BSPP Presidential Meeting 1996Unlocking the Future: Information Technology in Plant Pathology
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
Uyole Agricultural Research Centre, PO Box 400, Mbeya, Tanzania
School of Agricultural Sciences, Universidad Nacional, Heredia, Costa Rica
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
Keeping track of where pathogens are: Geographic Information
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:
- (1) the epidemic of canker of plane trees in
(2) a Phytophthora blight epidemic in the North-East of Switzerland
(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
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.