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.
E-mail: [email protected]
April 2004
1.
2.
3.
4.
5.
Summary
Introduction
Plant Health Diagnostic Resources
Software Identification Tools
4.1 Lucid identification software
4.1.1 The Lucid Professional/Lucid3 Toolkit
4.1.2 The Lucid Phoenix toolkit
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.
Back to Top
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.
Back to Top
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.
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.
Back to Top
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.
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 - http://biodiversity.uno.edu/delta/
Linnaeus/IdentifyIt - http://www.eti.uva.nl/
Lucid - http://www.lucidcentral.com/
XID - http://www.xidservices.com/
TAXIS – http://www.bio-tools.net/
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.
Back to Top
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.
4.1.1 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 www.lucidcentral.org.
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
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.
Back to Top
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
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.
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.
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.
Figure 6. Fact sheet for a specific weed species.
Back to Top
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.
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
www.lucidcentral.org].
KEY
CLIENT AGENCY
Mites, thrips, molluscs and weed seeds
Australian Quarantine and Inspection
Service (AQIS)
Mites, Elaterid beetles, scales and whiteflies
(Aleyrodidae) of quarantine significance for
North America
Animal and Plant Health Inspection
Service (APHIS), USA
Stone fruit Lepidoptera larvae pests in USA
APHIS
Seeds of federal noxious weeds of USA
APHIS
Conversion of Intkeys: World Fabaceae
(Legumes), Fruit fly adults/larvae
APHIS
Insects found in rice
AusAID, International Rice Research
Institute
Cotton insects
Aventis
Fruit Flies – Bactrocera dorsalis complex
California Department of Food and
Agriculture
Declared Plants of Australia
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 www.cbit.uq.edu.au for further information about these
diagnostic keys.
Back to Top
4.1.2 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
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.
•
•
•
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.
Back to Top
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
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 www.lucidcentral.org.
If you have a specific enquiries, please contact us at [email protected].
Back to Top