BSPP Presidential Meeting 1996

Unlocking the Future: Information Technology in Plant Pathology

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 40x40 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