keys to these databases. The willingness of quarantine agencies to share the keys they have contracted specialists to produce will also encourage increased development and deployment of Lucid keys and their translation into local languages. The Lucid Player has already been translated into several languages, including Thai, Bahasa Indonesia, Vietnamese, Chinese, Spanish and German and several multi-lingual and non-english keys have been produced. For more information about Lucid identification systems visit - If you have a specific enquiries, please contact us at enquiries@cbit.uq.edu.au.