BSPP1996 Abstracts Booklet – BSPP – The British Society for Plant Pathology

This is a subpage of our conference ‘BSPP1996: Unlocking the Future: Information Technology in Plant Pathology‘

Plenary session 1: BSPP Presidential Address and SA keynote paper

The incredible pace of change – Information Technology in support of plant pathology
Peter R Scott
CAB INTERNATIONAL, Wallingford OX10 8DE, UK.

Topics included

Handling facts to produce information
Handling the information explosion in plant pathology
Data management: bibliographic; nomenclatural; molecular; etc.

Interpreting information to produce knowledge
Taxonomic Information Systems
Geographic Information Systems
Multimedia; etc.

Using knowledge to support decision making
Modelling epidemics
Diagnostic tools
Expert Systems for disease management; etc.

Using knowledge to make predictions
Epidemic forecasting
Risk analysis

Passing on knowledge in education and training
New media
Interactive training
Distance learning; etc.

Storing and disseminating information

Intranets, the Internet, World Wide Web
Electronic publishing
Molecular Plant Pathology Online
Opportunities for developing countries.

Development of computer-based systems in systematics
Peter H A Sneath
Department of Microbiology and Immunology, University of Leicester, Leicester LE1 9HN, UK.

Systematics Association keynote paper

An overview will be presented of the way computers have been applied to systematic biology. Before the development of digital computers there were very few numerical applications to systematics. Systematics is a subject that requires the marshalling of numerous pieces of information, ranging from the estimation of resemblances between organisms to the preparation of regional checklists. Data processing based on information theory was therefore an essential.

These developments first required a logical strategy. Most early workers viewed systematics as so complex an art that it would be infeasible to reduce it to a science with logical rules. Numerical taxonomy defined a logical progression: from organisms and their characters to measures of resemblance between organisms; and then to finding taxonomic structure by cluster analysis, ordination and phylogenetic trees. These steps led on to databases on organisms; and thence to numerical methods for identification.

A growing field is the preparation of descriptions of taxa by computer methods, with extensions to ecology, pathology, geography and other areas. A good deal of computing is directed to molecular sequences, mainly for the study of phylogeny. But it is numerical identification that is especially relevant for the present meeting, which commemorates the 21st anniversary of a key symposium on this topic. Computing has made the early concepts practicable, and the field has diversified into sophisticated methods for diagnostic keys, polyclaves and taxonomic distance models. One particular benefit is the way in which, through probabilistic concepts, the reliability of identification systems can be assured.

Plenary session 2: Handling facts to produce information

Handling the information explosion: the challenge of data management
John E Anderson
BIOSIS, 2100 Arch Street, Philadelphia, PA 19103, USA.

“Rise up, my fellow biologists, and throw off the bonds of techno-tyranny!” Information technology is a servant, at most a colleague, not a ruler or tyrant.

Most scientists have suffered the plight of working with a knowledgeable colleague in a foreign language. Untoward time and energy is expended on communication, thereby reducing the effort and knowledge available for the issue at hand. For such a collaboration to grow, both parties must work toward learning the language of the other, otherwise the labour imbalance may become detrimental, even causing termination. Regarding an information/knowledge database as a servant or colleague gives rise to a healthy assessment of effort expenditure. Why should computer databanks not come as much to us (learning the language of science) as we to them (e.g. we have all learned some of the language of technology)?

In part because of the continuing information explosion, science MUST transfer more of the burden of communication WITH information technology TO information technology. If we, as the ultimate life form, do not delegate more responsibility to our tools (computer knowledge banks), we’ll not have time and energy to do what only scientists can do: SCIENCE.

What then can life science expect of its colleague, information technology? Life scientists can expect, and should demand:

To communicate with information technology in a manner more akin to that of humans – “natural language”.
To reach the knowledge in real time, beyond the abstract of a publication, beyond the publication, to the data/information/knowledge from which the publication was written, and even to the author/scientist.
To communicate via subject matter concepts with data technology, not merely the scientific “baby talk” of co-occurrence of a few terms which may or may not capture the concept.

The last of these three points is the subject of this paper. It is related to, and even dependent upon, the first two.

Keeping pests in their place: international plant quarantine data bases
IM Smith
European and Mediterranean Plant Protection Organization, 1 rue Le Ntre, 75016 Paris, France

The objective of plant quarantine is to prevent the spread of pests to areas where they do not occur. According to the International Plant Protection Convention (IPPC), phytosanitary measures are aimed principally at “quarantine pests”, i.e. pests of known economic importance, known to be absent from the area to be protected. These measures will be the more effective if they address pests of known identity, whose geographical distribution is precisely known, together with the pathways (usually consignments of plants or plant products) by which they are likely be moved through international trade. Moreover, official phytosanitary measures are non-tariff barriers to trade, and have therefore, for member countries of the World Trade Organization (formerly GATT), to be scientifically justified and commensurate with the risks involved. Today’s plant quarantine can no longer be based on highly restrictive measures against ill-defined risks; it has on the contrary to be based on detailed and transparent information, with due consideration to the quality, reliability, timeliness and significance of data. It is not enough, for example, to record that according to a stated bibliographic reference or a collected specimen a pest occurred in a country at some date in the past. The identity of the pest, the circumstances of the find, its relevance today, can all be called into question. On this basis, dubious poorly documented records may be included, provided they are appropriately assessed.

Informatic and experimental approaches to the elucidation of novel gene functions
S Oliver
Department of Biochemistry and Applied Molecular Biology, UMIST, PO Box 88, Manchester M60 1QD

The genome of the yeast, Saccharomyces cerevisiae, has now been completely sequenced. The picture of biology which is emerging from yeast and the other genome projects is that c. 50% of the genes identified are of completely unknown function. This is a sobering statistic and one must question why molecular genetics has failed to find these genes previously by its classical, “function first”, approach. A high level of redundancy is revealed by the informatic analysis of the genome and this undoubtedly has a lot to do with our previous failure to find these genes. In many cases, redundancy may be more apparent than real. I think we must consider the possibility that the way we do our science may have placed constraints on the set of genes that we have been able to discover. Most molecular genetics experiments are designed to provide qualitative answers. It may be that this has caused us to miss many genes whose contribution is a more quantitative one. If this is true, it suggests that a systematic approach, involving both bioinformatics and ‘wet’ experiments, will be required in order to elucidate the function of all of these novel genes. Like genome sequencing, the systematic analysis of gene function is certain to provide interesting and unexpected findings which, we hope, will lead us to new biological truths.

Handling facts to produce information – Where from here?
Simon B Jones
CAB INTERNATIONAL, Wallingford OX10 8DE, UK.

The paper will review developments in database and information retrieval technology to highlight how they will impact biological research in the future. The likelihood of successful application of each technology will be assessed through comparisons with early adopters. The paper will focus on three key developments:

Data warehousing, in which large collections of data from many sources are collected and managed together. Different approaches will be examined in which the data are pooled in a single database, or managed as separate, linked databases. The feasibility of “virtual” data warehouses with networked links between geographically separate sources will be explored.
The application of “data mining” technology, sometimes in conjunction with data warehousing, to derive conclusions which are not anticipated by the database structure.
New paradigms for databa
se management, especially object oriented systems, which allow greater flexibility for handling multiple and varying data types.

The emphasis in the paper will be on how to match the technology to the way in which scientific research work is carried out.

Distance learning; etc.

Storing and disseminating information

Intranets, the Internet, World Wide Web
Electronic publishing
Molecular Plant Pathology Online
Opportunities for developing countries.

Development of computer-based systems in systematics
Peter H A Sneath
Department of Microbiology and Immunology, University of Leicester, Leicester LE1 9HN, UK.

Systematics Association keynote paper

Plenary session 2: Handling facts to produce information

Handling the information explosion: the challenge of data management
John E Anderson
BIOSIS, 2100 Arch Street, Philadelphia, PA 19103, USA.

“Rise up, my fellow biologists, and throw off the bonds of techno-tyranny!” Information technology is a servant, at most a colleague, not a ruler or tyrant.

What then can life science expect of its colleague, information technology? Life scientists can expect, and should demand:

To communicate with information technology in a manner more akin to that of humans – “natural language”.
To reach the knowledge in real time, beyond the abstract of a publication, beyond the publication, to the data/information/knowledge from which the publication was written, and even to the author/scientist.
To communicate via subject matter concepts with data technology, not merely the scientific “baby talk” of co-occurrence of a few terms which may or may not capture the concept.

The last of these three points is the subject of this paper. It is related to, and even dependent upon, the first two.

Keeping pests in their place: international plant quarantine data bases
IM Smith
European and Mediterranean Plant Protection Organization, 1 rue Le Ntre, 75016 Paris, France

Informatic and experimental approaches to the elucidation of novel gene functions
S Oliver
Department of Biochemistry and Applied Molecular Biology, UMIST, PO Box 88, Manchester M60 1QD

Handling facts to produce information – Where from here?
Simon B Jones
CAB INTERNATIONAL, Wallingford OX10 8DE, UK.

Data warehousing, in which large collections of data from many sources are collected and managed together. Different approaches will be examined in which the data are pooled in a single database, or managed as separate, linked databases. The feasibility of “virtual” data warehouses with networked links between geographically separate sources will be explored.
The application of “data mining” technology, sometimes in conjunction with data warehousing, to derive conclusions which are not anticipated by the database structure.
New paradigms for database management, especially object oriented systems, which allow greater flexibility for handling multiple and varying data types.

The emphasis in the paper will be on how to match the technology to the way in which scientific research work is carried out.

Parallel session 3A: Support for decision making

PC-Plant Protection – a need-based decision support system for crop protection in Denmark
Bo J M Secher & N S Murali
Danish Institute of Plant and Soil Science, Department of Plant Pathology and Pest Management, Lottenborgvej 2, DK 2800 Lyngby, Denmark.

The decision, in 1986, on an action plan to reduce pesticide use in Denmark by 50% has led to increased research on the potentials for reduced dosages. A decision support system (PC-Plant Protection) developed by the Danish Institute of Plant and Soil Science and the Danish Agricultural Advisory Centre implements the research findings with a detailed use of threshold values to support decisions on treatment need, choice of pesticides and the appropriate dosage for the actual problem.

The pest and disease model of the system has been commercially available since 1993. In 1996, 2800 licences were in use at agricultural schools and with advisers and farmers. The system was evaluated by agricultural advisers in 1990, 1991 and 1993. Usability and usefulness of the recommendation model were judged to be user-friendly, and the model was considered to be reliable and to meet the requirements of advisers. In 1996 a farm survey of 488 farmers who had used the system in 1995 showed that the system has been well accepted by farmers, not only because of its reliable recommendations but also because of the good profitability that resulted from its use.

The recommendation model for pest and disease control has been validated in the field since 1990. Validation in winter wheat (62 trials), spring barley (62 trials) and winter barley (39 trials) has shown that the model is able to control pests and diseases to a satisfactory level, without affecting farmers’ gross margins. The model was able to regulate pesticide usage to the large annual variations. On average, pesticide usage in plots treated according to the model was well below the level in reference plots, and below the level for strategies commonly used by Danish farmers.

The models in PC-Plant Protection are undergoing continuous development. A weather module, taking into account detailed weather information, and an environmental module, giving farmers the opportunity to choose pesticides according to their environmental risk, will be implemented in the near future. Further planned developments include integration of the decision support system with site-specific (precision) farming, and multimedia presentation of biological and pesticide information.

Developing a model of expertise for a taxonomic expert system
Marion Edwards
Computing Laboratory, University of Kent, Canterbury, Kent CT2 7NF, UK
and
School of Sciences, University of Buckingham, Buckingham MK18 1EG, UK

This paper discusses the role of modelling in expert system development with reference to an expert system developed to investigate water mite identification. A model, usually termed a model of expertise, defines the behaviour that the expert system is required to exhibit. The model of expertise is usually, at least partly, based on the behaviour shown by a human expert when solving a problem. In this case the actions of an expert taxonomist when identifying water mite specimens were investigated.

A model of expertise is developed during the knowledge acquisition stage of an expert system project. Knowledge acquisition includes three activities:

the elicitation of the domain-specific knowledge (usually from an expert)
the interpretation of that knowledge
the formal representation of that knowledge.

This paper concentrates on the first two activities: elicitation and interpretation. First, the knowledge acquisition technique, which is a modified form of the twenty questions knowledge acquisition technique, is described. Second, the interpretation and analysis of the knowledge elicited is outlined, and the model of identification is described. The model was termed identification by confirmation and has four distinguishing characteristics.

A broad search strategy is used so that once a tentative identification is reached alternative identifications, which could be confused with the tentative identification, are specifically excluded.
Questions are repeated when there is reason to doubt the original answer either because the question was answered hesitantly or the answer contradicts existing evidence.
Different types of questions are recognized, most important are those used to confirm conclusions tentatively reached and questions answered hesitantly.
The taxonomic classification has a flexible representation.

This last characteristic showed that the expert neither rigidly followed the recognized classification nor discarded it entirely, rather it was used as appropriate.

The model of identification is described in an informal, implementation-independent format, and the implications of adopting a modelling approach to the development of taxonomic expert systems are discussed.

Parallel session 3B: Computer-based species identification: Applications I

Computer-based keys for botanical identification
R J Pankhurst
Royal Botanic Garden Edinburgh, Inverleith Row, Edinburgh EH3 5LR, UK.

Computer assisted identification first began about 30 years ago, and it is now 20 years since the publication of the first Systematics Association conference volume on identification methods. This paper traces the development of the principal types of method, elimination versus comparison, over this time. The DELTA format for morphological descriptive data continues to be of great importance for identification techniques. The relevance of various computing techniques, such as expert systems, hypertext, relational databases and computer graphics, will be discussed. Finally, priorities for new research will be given.

Identification of yeasts through computer-based systems
R W Payne
Statistics Department, IACR-Rothamsted, Harpenden, Herts, AL5 2JQ, UK.

The identification of yeasts presents a worthwhile and challenging application for computer-based identification systems. There are currently nearly 650 species and varieties to consider, and over 100 tests. These involve such attributes as the ability of the yeast to ferment certain types of sugar or to grow in particular media, as well as some morphological characters such as the formation of spores and filaments. The basic data for the identification is a species-by-test table indicating the possible responses that each yeast may give to each test. The response may be fixed: all strains of the yeast always give the same result (positive or negative) to the test. However, there are many variable responses, where different strains produce different results. Some responses are weak or delayed and thus must also be treated as variable, and others are unknown.

A further complication is that tests can take up to 14 days to observe. Consequently the standard sequential methods, used for example in botanical identification, are inappropriate. Tests are generally observed in batches, and it is more important to ensure that the identification can be completed within a specified time than to minimise the number of tests that are required.

Methods will be described for selecting the tests to be used during an identification, and for assessing the reliability of the conclusions that they generate. We will also discuss ways of allowing a suggested identification to be checked and of allowing for mistakes during testing. These will be illustrated by examples from the Yeast Identification Program of Barnett, Payne & Yarrow, and the keys and tables in the book Yeasts: Characteristics and identification (Barnett, Payne & Yarrow, 2nd edition, 1990, Cambridge University Press).

Probablisitic identification systems for bacteria
TN Bryant
Medical Statistics and Computing, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK.

Probabilistic identification methods for bacteria are based on the likelihood that the observed pattern of results of tests carried out on an unknown bacterium can be attributed to the known results of a taxon within an identification matrix. Typically, the known taxon is a recognized bacterial species, although this does not have to be the case, and the identification matrix contains species from a small number of related genera. Few attempts have been made to produce a general purpose matrix covering all genera. A number of approaches have been suggested for probabilistic identification; however the most commonly used method was proposed in 1973 by Lapage and his colleagues, which is based on Bayes Theorem.

The probabilistic approach depends on the availability of good quality phenotypic data in the form or a probability, or identification, matrix. Ideally, the probability that a taxon (species) exhibits an attribute is obtained from testing many isolates of that species. Developments in probabilistic identification can be divided into: bacteriological, involving the development of new tests and techniques that enable the creation of new, or better, identification matrices; and computational, through the development of software to perform the management, manipulation and evaluation of data as well as the identification process itself. The probabilistic approach forms the basis for some commercial identification kits although the exact algorithm used may not be published. In recent years there has been a lack of new identification matrices. This may be due to microbiologists pursuing new genotypic, or phenotypic techniques, neither of which produce data appropriate to the probabilistic method. Bacterial taxonomy, including identification, is now based on this polyphasic approach. In most routine microbiology laboratories, however, identification is based on the use of conventional tests which form the basis of probabilistic identification.

A general structure for biological databases
J Diederich*, R Fortuner**, J Milton*
* Department of Mathematics, University of California, Davis CA 95616, USA.
** 4, rue des Jardins, Montendre, 17170 France (Correspondant du Musum National d’Histoire Naturelle, Paris).

We argue that morpho-anatomical characters should best be stored in a general database as simple data because it is always easier to combine several simple pieces of data into a complex character, when one is needed, than to do the opposite, which may even be impossible in some cases.

A standardized decomposition is discussed, using the classical entity/property/value scheme. For each character, the entity is strictly defined as one of the existing biological structures, from the whole organism to systems, organs, tissues, and down to individual cells, organites and molecules. The property is taken from a short list of “basic properties” which are the same in most biological groups. The value is the traditional qualitative state or quantitative value, with some standardization made possible by the use of basic properties.

Other, non-morpho-anatomical, types of data could be decomposed in a similar manner, using the same entities with their own sets of basic properties. This would be naturally conducive to the definition of relations between different types of data.

Characters that are decomposed into elementary parts can be used as is, by specifically designed applications. In other situations, a database management system (DBMS) should provide sufficient support to use or view the data in more complex, or different ways. Some of this required support can be provided through generic capabilities of DBMS which are intended for a wide variety of users and are not directed at supporting biological applications per se.

There are some important requirements for biological databases to relate simple characters with more complex formulations, or with coded formulations. Here we will address some of these questions and will look at concepts we have defined or that need to be studied to support existing applications such as DELTA-based applications, cladistic programs, etc. In particular we will be looking at the requirements (the needs of biological applications) for the purpose of determining what a biological database management system, a BioDBMS, should be.

Plenary session 4: Computer-based species identification

Systems for computer-based multi-access keys
M J Dallwitz, T A Paine and E J Zurcher
Division of Entomology, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia.

Computer-based multi-access keys, also known as interactive keys, can offer several advantages over conventional keys:

A correct identification can be made in spite of errors by the user or in the data.
Characters can be used, and their values changed, in any order.
Numeric characters can be used directly, without being divided into ranges.
The user can express uncertainty by entering more than one state value, or a range of numerical values.

Other desirable features include:

Advice on the most suitable characters to use at any stage of an identification.
Character dependencies: certain character values making other characters inapplicable.
Provision for gaps in the values recorded for integer numeric characters.
Storing, searching, and displaying free-text information.
Locating errors which were circumvented by the error-tolerance mechanism.
Use of probabilities.
Provision for restricting any operation to subsets of the characters and taxa.
Glossaries and notes on interpretation of characters.
Illustrations of characters and taxa.
Provision for information retrieval.
Finding the differences and similarities between taxa.
Finding diagnostic descriptions.
The ability to handle large data sets efficiently.
Data sharing with other description-based applications: description writing, generation of conventional keys, and phenetic and cladistic analysis.

It is an inevitable consequence of the flexibility of interactive keys that much of the strategy involved in carrying out an identification is left to the user. Good strategies must be learnt if the keys are to be used to the best advantage.

Archiving biodiversity
Peter H Schalk
ETI, University of Amsterdam, Mauritskade 61, 1092 AD Amsterdam, Netherlands. Tel: +31 20 5257239. Fax: +31 20 5257238. E-mail: peter@eti.bio.uva.nl.

The end of this millennium is characterized by an oncoming or perhaps ongoing revolution in the field of information management and fast dissemination by means of the new media. With the large scale introduction of personal computers in the consumer market, the related developments in Information Technology have received an enormous impulse. The possibilities of the compact disk and the Internet have literally erased traditional borders. Information processing and knowledge dissemination have found a new dimension and influenced science and society in an irreversible way.

The demand for readily accessible biological expertise is growing. In the scientific community and in society there is an increasing need for up-to-date information on biological diversity, stimulated in no small way by developments in the context of the Convention on Biological Diversity. In the past, scientific data were mainly for the scientists. Now the information is needed by a far larger group of users for various purposes such as: pure or applied research, industrial processes, nature conservation, biodiversity inventories, policy making, etc. In all these cases the “up-to-date-ness” and validity of the information may be vital.

At the same time the size of the required information sets is growing: we know more, need to update more, and need to check our data against a bigger variety of existing information. Last but not least, we are more in a hurry than ever before. There is an increasing pressure by society to produce and access the latest data fast; both information providers and information users encounter deadlines. This calls for innovative instruments to archive, process and handle our information. Information Technology offers new possibilities.

ETI developed the Linnaeus II software package for biodiversity documentation and species identification. It is a multi-functional system that can be used by scientists on their own PCs to create multimedia biological databases, computer-assisted identification systems and geographic information systems for mapping distributions and biodiversity. Apart from these basic functional parts, supporting modules such as glossaries, literature databases and methodological sections can easily be added. At the same time Linnaeus II presents an electronic publishing tool, allowing fast dissemination of large information systems on CD-ROM or the Internet.

This paper describes in detail the data model and functional aspects of the Linnaeus II software, and discusses the why and how of ETI’s taxonomy networks: an internal cooperation of specialists to open up the knowledge of the world’s species and document biological diversity in a quality-warranted format.

Images as a basis for identification
D McL Roberts, G Novarino, G Kennaway & S Hope
Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.

Identification of a specimen has traditionally relied on it appearance, that is to say visual inspection should reveal sufficient characters to enable the specimen to be identified. This system had shortcomings when applied to very small organisms which, because of their sheer size could not carry sufficient visually accessible characters to allow straightforward identification. The almost universal move towards phylogenetic classification schemes also demonstrated the paucity of characters suitable for establishing relationships between taxonomic groups.

The development of high resolution techniques, particularly the transmission electron microscope, and non-visual methods, particularly molecular biology, has allowed much progress towards defining taxonomic groups, but has also necessitated the observation of difficult or obscure characters. The problem of identification has been greatly helped by the development of multi-access keys (see Dallwitz et al., above).

Some characters, e.g. movement in life or environmental context, have not been used in establishing taxonomic relationships but are almost universally used by those skilled in identification.

Here we will review some practical techniques in microscopy to enhance the visibility of obscure characters, the use of video and computers to make other characters accessible, and their use in distance learning. Examples will be taken from a group generally regarded as “difficult”, the unicellular eukaryotes.

Garrett Memorial Lecture

Building models of epidemics to help take decisions
MJ Jeger
Department of Phytopathology, Agricultural University, POB 8025, 6700 EE Wageningen, Netherlands.

The concern of plant epidemiology is with an understanding, not merely description, of interactions between host and pathogen populations. Based on this understanding it may be possible to make decisions at different levels relating to disease management tactics, strategy and policy. Mathematical modelling, as part of the normal process of scientific inquiry, can contribute both to understanding and to the decision process. Models are used for different purposes: in exploratory analysis; to formalize concepts relating to epidemic processes; and to span biological hierarchies or levels of integration. Examples will be given of how these model types have contributed to decisions in disease management. Most epidemic models attempt to deconstruct an epidemic into component processes and then either identify key processes and their determinants, or to reconstruct an epidemic using computer simulation. Modelling of apple scab (Venturia inaequalis) will be used to illustrate the strengths and weaknesses of different approaches and their contribution to disease management.

A common fallacy is that modelling demands data before it can start. There are many examples of models which have been formulated at an early stage of, and indeed provided the initial stimulus for, an experimental programme. The decisions made by researchers on which directions to follow can be influenced by modelling. In recent years there has been a productive exchange between theoretical models from human/animal epidemiology and plant epidemiology. A fundamental quantity derived in these models (but with antecedents in plant disease) is that of the basic reproductive number. This quantity will be defined and illustrations made of its use for making strategic decisions, in particular in relation to some of the more difficult problems in plant epidemiology: dealing with inter-organismal interactions; combining population dynamic and genetic approaches; integrating different control practices; and quantifying epidemic processes below ground. The availability of powerful computing facilities and the development of numerical algorithms have expanded greatly our abilities to obtain qualitative and quantitative insights into the consequences of different disease management decisions.

SD Garrett (1970) summarized his views on the concepts of inoculum potential in relation to infection and colonization of a substrate, both dealing with ‘energy of growth’. These concepts have proved useful for soil-borne pathogens but have not found universal acceptance by epidemiologists because of essential problems in quantification. An energy-based model of soil colonization by a mycoparasite attacking a sclerotium-forming fungus will be outlined. This model bears similarities to the theoretical epidemic models but has physically consistent parameters and derived properties. It may be possible to redefine and operationalize the concept of inoculum potential, and to assess its relevance for decisions in disease management.

Posters and hands-on demonstrations

A plant virus notebook for IBM-compatible computers
J Antoniw
Institute of Arable Crops Research, Rothamsted Experimental Station, Harpenden, Hertfordshire AL5 2JQ, UK.

Automated ribotyping creates a European article numbering system for microorganisms
J Banks
Campden & Chorleywood Food Research Association, Chipping Campden, Goucestershire GL55 6LD, UK.

Dade Microscan 2.5hr system
S Bascomb
15 Grosvenor Mews, Southampton Road, Lymington SO41 9JY, UK.

Investigations into the classification of rhododendron powdery mildew using molecular biology and scanning electron microscopy
Paul Beales and Avice M Hall
Plant Pathology, Environmental Sciences, University of Hertfordshire, College Lane, Hatfield AL10 9AB, UK.

Though rhododendron powdery mildew has become an increasing problem for growers in the past 10 years, the identity of the causal agent is still unknown.Whilst it is obviously a member of the Erysiphales, the genus and species are by no means clear; in fact there have been four or five suggestions made in the literature. The aim of this presentation is to show that anatomical studies, using light and scanning electron microscopy coupled with preliminary molecular studies, can be used to eliminate some of the possible genera and the results used to direct further research for final confirmation.

MORPH, an integrated forecasting model launcher
Andrew Binks, Paul Sayers and John Clarkson
Horticulture Research International, Wellesbourne, Warwick CV35 9EF, UK.

Horticulture Research International (HRI) has realized the need for an application that can incorporate current disease and pest forecasting models on several crop types into an integrated package with the flexibility to accept new models as they are developed. MORPH provides a Windows mechanism that allows any compatible disease forecasting model to be launched using any type of met data collector and produces a large choice of text and graphical outputs. This is achieved by the provision of independent components which are accessible to all models. New components can be added or removed, as and when required. The ‘sharing’ nature of MORPH’s structure allows the deployment of the very latest modelling technology, to the industry, in a fraction of the time that is normally required. All new HRI disease forecasting models will run under MORPH. Most of HRI’s current models are now being updated to run in the new technology.

Species 2000: indexing the world’s known species
F Bisby
Species 2000, University of Southampton

LegumeWeb: access to the world database of legumes
F Bisby
Species 2000, University of Southampton

APPLESCAB: pest management game
Philippe Blaise
Institute of Plant Sciences, Section Phytomedicine/Pathology, Swiss Federal Institute of Technology, Universittstr. 2, CH-8092 ETH-Zrich, Switzerland.

Colour analysis of Lepidoptera for species identification
E D Chesmore
Environmental Electronics Research Group, Department of Electronic Engineering, University of Hull, Hull HU6 7RX, UK.
S Flandin
cole Nationale Suprieure de Physique de Strasbourg, Parc d’Innovation, Bld. Sebastien Brant, F 67400 Illkirch, France

The commonest method for identification of Lepidoptera (butterflies and moths) is by comparison with high-quality photographs or drawings in conjunction with dichotomous keys, and dissection for examination of genitalia when necessary. The identification process can be slow and difficult. Computer-aided species identification (CASI) can speed up the process and alleviate the difficulties associated with inexperience and intra- and inter-observer variability which is sometimes a major problem.

Research in the Environmental Electronics Research Group at Hull is directed towards the application of advanced signal and image processing techniques to biological problems, especially in Lepidoptera. Recent work has concentrated on the analysis and classification of the colour forms of the Large Yellow Underwing moth (Noctua pronuba) which exhibits a total of seven possible forms including sexual dimorphism. The approach adopted was to develop classification techniques based on features from RGB or HSV colour spaces and edge densities. Following feature extraction, a statistical classification in principal component space by clustering using k-means was carried out; results show that the classification method is suitable for colour form discrimination.

The poster will give details of the work together with results for 50 locally caught specimens of five colour forms. It will also discuss future directions for the research including increasing the classification accuracy using many more specimens from museums, and investigations into other image processing methods such as texture analysis, co-occurrence matrices, colour moments, wing morphology, neural networks, etc. It will also address the possibility of using colour analysis for discrimination between closely allied species and of general species identification.

DELTA and INTKEY
M J Dallwitz, T A Paine and E J Zurcher
Division of Entomology, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia. Fax: +61 6 246 4000.

The DELTA system is an integrated set of programs for recording and processing taxonomic descriptions. The facilities available include the generation and typesetting of descriptions and conventional keys, conversion of data for use by classification programs, and the construction of INTKEY packages for interactive identification and information retrieval. The system has been developed by the CSIRO Division of Entomology over a period of 25 years, and is in use worldwide for diverse kinds of organisms, including viruses, corals, crustaceans, insects, mites, fish, fungi, plants, and wood. The programs are continually refined and enhanced in response to feedback from users. The DELTA data format has been adopted as a standard for data exchange by the International Taxonomic Databases Working Group.

INTKEY is available for MS-DOS and MS-Windows, in English, French, German, Italian, Malay, Portuguese, and Spanish. It offers better and more comprehensive features than any similar program. These features include: entry and deletion of attributes in any order during an identification; calculation of the ‘best’ characters for use in identification; the ability to allow for errors (whether made by the user or in the data); the ability to express variability or uncertainty in attributes; notes on characters; direct handling of numeric values, including ranges of values and non-contiguous sets of values; restricting operations to subsets of characters or taxa; listing similarities or differences between taxa; generating diagnostic descriptions for specimens or taxa, to specified degrees of redundancy; coalescing descriptions (e.g. to generate accurate generic descriptions from species descriptions); illustrations of characters and taxa, with provision for sound and video; access to illustrations via the Internet; complete on-line help; and acceptable response times with large sets of data.

The following data sets, in the form of INTKEY packages and HTML descriptions, will be available in the demonstration session.

Butterflies and moths (a toy dataset usable by children)
Grasses of the Canadian Arctic Archipelago
Larvae of the Elateriformia (Coleoptera)
The Families of Flowering Plants
The Grass Genera of the World

VIDEdB
A J Gibbs
Research School of Biological Sciences, Australian National University, Canberra

DAINet: an extensive information system for food, agriculture and forestry on the Internet
Katja Hasky-Guenther
Centre for Agricultural Documentation and Information, Bonn

Identification of trees in Borneo
James K Jarvie
The Arnold Arboretum of Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA.

Presented here is a DELTA-coded system for identifying the tree genera of Borneo. Until now, there has been no resource available to identify a USA specimen from the more than 500 genera recorded from the island, unless its family was already known, and a family treatment was available. Available treatments are scattered, usually text-based in a technical version of English, and are rarely well illustrated. They can be excellent information resources, but only to specialists. The needs of wider audiences who could use the data are not met.

Conservation planners recognize that knowledge of the taxa within protected areas, accessed through taxon names, is a prerequisite to implementation of field activities based on prioritizing species and habitats under threat. Teachers at school and college levels need appropriate methods to instruct and involve students in conservation and biology. Through dialogue with these and other potential users, a need was identified for a method to identify tree genera of Borneo in both English and Indonesian.

The DELTA system was used to develop parallel English and Indonesian formats capable of using the same numerically coded taxon information. Descriptive characters, such as fruit and inflorescence types, were separated into their component characters to facilitate identification and make descriptions clearer. 135 characters are used in the keys. Files were fine-tuned so that the data used to produce interactive keys could, in either language, be used to provide hard-copy and Web-based descriptions. Taxa and character illustrations were included. A draft edition was put on the Web for comment. Feedback has been critical in revising content and format, and the first edition release is set for early in 1997.

This project has highlighted the gap between the knowledge held by taxonomists, collections and libraries, and the knowledge and tools available to technical and non-technical users who need information for education and resource management applications such as conservation. The gap between the two groups is easily bridged using appropriate Information Technology (IT) tools. There is great scope for further examples of using IT for conservation applications of basic research. They will benefit taxonomy, education and conservation practice.

Pl@nteInfo – A WWW-based platform for the dissemination of up-to-date crop protection information
Bo JM Secher
Danish Institute of Plant and Soil Science, Department of Plant Pathology and Pest Management, Lottenborgvej 2, DK 2800 Lyngby, Denmark.
Allan Jensen and Jens G Hansen
Postboks 23, DK – 8830 Tjele, Denmark.

New and reliable information on the development of pests and diseases in crops during the growing season is of great value for farmers and advisory services. Such information has traditionally been disseminated using newsletters, faxes or text-tv. The Internet and WWW have opened a new and well suited platform for the dissemination of such information. Information can be easily updated or generated automatically and illustrating maps can be presented, supplemented with relevant information. Information can be reached easily by modem.

To demonstrate the potential value of a crop information system on the Internet, The Danish Institute for Plant and Soil Science (DIPS) and The Danish Agricultural Advisory Centre (DAAC) has developed the “Pl@nteInfo” (http://www.sp.dk/planteinfo) crop information system. The following crop protection information has been distributed via Pl@nteInfo:

Up-to-date calculated risks based on weather data:
- Septoria species on winter wheat
- Drechslera teres and Rhynchosporium secalis on barley
- Oscinella frit
- Dasineura brassica
- Phytophthora infestans
Records from national pest and disease surveys of all major pests and diseases in:
- Winter wheat
- Winter barley
- Spring barley

The weather-based risk calculations were presented in maps of Denmark divided into 40×40 km grids. The grids were coloured according to the calculated risk: green if no risk, yellow if close to risk, and red if at risk. In each grid a comparison to the developments in previous years could be retrieved in a sublayer. Linked to the maps was information on the pathogen or pest, the model used to calculate risk, and comments from crop protection specialists.

Records from the national surveys on pests and diseases were presented in tables generated from the database at the DAAC.

DIPS and DAAC will improve the information and presentations in Pl@nteInfo for the growing season 1997. Information related to crop development, irrigation and fertilizers will be included.

Making books interactive: an electronic experiment
Pierce Jones
Agricultural and Biological Engineering Department, University of Florida, PO Box 110570, Rogers Hall, Gainesville, Florida, 32611 USA.

See Parallel session 5A

The Plant Pathology Internet Guide Book (PPIGB)
Thorsten Kraska
Institute for Plant Diseases and Plant Protection, University of Hannover, Herrenhuser Str. 2, D-30419 Hannover, Germany.

The project to make a compilation of plant pathology Internet resources started at the beginning of 1996 with not more than 50 sites. In its third version it now has more than 600 links and is still expanding every week. In the mass of Internet sites available, PPIGB is intended as a service where one can find relevant information about plant pathology in its broadest sense, sorted into thematic sections. But why create PPIGB for this purpose and not use one of the available Internet search engines? Search engines give a mass of sites in response to a given search query, but often only a few of the results contain relevant information for the user. PPIGB in contrast functions as a starting point. It is not an automatic spider, which lists all results to a given search query; it is a subject-oriented Internet resource guide, where sites with relevant plant pathology information are included. Clicking on a thematic section (e. g. Departments, mycology, pesticides, IPM . . .) will display a list of relevant sites with brief descriptions, often submitted by the authors of the Web sites. Clicking on a link will lead the user to Web sites of interest. If several sites covering the same aspect are available in one section, they will displayed together (e.g. on Karnal bunt in the section on mycology). The author of PPIGB check the links from time to time and searches for broken links. Also the user has the possibility of reporting broken links or sending comments to the author. New thematic sections will be included if there is a need for them. Online forms for submitting URLs and information about meetings or jobs are available. This ‘interactive’ aspect of PPIGB links the user to the author of PPIGB and makes it possible for PPIGB to be adapted to the needs of users. PPIGB is updated every week, or after information on one page has been changed.

The German Phytomedical Society on the Internet – DPG Online
Thorsten Kraska
Institute for Plant Diseases and Plant Protection, University of Hannover, Herrenhuser Str. 2, D-30419 Hannover, Germany.

The ‘DPG Online’ service was created on the occasion of the 50th German Plant Protection Congress in Mnster (Germany) in September 1996. The first full version will be available in December 1996. The DPG is the mouthpiece of the phytopathologists in Germany. DPG Online will provide general information about the society and their activities. It will also give up-to-date information in members’ and non-members’ sections. In the near future it is planned to set up a service called ‘Phytopathology in Germany’ with information about Departments, their research topics and contact addresses. For young scientists a listing is currently created where they can find information about working groups and scientists in their field of interest. This will be a searchable database. Online Discussion Groups will be created on members’ requests. The working groups of the DPG will present abstracts of their annual meetings. Online forms will help the user to give feedback to the society. There will also be a place for general questions. A full first English version will be available soon.

We hope that DPG Online will be a platform for all plant pathologists to find information and to exchange ideas.

Image capture, analysis and archiving as an aid to fungal diagnosis
C. Lane
Central Science Laboratory, Sand Hutton, York YO4 1LZ, UK.

Environmental Management in Agriculture
Kathy Lewis and Avice M Hall
Plant Pathology, Environmental Sciences, University of Hertfordshire, College Lane, Hatfield AL10 9AB, UK.

This decision support system, funded by the Ministry of Agriculture, Fisheries and Food, aims to encourage and promote best practice in arable agriculture. The system is a computer-based, interactive system which includes a comprehensive hypertext information system, and a method of eco-rating individual pesticides and farming practices.

The pictorial computerized identification system BIKEY as a part of the DIALOBIS biological encyclopaedias on CD-ROM
A Lobanov, M Dianov, A Ryss
Zoological Institute of the Russian Academy of Sciences, Universitetskaya emb. 1, St. Petersburg, 199034 Russia.
W Schilow
“Dialobis Edition”, Ebereschenallee 11, 2623 Berlin, Germany.

Identification of specimens plays a significant role in computerized biological encyclopaedias. Pictorial multi-entry polychotomous identification keys are the only ones that correspond to the level of modern multimedia technologies. The main programs of the computerized identification system BIKEY have been used to create the DIALOBIS biological encyclopaedia series on CD-ROM.

The DIALOBIS concept is based on the idea of the initial set of taxa which can be investigated interactively and reduced in different ways. Eight specialized applied programs are used as filters. They can be started by the following eight screen buttons of the main interface: “Higher Taxon”, “Queries to Database”, “Distribution Map”, “Picture Gallery”, “Text Key”, “Pictorial Key”, “List of Taxa” and “Classification Tree”. DIALOBIS has the following advantages over the analogous multimedia database systems. You can:

Find the taxon by the name fragment
Move quickly between and within the classification levels
Obtain the list of taxa inside borders traced by the user on a map
Address requests consisting of up to seven different conditions (distribution, habitat, feeding habit, etc.)
Use a distribution thesaurus reflecting the subordination links of regions.

Subordinate programmes of the DIALOBIS package have the following advantages:

“Pictorial Key”:

Uses images during selection of character states (text explanations serve as auxiliary means only)
Proposes the characters in descending sequence depending on their diagnostic value (not at random!)
You can finish an identification at every step by directly browsing all the images, without thorough selection of character states (“peephole” mode).

“Distribution Map”:

The map is synthesized from several layers (land contours, river networks, lakes and water basins, settlements) in real time
You can set any map scale you like
Species and higher taxon distribution is shown by pictograms of real record points (not as generalized regions). You can change the shape, size and colour of pictograms.

“Picture Gallery”:

An original program to browse images of taxa, with a simultaneous study of their classification.

“Classification Tree”:

A program to browse and choose taxa from the classification tree remaining after reduction by other filter programs.

GENCOMEX: a computerized key to identify the genera of Asteraceae of Mexico in the PC-Windows environment
Miguel Murgua
Asociacioacuten de Bilogos Amigos de la Computacin, A. C. Av. San Jernimo 507, Col. San Jernimo Ldice, 10200 Mxico D.F., Mxico.
Jos L Villaseor
Instituto de Biologa, U.N.A.M. Department of Botany, Apartado Postal 70-367, 04510 Mxico D.F., Mxico.

See Parallel session 5B

Multi-media tools for diagnosing and managing pest and disease problems
Geoff Norton
Cooperative Research Centre for Tropical Pest Management, Gehrmann Laboratories, The University of Queensland, Brisbane, Queensland 4072, Australia.

See Plenary session 7

Computer-based keys for botanical identification
R J Pankhurst
Royal Botanic Garden Edinburgh, Inverleith Row, Edinburgh EH3 5LR, UK.

See Parallel session 3B. The demonstration will include the PANKEY package of identification programs, and identification data in the PANDORA database.

GENSTAT for Windows
R W Payne
Statistics Department, IACR-Rothamsted, Harpenden, Herts, AL5 2JQ, UK.

Archiving biodiversity
Peter H Schalk
ETI, University of Amsterdam, Mauritskade 61, 1092 AD Amsterdam, Netherlands.

See Plenary session 4

A computerized identification system for poisonous plants and fungi
EA Dauncey*, VSG Murray, TGJ Rayner* and DA Shah-Smith*
Medical Toxicology Unit (MTU, formerly Poisons Unit), Guy’s & St Thomas’ Hospital Trust, London, UK.
*MTU, c/o Centre for Economic Botany, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK.

The Medical Toxicology Unit (formerly Poisons Unit) of Guy’s & St Thomas’ Hospital Trust and the Royal Botanic Gardens, Kew are collaborators in the design and development of a computerized system for identifying poisonous plants and fungi. Designed primarily for the use of medical professionals, the first products of this collaboration are the award-winning** Poisonous Plants in Britain and Ireland on CD-ROM (1995), and Poisonous Fungi in Britain and Ireland (due to be published in autumn 1997). The identification system is comprised of three parts:

A dataset consisting of five files largely based on the DELTA (Description Language for Taxonomy) format, including a list of distinguishing characters and a list of taxa or ‘suspects’
An ‘identification engine’ coded in C and written specifically for the project by System Simulation Ltd.
A highly visual user interface written by the Computing Section, Royal Botanic Gardens, Kew in Visual Basic to run in Microsoft Windows.

The interface prompts the user to identify a plant or fungus by answering non-technical questions, many of which are illustrated by graphic images. According to the user’s answer the ‘engine’ recalculates the number of taxa or ‘suspects’ and selects the next ‘best’ question to achieve an identification by asking the least number of questions. The selection of the ‘best’ question is made using an information theoretic measure based on the ID3 algorithm. A second algorithm, the minimax game tree algorithm, is also available.

When sufficient questions have been answered to reduce the number of ‘suspects’ to five or fewer the user can ‘view’ the suspects. Identifications are visually confirmed by the examination of photographic images, many of which show close-up images of important morphological characters. There are up to ten images for each taxon. The user is then able to view toxicological and morphological descriptions.

At present the system is designed for the identification of poisonous plants and fungi. However, the software is generic and can be used for many other applications. For example we are currently developing a tool to teach the differences between electrocardiogram (ECG) traces, and we are keen to form further collaborative links.

**British Computer Society Award (1994), Directory Publishers Association CD-ROM Directory of the Year Highly Commended (1996)

Poisons Unit of Guy’s & St Thomas’ Hospital Trust and Royal Botanic Gardens, Kew (1995). Poisonous Plants in Britain and Ireland on CD-ROM. HMSO, London, UK. [2 versions: medical, general]

The Crop Protection Compendium
A Sweetmore, C Y L Schotman, Bin-Cheng Zhang, S A Rudgard and P R Scott
CAB International, Wallingford, Oxon OX10 8DE, UK.

See Parallel session 8A

ADEM – an integrated disease warning system for apple
XiangMing XU
Horticulture Research International, East Malling, Maidstone, Kent ME19 6BJ, UK

Parallel session 5A: Passing on information in education and training

Electronic teaching aids for students and practitioners
Gail L Schumann
University of Massachusetts, Amherst, USA.

This paper examines some of the pedagogical advantages and disadvantages of newly emerging teaching technologies. Probably the greatest benefit from the use of instructional technologies for plant pathology students is access to quantities of high quality images. An important first step in the study of plant pathology is to develop mental images of the microscopic pathogens and typical disease symptoms referred to in most of the scientific literature. The limited photographs in textbooks and the brief exposure to photographs in the classroom impair the ability to quickly visualize the basics of plant pathology. Examples of the current technologies discussed are videodisc, CD- ROM, Web pages, and simulations for decision-making, with their relative advantages and disadvantages.

Some of the limitations of teaching technology are technological. These include student access, hardware and software incompatibilities, and technical support for faculty in the time-consuming and rapidly changing formats for instructional technology. More important problems are probably associated with possible misinterpretations of how technology may or may not help students learn. Instructional technology is so new that the instantaneous gasp at how beautifully images can be presented and interact in a three-dimensional cyber-environment must now give way to an analysis of the quality of the material presented. There is no doubt that technology can improve a student’s ability to quickly become familiar with some important aspects of plant pathology, but the “point and click” superficiality of “screen literacy” is no substitute for laboratory experience with diseased plants and their pathogens. It is also no substitute for an in-depth consideration of the concepts and theory of plant pathology which may mature into the ability to critically evaluate the science behind the flashy images. We must find a way to integrate the full range of intellectual skills for the education of future plant pathologists.

In the modern world, it is not unusual for people to have a paradoxical attitude toward information. On the one hand, daily life’s complex interactions seem to require ever increasing access to specific, accurate information. On the other hand, there seems to be an expanding overabundance of information. From their inception, computers were touted for their capacity to manipulate, store and retrieve information (data). This paper describes two electronic publishing projects with the stated goal of improving access to information.

NASD’95, the 1995 edition of the National Ag Safety Database, funded by the National Institute for Occupational Safety and Health (NIOSH), provides an extensive compendium of educational and information resources targeted to support programs in county Cooperative Extension Service (CES) offices. NASD’95 was publicly released on CD-ROM at the 1995 National Institute for Farm Safety Summer Meeting in Saratoga, New York. In November 1995 the database was reformated in HTML and served up on the World Wide Web. Since its inception, activity on the database was monitored. Between November 1995 and July 1996, total visits grew from 1,053 to 16,705. More sophisticated tracking tools are being implemented to better understand activity on the National Ag Safety Database.

HazCom Interactive delivers information on hazardous chemicals on personal computers. The project is based on the International Chemical Safety Card (ICSC) database developed by the International Programme on Chemical Safety (IPCS). The ICSC uses standard phrases in multiple languages to describe the characteristics of ~1,200 hazardous chemicals. Pictographs were created that correspond to many of the standard phrases. Text and associated pictographs are displayed in combination both on the computer monitor and auxiliary printed posters and labels. Audio files can be activated to “read” the textual descriptions of the chemicals. HazCom Interactive provides specific, high quality information and training on hazardous chemicals that can be delivered on construction sites where personal computers are present.

Both projects intend to improve access to targeted sets of information. Both are designed to achieve this goal through paying careful attention to storage and retrieval issues, developing a critical mass of materials in the targeted area, ensuring version control, and maximizing the interconnectivity of the information in the collections. Examples are given.

Crop protection: Information Technology and ecosystem health
ZuoRui SHEN
Department of Plant Protection, College of Plant Science and Technology, The China Agricultural University, Beijing 100094, China.

The Strategy of Precaution Priority and Integrated Management has been implemented for 20 years in China and today proves more convincingly to be wise in the trend towards sustainable development in agriculture. Historical facts demonstrate that this Strategy cannot achieve complete sustainability without ample information on ecosystem health. This is concerned with crops, insect pests, plant diseases, weeds, other harmful organisms, their natural enemies, so-called “resource biota”, components of the physical environment, and structures connecting and relating all of them in food webs and biogeographical cycles. In addition, history reveals that to realize sustainable success by this Strategy the scale of the ecosystem that is monitored, diagnosed, and taken to precaution or protection should be substantial. It should be enlarged from the level of physiological ecology, individuals, populations, communities, and fields, to the level of farms and even whole regions. Information Technology will play a more and more important role in the scaling-up, and will be used in more diverse and advanced ways. To demonstrate how the Strategy can be used in the context of the information revolution, case studies from China will be presented.

Having collected data and experiences from vegetable production and pest control practices for many years in the Beijing region, the author’s laboratory is conducting a project to develop a software system, BJ-CABBAGIS, for vegetable production information management and decision support. It is designed to be GIS-based and consists of four subsystems: social and natural information management, vegetable production information management, vegetable protection information management, and pest diagnosis and IPM decision support.

Another case is the development and use of a multi-media system, PQ-INFORMIS, from which information on plant quarantine insects (58 species) can be retrieved and managed. The information includes text for many items such as English and Latin names, host plants, geographical distribution (countries), quarantine treatments, and also images of identifying morphological characteristics. It offers a Prolog program to help quarantine staff to distinguish similar species. The software is proving popular at about 70 importing port quarantine stations throughout China.

These two cases illustrate successful application of information technology to plant protection. An important component of the methodology is the participatory approach which unites university researchers, government administrators, plant protection practitioners at quarantine stations and farms, and information experts.

Computer games and other tricks to train field pathologists
Terry Stewart
Department of Plant Science, Massey University, Private Bag, New Zealand.

Problem-solving exercises are recognized as having a high educational value. Incorporating such exercises into plant pathology courses is important, as the diagnosis and management of plant diseases requires such skills. Of these learning aids, well- designed computer-based games, used properly, can be ideal training tools.

Diagnosis for Crop Protection is an example of a problem-based training aid, that came about as a solution to a teaching problem. The problem was how to allow students to acquire the “art” of disease diagnosis as distinct from simply being able to identify a pathogen. In Diagnosis, students are placed in an “adventure game”-type simulation where they must actively seek clues and interpret observations on the cause of plant problems. Unlike an expert system, it is assumed the expertise lies with the student. In this way, they are challenged to use their knowledge and any resources available, to come up with a justifiable diagnosis and recommendation. The plant problem simulations, or “scenarios”, can be tailored to the student, both in the level of interpretation offered, and the crops and pathogens encountered. The programme can monitor student progress and provide feedback. Games such as Diagnosis are useful integrating tools, forcing students to take a holistic view of cropping systems and giving them practice at solving real-world problems.

Where from here? The need to rebuild our university educational systems on an Information Technology basis
Peter H Schalk
ETI, University of Amsterdam, Mauritskade 61, 1092 AD Amsterdam, Netherlands. Tel: +31 20 5257239. Fax: +31 20 5257238.

Financial cut-backs have severely affected the capacity and quality of university educational systems, especially in the “developed countries”. Traditional classroom situations with a teacher vocally repeating printed information is out of date as well as inefficient. Moreover, the computer-“savvy” new generation of students expect more from their education than is presently offered. Self study will (and should) become more and more important for the students of the future.

The so-called “new media” and other developments in Information Technology offer wonderful opportunities to modernize and revitalize our university educational systems. Interactive multimedia software tools, reference works on compact disc, in combination with links to continuously updated information on the Internet, can be used to increase both the efficiency and quality of education at the university and high school level.

In this “Where from here?” paper I would like to make a strong plea for applying the new media in the educational system. This would not only improve the quality of education at our universities, but it would also create an entirely new “export product” allowing students in other (developing) countries to tap into our educational resources and to benefit from them.

Parallel session 5B: Computer-based species identification: Applications II

Computerized insect identification: a comparison of differing approaches and problems
Ian M White and Graham R Sandlant
International Institute of Entomology, 56 Queen’s Gate, London SW7 5JR, UK.

The advantages and disadvantages of computerized dichotomous and multiple entry keys are discussed. While both approaches allow pictorial presentation and space for explanation of terms, the multiple entry key also has better retention of information, greater user efficiency, and the power to allow users some control of the path to an identification. A theoretical comparison was made of how well each approach represents an information space (a data matrix of taxa by characters); multiple entry keys can represent the entire information space; conversely, a dichotomous key could in some cases contain under 10% of that information. For example, a dichotomous key to mosquito genera was found to contain only 17% of the possible information that the author would have had to consider in some way during the construction of that key. Multiple entry keys also have greater user efficiency in terms of the mean number of questions that have to be answered to achieve an identification.

An experiment compared dichotomous and multiple entry keys to 120 species of tephritid fruit flies. A selection of 20 pest species was run through each key and it was found that 179 decisions were required to use the multiple entry key compared to 244 with the dichotomous key, an increase of 36%. In general the multiple entry key approach is to be preferred, both for its greater information content and user efficiency. However, in some circumstances there may be good reason to simply convert an existing printed dichotomous key into computerized form in order to gain the advantages of improved presentation and links to other information. Furthermore, multiple entry keys can be difficult to apply in some circumstances, in particular where the taxa are of genus level or above. For example, some mosquito genera appear to be unnatural groups of species and some questions have to contain combinations of two or more characters.

A subjective comparison of the application of the multiple entry key approach to species (fruit flies), genera (mosquitoes) and families (beetles) suggests that this technique gets increasingly more difficult to use with increasing taxonomic level.

GENCOMEX: a computerized key to identify the genera of Asteraceae of Mexico in the PC-Windows environment
Miguel Murgua
Asociacioacuten de Bilogos Amigos de la Computacin, A. C. Av. San Jernimo 507, Col. San Jernimo Ldice, 10200 Mxico D.F., Mxico.
Jos L Villaseor
Instituto de Biologa, U.N.A.M. Department of Botany, Apartado Postal 70-367, 04510 Mxico D.F., Mxico.

The Asteraceae is a family of flowering plants distributed worldwide, and is the richest in number of genera and species. In Mexico the family has found one of its main centers for its diversification, and the country stands as one with the richest Asteracean floras in the world.

Because of the large number of genera present in any flora and the kinds of characters used under traditional methods, identification of members of the Asteraceae has always been a difficult task. However, it is highly necessary, because any flora has the Asteraceae as one of its most important elements.

Written in Turbo-Pascal for Windows, an interactive key was developed for identifying the genera of Asteraceae occurring in Mexico. The program uses a data matrix of 343 genera and 100 character states, these latter ranging from vegetative to reproductive characters, as well as patterns of distribution of the genera among the political states into which Mexico is divided.

The program was developed following a theoretical model we call “Dynamic Identification”. It consists in the traditional character-taxon selection, where a positive matching between the character shown by the specimen under identification is scored; thus, taxa are eliminated each time the character selection is done. However, additional taxon-character selection is also possible. It consists in selecting a possible hypothesis (a taxon that one suspects the specimen belongs to), and once the program displays the characters that distinguish this taxon, we can corroborate our hypothesis or, if it is rejected (the specimen does not belong to the taxon selected), the identification process can continue until a possible identification is reached. By playing with different colors in the screen, the two different processes can be distinguished and easily understood.

The program can display a dictionary (glossary) that explains all the technical terms used in the key. It also includes a set of drawings (iconothec) that helps the user to understand better different structures that are important for the proper identification of the genera of Asteraceae.

The use of this key during the last six months has proved its efficiency. This led us to conclude it is an important resource that will be useful to people interested in the identification of the flora of Mexico. The program thus developed is now being used in the process of generating computerized identification keys for other Mexican groups of plants. For example, a key to identify the families of flowering plants occurring in the country is in the final stages of completion.

The BEG Expert System – A multimedia identification system for arbuscular mycorrhizal fungi
J C Dodd* and S Rosendahl**
*International Institute of Biotechnology / Department of Biosciences, University of Kent, Canterbury, Kent CT2 7YW, UK.
**Department of Mycology, University of Copenhagen, ster Farimagsgade 2D, DK-1353 Copenhagen K, Denmark.

Knowledge of the biodiversity of arbuscular mycorrhizal fungi is limited and keys for identifying them are not in a user-friendly format for the non-expert. An Expert System, linked to the BEG (Banque Europenne des Glomales), has been developed on a CD-ROM to produce a multimedia identification system for these fungi with this aim in mind. An Expert System has been defined in many ways but D A Waterman (cited Edwards & Morse, 1995) proposed sophisticated computer programs that manipulate knowledge to solve problems efficiently and effectively in a narrow problem area. The BEG Expert System was done to show the potential of such a system with a limited number of well-defined species of arbuscular mycorrhizal fungi. The system was put together using Linnaeus II software (Expert Centre for Taxonomic Identification, ETI, University of Amsterdam, Netherlands) which has been developed for biodiversity documentation and species identification. It includes much unpublished data and photographic images on a CD-ROM suitable for computers with Windows or Macintosh platforms. The CD-ROM can be run on a Macintosh/PowerMac platform running System 7.0 or higher with a minimum 4 Mb RAM. The Windows version requires system 3.1 or 95 and 4 Mb RAM.

Our initial philosophy was to make descriptions of the different species consistent in their presentation on the CD-ROM and so we have made several alterations to the published taxonomic descriptions. A consistent taxonomy is necessary for creating the identification system which is based on ETI’s ‘IdentifyIt^TM‘ multiple-entry taxonomic key. This software is based on a character and state matrix and we have input the characters considered most important for identification of AMF across the five genera used on the CD-ROM. There is a different ‘card’ for each character which allows the selection of states to include or exclude in the search pattern. Images and clarification of terminology accompany these cards to aid the user. This still requires the user to view spores under a stereomicroscope for some information and slide mounts on a compound microscope to select the correct character states! Having identified as many character states as possible applicable to the specimen or isolate, ‘IdentifyIt^TM‘ will perform a search on the selected states for the closest resembling AMF species, with results indicated as successful hit percentages next to the species names.

The aim of this venture has been to stimulate renewed interest in the accurate collection of ecological information on the global diversity of these fungi by simplifying the identification procedure. It is a positive attempt to move the taxonomy forward and is open to suggestions from any user.

In trials with colleagues in COST Action 8.21, there has also been considerable enthusiasm for its potential use in teaching. Copies are still available (free) for people wishing to test the CD-ROM and requests should be sent to either author at the two above addresses or via e-mail (soerenr@bot.ku.dk or j.c.dodd@ukc.ac.uk).

More details are provided in the following article:
DODD, J.C. & ROSENDAHL, S. (1996) The BEG Expert System – A multi media identification system for arbuscular mycorrhizal fungi. Mycorrhiza 6, 275-278.

The BEG WWW site is at http://www.ukc.ac.uk/biolab/beg/index.html

P H Gregory paper-reading competition for young researchers

The genetics and pathogenicity of pigment mutants of the take-all fungus Gaeumannomyces graminis
CP Kelly*, AE Obsourne** and CE Caten*
* School of Biological Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
** The Sainsbury Laboratory, Norwich Research Park, Colney, Norwich NR7 4UH, UK.

Pigmented hyphae of the take-all fungus Gaeumannomyces graminis (Gg) are observed both on infected host tissue and when the fungus is grown in vitro. The pigment has previously been partially purified and has properties characteristic of melanin. Growth of isolates in the presence of inhibitors of melanin biosynthesis such as tricyclazole and pyroquilon gave rise to characteristic changes in hyphal pigmentation, but did not affect growth rate. Melanin has been shown to be essential for pathogenicity in some other fungi (Bell & Wheeler, 1986 Annual Review of Phytopathology 24, 411-451) and in order to determine whether this is also the case in Gg, we set out to isolate pigment mutants and to examine their pathogenicity.

An albino and several pale mutants were isolated following irradiation of protoplasts with ultra-violet light. The pale mutants produced only mild disease symptoms on wheat and oats, when compared to the wild type, and the albino was non-pathogenic. Attempts have been made to cross these mutants back to their wild type parent in order to determine the genetic basis of the mutant phenotype and to test whether reduced pigmentation and reduced pathogenicity co-segregate. However, only two crosses have been achieved because of the normal homothallic breeding system of Gg. The first cross, involving a white waxy mutant, indicated that the mutant phenotype was determined by a single gene. All the mutant progeny showed reduced pathogenicity, confirming that the loss of pathogenicity is associated with the pigment loss. In the second cross, a pale brown phenotype was again the result of a mutation in a single gene, but the precise relationship of this to pathogenicity appeared more complex. These results suggest that melanin production is essential for pathogenicity in Gg.

Identification of species of Pestalotiopsis using artificial neural networks based on spore morphometric data
Alexandra Morgan
School of Pure and Applied Biology, University of Wales, Cardiff, UK.

Numerous species of Pestalotiopsis, a fungal plant pathogen, have been described, the majority of which are separated by small differences in dimensions, pigmentation and appendage characters of conidia. Conflicting descriptions of several taxa are typical of the problems involved in clearly defining species boundaries. Radial basis function (RBF) artificial neural networks (ANNs) were trained and optimized for the identification of 23 species of Pestalotiopsis and the related species Truncella truncata based upon morphometric measurements of spores.

Cloning a gene which encodes a glycoprotein present at the fungal-plant interface formed in the Colletotrichum – bean interaction
Sarah Perfect*, Richard O’Connel** and Jonathan Green*
* School of Biological Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
** IACR Long Ashton Research Station, Department of Agricultural Sciences, University of Bristol, Bristol BS18 9AF, UK

Colletotrichum is a large genus of plant pathogenic fungi which cause anthracnose diseases on a wide range of temperate and tropical crops. C. lindemuthianum is a hemibiotrophic species causing anthracnose of bean, Phaseolus vulgaris. During the initial biotrophic stage of infection, the fungus differentiates infection vesicles and primary hyphae within host epidermal cells. These specialized intracellular hyphae invaginate the host plasma membrane, from which they are separated by a matrix layer. Monoclonal antibodies (MAbs) raised to isolated infection structures have been used to identify proteins present at the fungal-plant interface.

One of these MAbs, designated UB25, recognizes a protein epitope in a 40kDa N-linked glycoprotein specific to intracellular hyphae. Indirect immunofluorescence and EM-immunogold labelling show that the glycoprotein is present in the infection peg, and the fungal walls and matrix surrounding the intracellular hyphae. However, the glycoprotein is not present in intercellular hyphae or secondary necrotrophic hyphae, which suggests that it is specific to biotrophic structures growing in contact with host protoplasts. The glycoprotein may therefore be involved in the establishment and maintenance of biotrophy.

A cDNA library has been constructed from total RNA isolated from infected bean hypocotyl epidermis. The MAb UB25 hs been used to immunoscreen the library and positive clones have been isolated and sequenced. Analysis of the deduced amino acid sequence revealed the presence of two distinct domains, one of which is rich in serine, threonine and proline. The functional significance of this will be discussed. In addition, Southern analysis indicates that the glycoprotein recognized by UB25 is fungally encoded and is present in several Colletotrichum species.

Stem tip dieback of cassava: identification and virulence of the causal organism
Emmanuel Moses
Department of Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, UK.

A disease of cassava characterized by prominent dieback symptoms was first described in Zaire in 1989 but the causal agent was not established. A similar disease is widespread in Ghana and isolations from affected plants consistently yielded a fungus with morphological features corresponding to the genus Colletotrichum. When four Ghanaian cultivars of cassava were inoculated with these isolates they developed symptoms which were indistinguishable from those of the plants from which the isolations were made. Koch’s postulates were completed by reisolating the fungus from the inoculated plants and showing that its morphology was the same as the one originally isolated.

The identity and taxonomic position of the cassava pathogen was established by sequencing domain 2 of ribosomal DNA and comparing the nucleotide sequences with those of other members of the genus whose identities are well established. Out of 193 nucleotides analysed, the cassava isolate differed from authentic C. gloeosporioides isolates by only one, demonstrating that the cassava pathogen was a form of C. gloeosporioides.

The host range of the casssava pathogen was tested by inoculating other plant species that are widely grown as crops in Ghana. Fruits of tomato, banana and pepper developed lesions within two days of inoculation and lesions were especially severe if the fruit were wounded.

The early occurrence of water-soaking symptoms in inoculated stems of cassava suggested that the fungus was affecting the permeability of the plasmamembranes of host cells. When the fungus was grown on Czapek-Dox nutrients supplemented with cassava extract or citrus pectin, the culture filtrates killed cells of the plant isolated from leaves by enzyme digestion.

On dialysis of culture filtrates, about half of the cell-killing activity was found in the high molecular weight fraction and the same proportion was precipitated by 60% acetone. The acetone precipitate also possessed macerating activity as determined by the reduction of weight of cucumber slices and pectate lyase activity as determined by the increase in absorption of light at 232 nm of a reaction mixture consisting of acetone precipitate, sodium polypectate, calcium chloride and buffer at pH 9.5.

When the acetone was removed by evaporation from the acetone supernatant of culture filtrates, most of the residual cell killing activity partitioned into ethyl acetate. This ethyl acetate fraction was further separated by flash chromatography on silica gel. Three toxic compounds were isolated which, on mass spectrometry, were found to share a prominent peak at m/z 355 as well as several peaks at other m/z values suggesting that all three compounds were similar.

In conclusion, the work has shown that dieback of cassava is caused by C. gloeosporioides and that the fungus is capable of producing enzymes and toxins which may be of importance in its virulence.

Plenary session 7: Knowledge dissemination

The number and range of computer-based aids for the prediction, diagnosis and management of insect pest and disease problems has steadily increased over the past 25 years. As new developments occur in Information Technology, the potential value of computer-based systems in improving pest management is increased accordingly. However, to realise this potential, the lessons of the past need to be heeded. The reasons why computer-based systems have not had more impact include their being –

science or technology driven, rather than being designed to meet specified user needs
constructed by biologists with computing ability rather than by specialist programmers
developed de novo, with the “software wheel” often being reinvented
produced with short-term funding, and lacking resources for up-grading and maintenance
seen as competing with, rather than complementing, existing research and extension effort

The Cooperative Research Centre for Tropical Pest Management (CTPM) is a joint venture between four participant organizations – two State Departments, CSIRO and The University of Queensland. Within this joint venture, a suite of software products for pest management is being developed to complement other activities – specifically, problem specification, generic and specific research and development, and education, training and communication. Within this context, the main features of the software products developed are –

they are produced by a team of 10 programmers, working closely with other scientists and users
wherever possible, the software is developed generically, providing large economies of scale
builders are provided with a number of products, allowing easy adaptation and use
training manuals are supplied or being developed for educational forms of the software
monitoring and evaluation of prototype and finished products is standard practice
“extension software” is being developed in close collaboration with industry and State Departments

This paper outlines the Centre’s IT strategy. Demonstrations of software products, to illustrate their use for diagnosing and managing pest/disease problems, include –

LucID – an easy to use, interactive taxonomic/diagnostic key and builder.
BugMatch – crop- based information systems (on CD) for citrus and cotton (a joint development with Rhone-Poulenc Australia).

CD-ROM as a dissemination medium in practice: crop protection case studies in Africa
Sulayman S M’Boob
FAO Regional Office for Africa, PO Box 1628, Accra, Ghana.

In Africa, as elsewhere in the developing world, there is an urgent need for improved delivery of information to support the effective implementation of Integrated Pest Management. FAO, through its Regional Office for Africa, has a special responsibility for supporting information needs in plant quarantine. The FAO Regional Office has a programme to establish information and training networks throughout Eastern and Southern Africa to support the needs of plant protection staff in National Plant Protection Services. In several projects carried out in partnership with CAB INTERNATIONAL, FAO has supplied National Plant Protection Services in Africa with extensive information resources on CD-ROM, backed by hardware, training and technical support. Typically, plant protection specialists who gain access to such resources for the first time display obvious excitement, and gain considerably in professional confidence. The CD-ROM medium appears well suited to delivering substantial information resources to developing countries. Up to now, FAO has focused on providing bibliographic databases in this way. There are now good prospects for further strengthening information resources in African plant protection services through provision of user-friendly information in multi-media format. At present, CD-ROM remains a preferred medium. In due course, the Internet may play a significant complementary role.

Networked communications in extension
Reuben Ausher
Ministry of Agriculture and Rural Development, Extension Service, Department of Crop Protection, Tel Aviv 61070, P.O. Box 7054, Israel.

The conceptual differences between the need for data, information and knowledge are discussed. Networked communications in extension have been tried out in the framework of the extension service in Israel in recent years. The experience was successful in the case of the dairy cattle industry. It failed with poultry and beef cattle. Flower growers connected in the past by e-mail to the auctions in the Netherlands have downgraded the technology level and switched to facsimile communication with the marketplace.

The following types of networks have been established or accessed by extension in Israel:

state or regional farmer-operated networks
in-house crop-based projects and databases operated by extension
Internet-based services.

Crop protection extension is a component of several of these programs.

The following critical success factors have been identified:

frequently updated information
bearing on farmers’ decision-making
available in local language
charged for actual use only
easy handling (log-in and log-out).

The following means of communication with farmers and farmers’ groups are compared in terms of farmers’ needs and the development of new extension methodologies:

face-to-face
letters
telephone and cellular phone
facsimile
Internet-based telecommunications
Internet-based telecommunications for work groups.

Being constantly reduced in staff, the Extension Service in Israel has to amplify the communication channels with its clientele, and among its professionals. Networked communications are a promising but lengthy avenue.

Modern communication needs in agriculture for developing countries
S Nagarajan
Directorate of Wheat Research, Indian Council of Agricultural Research, Karnal 132001, Haryana, India.

In the expanding Indian agriculture, communication plays a vital role in linking policy makers, scientists, farm level agro-consultants, market operators and international institutions. India, in the process of transforming its agriculture, has fully utilized publishing media, audio systems, audio-visual appliances, street drama and performing arts to quickly communicate with farmers, who were not necessarily formally educated, on the need to adopt modern practices to maximize yield. In academic schools, in-service education and in advanced research, the information explosion is being handled through computers.

India is integrated by the INSAT network and is telelinked throughout its 600 or more districts. Flow of weather information, transmission of banking data, and other vital information linkages therefore occur readily. Creating information on the genetic resources of wheat, analysis of a billion information points on common wheat improvement trials conducted at forty places, and computerizing the plant breeder’s crossing note book are all nearing completion. Areas remaining to be explored include usage of GIS systems, computer-aided identification of crop varieties and pests, farmer-friendly advisory services, on-line connection to monitor national and international prices of commodities, and farmer education through multimedia slide shows. Usage of CD-ROM systems and computer usage in post-graduate education are well established. To attain a sustainable agriculture, the need to harness the knowledge explosion through electronic handling of information is well recognized.

Electronic publishing in plant pathology: predicting the unpredictable
Robert Campbell
Blackwell Science Ltd, Osney Mead, Oxford OX2 0EL, UK.

Information technology is full of examples of hopelessly wrong predictions and one way out of this is to conclude that the present is determined by the future. Certainly the current management school fashion is to focus on purpose, people and process and away from detailed predictions with meaningless mission statements. The latest forecasts from the European Commission are safely vague and warn against information overload and disorientation.

The predictions around 1980 of future publishing systems based on more powerful interconnected computers with the journal article moving through the publishing process in machine-readable form have now largely been fulfilled. Perhaps we can conclude that the promise of the future determines the present. Systems for searching the literature (discovery) are now much improved, with exciting innovations such as “search agents” (software that will search the WWW for required information) just round the corner. Once found, however, the delivery of an article still holds problems which may be resolved by Internet II.

New primary publishing models are being tried but it is most likely that the electronic version of established journals will dominate as they have the status to attract the high quality work. The market will demand some value innovation in this change from delivering hard copy at a fixed subscription price to giving access to digital files with scope for new, and perhaps fairer, ways of charging.

The new concept of the electronic textbook is also evolving, based on inter-action between the student and a comprehensive range of contents. These will be expensive to develop but may find favour with policy makers convinced that self-tuition systems will enable universities to teach more students at lower unit cost.

In conclusion, once the speed of delivery matches the new discovery facilities there may be a period of slower development as we adapt to the new more powerful and efficient publishing systems and focus on the financial aspects and ways of evaluating published work.

Parallel session 8A: Interpreting information to produce knowledge

Building an information system to interpret diversity in Colletotrichum
JA Bailey, C Nash, LM Morgan
IACR – Long Ashton Research Station, Long Ashton, Bristol BS18 9AF, UK
F Malweygo
Uyole Agricultural Research Centre, PO Box 400, Mbeya, Tanzania
G Rivera
School of Agricultural Sciences, Universidad Nacional, Heredia, Costa Rica
M Dron
Institut de Biotechnologie des Plantes, Universit de Paris Sud, 91405, Orsay, France

A study of the genus Colletotrichum has concentrated both on diversity between different species and that within a single species, C. lindemuthianum. The information is held on two databases created in Microsoft Access. LARSCOLL is a description of nearly 1000 isolates of pathogenic fungi, mostly species of Colletotrichum, stored at Long Ashton Research Station (LARS). The collection has been built up over more than 20 years and contains isolates from many different crops worldwide. LARSCOLL holds information about the origin of the isolates, including all original supplier codes, many morphological and cultural characteristics, and for some isolates there are novel diagnostic features and rDNA sequences. The second database, COLLBEAN, is central to an EU-funded project “Improved control of bean anthracnose in Latin America and Africa”. This database is devoted to information about the specific virulence of isolates of C. lindemuthianum causing bean anthracnose in Europe, Africa and Central and South America. In this database, which also records details of origin, emphasis is placed on recording the reactions of a differential set of bean cultivars to different isolates of the pathogen. The information has been compiled using similar methods in different laboratories and is being used to determine the number of different races and their distribution in all these countries. This information will help the selection of resistant germplasm appropriate to the different countries. The Access databases have also contributed greatly to taxonomic studies, as they allow ready comparison of isolates and selection of diagnostic criteria. Many errors in the diagnosis of disease and identification of these pathogens have been discovered and close relationships between isolates, previously considered as distinct species, have been discovered. New diagnostic morphological criteria have been found, and these are used routinely to rapidly confirm the identify the bean anthracnose isolates.

New knowledge about the taxonomy/diversity of Colletotrichum is essential if the biology of different species is to be understood and if effective quarantine measures are to be enforced. The wrong identification of the causal agent of lupin anthracnose in Europe, Australia and America appears to have allowed the pathogen to by-pass established quarantine regulations. An important conclusion from this work is that the powerful methods of handling, comparing and distributing data are to be encouraged. However, when such methods are applied to plant disease problems, it is essential that the knowledge concerning the individual pathogens be correct. For anthracnose diseases, at least, inaccurate taxonomic information remains a major deterrent to progress toward effective disease control and there is an urgent need to increase the knowledge base before information is made available.

Keeping track of where pathogens are: Geographic Information Systems
Philippe Blaise
Institute of Plant Sciences, Section Phytomedicine/Pathology, Swiss Federal Institute of Technology, Universittstr. 2, CH-8092 ETH-Zrich, Switzerland.

An important part of a scientist’s work is to think of ways to represent information so that underlying processes can be better understood. This is specially important in the analysis of spatial data with which epidemiologists are faced as soon as they leave the two dimensional space-time-severity to consider dispersal and spread of pathogens. The range extends from restricted-scale studies such as analysis of patterns of spread of soil-borne pathogens to large-scale studies dealing with the spread of airborne pathogens that can travel over hundreds of kilometers. However, working with data that include a spatial component is difficult since quantification is not reduced to a single value. Being the main scientific community concerned with spatial data, geographers have developed already in the 1960s special tools called Geographical Information Systems (GIS), which are distinguished from other data management systems by their inherent ability to maintain spatial relationships of variables as well as their attributes. A GIS can be defined as a set of tools used to handle objects defined in terms of their position with respect to a coordinate system and their attributes that are unrelated to position (e.g. soil type, plant variety, disease incidence etc.). Although the use of GIS is well established in some fields like land-use, natural resources and environment management, landscape ecology and remote sensing, biological sciences only discovered these tools recently and applications in pest management are sparse. This may be due to the fact that GIS have been traditionally regarded as very high-tech, requiring vast hardware, software and data resources to render them useful. Such systems still do exist but fortunately, thanks to the increasing power of microcomputers, GIS are becoming a common tool on desktop computers, ready to use for plant pathologists. After a brief introduction in GIS, a short review of GIS applications in pest management will be presented, followed by a more detailed presentation of some case studies made in our institute with the help of GIS. The value of GIS in plant pathology will be examplified by spatial studies on:

Phytophthora

(3) a survey of the plant protection measures taken in apple orchards in the canton of Zrich.

Integrated information management: a multimedia system for crop protection
A. Sweetmore, C.Y.L. Schotman, Bin-Cheng Zhang, S.A. Rudgard and P.R. Scott
CAB International, Wallingford, Oxon OX10 8DE, UK.

Crop protection research has traditionally been a discipline-based activity; in contrast, crop protection practitioners, particularly farmers and those supporting them in small-scale, intercropped systems in developing countries, have long been taking a more holistic approach. This difference in outlook has led in many cases to a gulf between the activities of the research community and the needs of farmers and their advisers. The difficulty has been recognized by a number of national and international crop protection research institutes, who have tried to break down the barriers between traditional, discipline-based departments and build a more interdisciplinary structure.

The electronic Crop Protection Compendium, a multimedia tool supplied on CD-ROM, addresses this problem by giving the user immediate access to information on all of the component disciplines in a variety of formats. Elements of the system include text, images, geographic data and maps, bibliographic data, taxonomic information, statistical data, and diagnostic aids. Information is organized by pest species (including pathogens and weeds), countries and crops. In the first Module, with a focus on South-East Asia, southern China and the Pacific, approximately 1000 such items are covered in detail, with outline information on many thousands of other species. All these are interlinked in a powerful relational database structure. In addition, ‘soft’ hypertext-like links can be made spontaneously when the user needs them, wherever the system detects a match between text and database index terms. The software is designed with open architecture, allowing connections to be made to external systems and information resources, locally or over the Internet. Rapid access is thus available to a large bulk of information, coupled with the ability to make an infinite variety of connections within the system.

This will aid users to gain a greater understanding of the complex interrelations within agronomic systems, and to take a more integrated approach to crop management and crop protection. It provides a strong generic background to the practical application of Integrated Pest Management, by users with knowledge of the local context.

Interpreting information to produce knowledge: Where from here?
Adrian C Newton, “BSPP Web Manager”
Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK.

Every user comes into a network when trying to access information of any form. The objective of an information system is to provide comprehensive but easy-to-follow routes through the network to all points the user needs to access. The objective is not to impress the user with the size of the network and their location in it, as this will either confuse, bewilder or daunt. To access information about, for example, potato late blight (Phytophthora infestans), potential sources of information and resources of interest may be: books, scientific papers, bulletins, crop intelligence reports, conferences, published statistics and surveys, agrochemical control measures available, practical and anecdotal information from agricultural advisors, agricultural policy documents, current work being carried out on research grants, agricultural advisors, germplasm collections of potato, its wild relatives and P. infestans and its relatives etc., genetic maps or databases of host and pathogen, lists of scientists working in the field, research employment opportunities, and many others. There is therefore a need for a structured information system whereby such sources can be linked together in a logical and helpful format and such that providers of information can make it available in suitable formats.

A key component of such information systems is how user-friendly they are. For example, the list of requirements could be: a Windows-based package, “intuitive” system of use (as few bother to read manuals), rapidly set to the user’s level of competence, rapid access to information so with facilities to update and store information locally whenever possible rather than relying upon slow internet connections, include self- training and automatic prompting, a user-friendly query interpreter, and the ability to handle query uncertainties. A key dimension which can be integrated where societies such as BSPP are involved is the inclusion of active researchers in whatever field is being considered. No information system can replace experience, and there is no satisfactory way of accessing anecdotal information or making the connections which only active researchers can make, and it is essential to involve people in the continuous development of information systems to maintain and develop their usefulness. Furthermore, once a coherent structure is in place many other suppliers of information will be encouraged to make their resources available in the most useful format.

One of the biggest problems in developing information networks will be compatibility and accessibility of information resources. The web interface will allow hitherto incompatible formats to be made accessible without having to access the software directly. The user need not know where the information is stored, what electronic format is used, or what software is being run to access it. The user will only see simple windows-type buttons or sliders to operate, lists to select from, or boxes to make entries in, all of which will be familiar to pc or Mac users. Options, preferences and permissions can therefore be tailored to users’ requirements, allowing different levels of access for different needs.

In the past, BSPP has served the needs of its members by disseminating information in Plant Pathology, in BSPP News, in books and at conferences. It has also represented plant pathologists on national and international committees etc. BSPP will continue to do these things, but it has also developed some new ways: it has established a web site for information about BSPP and its activities, improved availability of its own hard-copy publications in electronic format on the web, and developed a new electronic publication (Molecular Plant Pathology On-Line); it has provided on-line conference information and booking facilities including availability of pre-conference material, abstracts (such as this) and other notes, established a searchable and updatable database of members’ interests, and provided a list of pathology-related internet resources.

There is a clear role for a professional society such as BSPP in initiating and co-ordinating such developments, to serve the interests of its members and to involve them actively in the process, linking and associating information from different sources and at different levels. We should be providing rapid and mutually beneficial channels of communication, discussion, interpretation and data dissemination for our members at whatever is the required level of information technology access or expertise. I welcome discussion of these concepts, so please contribute to BSPPLIST and I will try to encompass any useful ideas in my paper on 19 December.

Parallel session 8B: Computer-based species identification: Novel developments

Development of neural networks for identification
Lynne Boddy*, Colin Morris** & Alexandra Morgan*
* School of Pure and Applied Biology, University of Wales, Cardiff, UK.
** Department of Computer Studies, University of Glamorgan, UK

Artificial neural networks (ANN) were initially developed to mimic the brain, but have been used successfully in many fields, including pattern recognition. Unlike most identification approaches they are not rule-based, but rather ‘learn/train’ from patterns presented to them. They can cope with incomplete, partially contradictory ‘fuzzy’ data, and hence are well suited to biological problems, including identification. A variety of ANN paradigms are suitable for identification, and the way in which some of these (multilayer perceptron, radial basis function and learning vector quantization) operate and the relative merits of each will be reviewed. Training and testing ANNs will be illustrated with data from the genus Pestalotiopsis (fungal pathogens of plants) and from marine phytoplankton. The ability to cope with missing data and novel data, and the pros and cons of using ANNs for identification will be discussed.

Automated analysis of insect sounds using TESPAR and expert systems – a new method for species identification
E D Chesmore, M D Swarbrick and O P Femminella
Environmental Electronics Research Group, Department of Electronic Engineering, University of Hull, Hull HU6 7RX, UK.

The production of sound in insects can be derived from several sources – deliberately generated signals for communication as is found in the Orthoptera, sounds created by movement such as flying and those produced by eating. In many cases, it is considered that the acoustic signals produced can be used to identify to group or even species level; it is this potential that is the subject of the research.

The paper describes work carried out in 1995/6 as a final-year undergraduate project in the Electronic Engineering Department at Hull. The project investigated the analysis and recognition of British Orthoptera although the techniques developed are equally applicable to other insect groups (Hemiptera, Coleoptera, etc.) and other phyla. The project made extensive use of digital signal processing (DSP) and expert system techniques to achieve the following:

Extraction of information on the sound production mechanism, e.g. tooth impact rate, resonances, etc.
Compression of the information by “recognizing” structure such as syllables
Recognition of species and discrimination between call types.

The software package, written in ‘C’ under Windows, is called ISAR (Insect Sound Analysis and Recognition) and utilizes various DSP tools to analyse signals, passing the results to a multiple expert system, known as a ‘blackboard system’, for further analysis and recognition. Conventional frequency domain analysis and time domain characterization (e.g. average zero-crossing rate, average energy, amplitude density, autocorrelation) together with Time Encoded Signal Processing and Recognition (TESPAR) are applied to sampled sounds to extract a set of statistical biometric features. The features are then passed to the blackboard system for hierarchical determination of the sound, e.g. syllable, chirp/trill and phrase/song type. Hypotheses about these song units are posted to the blackboard for examination by knowledge sources (KS) which may in turn post further hypotheses. The top level of the blackboard is species.

The paper will describe the techniques involved in the ISAR system, concentrating on the TESPAR signal analysis which has been used successfully in the past for speech analysis and acoustic condition monitoring of machinery. The results of the analyses for Orthoptera will be presented. These indicate that species-level identification is feasible with low-cost computing. The applicability of this approach will also be discussed. A demonstration will also be given if time permits.

Mixing elements from different identification systems
Paul Bridge
CABI International Mycological Institute, Bakeham Lane, Egham, Surrey TW20 9TY, UK.

The identification process, whether computer assisted or manual, must involve a final decision making step. This final step is arrived at either through a series of earlier decisions, as in keys and expert systems, or as a result of a numerical value in probability and identification score based schemes. Many manual schemes such as some dichotomous keys cannot fail to give a final identification, whereas numerical systems generally employ some form of critical cut-off value in order to validate the final identification. Increasingly, computer- assisted identification systems will use combinations of elements from keys, probability scores or profile matching to make a final decision on the validity or likelihood of the final identification. This process may not only validate the identification but may also be able to provide insights into the reasons for a poor or unsatisfactory identification.

Any identification system will always be placed under limitations imposed by the quality of the reference data, particularly in biology where the reference data must be sufficiently comprehensive in order to reflect the natural variablity within a taxon. All identification systems are subject to this shortcoming, and numerical systems that rely on a critical cutoff level can be particularly sensitive. Different identification coefficients will react differently to aberrant or atypical data, and combining the results from more than one coefficient can result in a more “robust” scheme.

This paper demonstrates how results obtained from different numerical coefficients can be correlated to give further information on the validity of an identification. The relationship of the numerical schemes to both profile matching and key character approaches will also be considered. The combination of these different elements can be used to provide a single robust identification program which will be demonstrated with a frequency matrix of taxonomic characters for a defined group of fungi.

The role of the user in computer-based species identification
GM Tardivel and DR Morse
Computing Laboratory, University of Kent at Canterbury, Canterbury, Kent CT2 7NZ, UK.

Other papers at this conference will review many of the technologies which are used in computer-based species identification. These techniques range from the multi-access key to neural networks and expert systems. While their relative merits have, and will be, hotly debated from a technical viewpoint, it appears that rather less work has been done on comparing and evaluating their usability, efficiency and effectiveness from the user’s perspective. This paper represents an attempt to redress that balance.

The paper describes a series of empirical evaluation experiments where a paper dichotomous key to woodlice, several versions of a hypertext version of the key and a multi-access key were compared. In each experiment, subjects were asked to identify one specimen of woodlouse. Each subject’s ability to reach an identification, the accuracy of that identification and the time taken to reach it were recorded, as were their opinions of the key they had used. In one experiment, with second-year undergraduate zoology students, the students were also asked to record the confidence which they placed in the accuracy of their identification.

In the latter experiment, all students achieved an identification, of which 74% were correct. The success rate was similar for all three identification methods, with students using the paper key being slightly more accurate than the two computer-based approaches. The latter were slower than the paper key. In all media the correct identifications were on average 4 minutes slower than those which were incorrect. Students using the multi-access and paper keys had equal confidence in their identification but their confidence was more often misplaced using the paper key. Students were generally most confident of their identification using the hypertext key, although this medium was slightly less accurate.

The comments which have occurred most frequently in all our evaluation experiments have concerned usability and navigation issues. In particular, our volunteers have commented on the frequently encountered problem of finding their way round the paper key. In general, volunteers found both computer-based keys easy to use but the diagrams and colour plates in both keys were criticized, either because they weren’t there, or because of the poor quality of some of the images. The former comment concerning usability was one or our original motivations for developing hypertext versions of paper keys. The latter comments could be addressed in future versions of the computer-based keys and do not pertain to all such keys.

Finally, an attempt has been made to discover where and how subjects went wrong in their identification and which decisions they found difficult, in order that the efficiency and accuracy of the identification process can be improved. Better software monitoring techniques are required in order to find out exactly what people are doing during the identification process. However, the experimental protocols and results described in this paper are a useful first step in putting the user back at the centre of the debate on the development of computer-based species identification tools.

OPEN FORUM: Biology and Information Technology: The Road Ahead

The IT revolution: how it may support or disturb biology
Peter Cochrane
British Telecom Laboratories, Martlesham Heath, Ipswich IP5 7RE, UK.

A member of the Artificial Life community recently pleaded that we should not anthropomorphise machines because they might not like it. Well, I feel as if I am being Silicomorphised by technology – and I don’t like it either. Even before the start of the electronics revolution in 1915 we have been bending people into technology. Well, it really seems high time to start bending technology into people – it is supposed to help and not hinder us. But our technology has been limited, and only recently have we been able to start the process of humanising machines. If information access equates to power, then usability becomes a moral issue, and the have and have-nots are all at risk. The question is – can we rise to the challenge – do we know enough about humans to realise better environments? Artificial life, or machines that think, provide the way ahead for human-machine interaction. They will create a technology interface for a far broader range of user, they will perform ever more complex tasks on our behalf, and they will enable us to live and work in our increasingly chaotic world.

THE BOOK OF THE CONFERENCE

A book, Information Technology, Plant Pathology and Biodiversity edited by Peter Scott, Paul Bridge, Peter Jeffries and David Morse, will be based on the Conference. It will be published in 1997 by CAB INTERNATIONAL, and will be available at a special price to those who attend the meeting and to Members of the British Society for Plant Pathology and the Systematics Association. For further information or to place an order, contact Lorraine Rogers, CAB INTERNATIONAL, Wallingford OX10 8DE, UK. Fax: +44 (0)1491 833508. E-mail: L.Rogers@cabi.org