International Symposium
"Data Retrieval Systems in Biodiversity Research"

St. Petersburg, Russia, May 22 - 28, 1999


Plenary Session


Computerization of the biological institution: Zoological Institute RAS

Main direction of research conducted by the Zoological Institute RAS - systematics, faunal studies, zoogeography and evolution of animals of Russia and neighbouring countries, essential for the conservation of biodiversity. Aims of computerization are to create the efficient system to help the main research activities.

Fields of computerization of the institute are the following:

1) Collection databases and databanks should operate information of millions unique collection materials deposited in ZIN RAS, including type specimens. Both types of collection databases: the relational DBs and the post-relational net hierarchical one ("Collectsia") are being developed in laboratories. Both versions include databases of taxa names with synonyms, geography, ecosystems types;

2) Consequently, the local net is developed to make an information exchange within/between labs more active;

3) Taxonomic Diagnostic Identification Systems (BIKEY, PICKEY) to identify the taxa (for world fauna and fauna of Russia) are the new electronic publications which made according to structure accepted for the well-known series of (paper) taxonomic monographs "Opredeliteli po Faune Rosii [Identification books on Russian fauna]" and "Fauna Rossii [Fauna of Russia]" published by ZIN RAS for decades;

4) Geographical Information Systems (GIS) are being developed as a part of collection and diagnostic identification system packages;

5) Computer Image Analysing is developed for efficient study of the mass collection materials, to create pictorial collection catalogues, and for ecological purposes - to distinguish a taxon in species mixtures and to calculate the species density and biomass;

6) Simulation models in biodiversity and ecology research for prognosis of the development of communities under antropogenic stress;

7) Development of information exchange via Internet in frames of the international collaboration agreements;

8) CD-ROM publications using the multimedia technologies ("Mammoths", "World of beetles", etc.).

Zoological Institute RAS, 199034 St. Petersburg, Universitetskaya Embankment, 1. Tel. (812) 3280011, 3280311, Fax: (812) 1140444. E-mail:


Results of development and use of zoological retrieval systems

The informal inter-laboratory group (ILG) (authors of the report are constant participants of it) attends to development and use of various zoological information retrieval systems more than 10 years. The structure of group has been changed from project to project and these circumstances promoted to search of the non-standard decisions for each new participant and brought new problems and new sight on methods of their  overcoming. Results of the most interesting projects and research fields of the group are presented in separate Symposium reports. Therefore in this introduction we would like to make only some general conclusions. The conception of representation of multilevel hierarchies in relational databases (ZOOCOD), that has been developed and permanently improved by ILG, is of special significance. This conception is used to reflect the biological classifications in all projects of ILG. S. Medvedev has applied principles of ZOOCOD to databases of geographical names and morphological features, N. Kluge promoted the solution of a problem of representation of set of different classifications for the same taxonomic group in one DB table. S. Stepanjants and A.Ryss have introduced the large contribution in the development of diagnostic systems BIKEY and PICKEY to create the computerized identification keys. The long-term work with collection databases has given the whole tree of branches. The central trunk was allocated in integrated system ZOOINT, in which many problems are decided by help of E. Sokolov and A. Stekolnikov. One branch has given the system named OCEAN, which is used collectively in the laboratory of marine researches and improved by A. Golikov. The second branch (developed in cooperation with V.Panov and P.Krylov) is the INVADER system for accumulation and analysis of the data on aquatic invasive species. Experience of development of mapping system ZOOMAP/dBaseMap allows to make interesting generalizations. Integration of all listed directions is DIALOBIS that is the concept of construction of complex biological manuals on compact discs with the use of multimedia elements. Support: RFBR, grants 96-07-89086 and 99-07-90315.

Zoological Institute RAS, St. Petersburg, Russia, E-mail


CD-ROM products of information and identification systems for pest management

(SASD; OOP; Microsoft Visual BASIC)

IPMIST is a laboratory special for IPM Information and Software Technology at the China Agricultural University, Beijing, China. The aim of this lab is to foster young scientists with multidisciplinary knowledge ranging from ecology, agronomy, entomology, plant pathology, and plant protection, to information and software technology, while doing research projects, education programs, consultancy and information service. Consequently, IPMIST has developed software products and electronic publications that can be used for plant protection, agricultural industry, environmental and biodiversity management. Among several categories of IPMIST's achievements in database, expert system, GIS, and Internet applications only CD-ROM products are selected and introduced in this paper. The following products have been commercialized in China.

PQ-InforMIS is a system for managing information with text and illustrations of 58 species of plant quarantine insects that are as a whole listed in documents by the Chinese governmental authority. The information stored includes: name and classification status of the species, their morphological description with texts and images, host plants, geographical distribution in the world, spread approach, record of capture, etc. In addition, the system can work as a consultant to guide quarantine staff to identify a species of quarantine risk, with a knowledge base and in terms of dialogue.

PestDiag is a multimedia expert system and can be used to identify common vegetable insects of more than 80 species in north China. Designed with the technology of SASD (Structural Analysis and Structural Design) and OOP (Object Oriented Programming), the system has been encoded by Microsoft Visual BASIC. PESTDIAG proves useful in assisting vegetable insect pest management for agricultural administrative agencies, plant protectionists and farmers. It helps users to identify vegetable insect pests in the field and then provides them with knowledge of integrated management of the pests. In addition, the system actualizes a new way to professional education and training either at agricultural university level or peasant level. It has the following thoughtful characteristics: (1) Knowledge of vegetable insect pests and their management is reliable. (2) Multimedia technique makes this system user-friendly, more vivid and vigorous. (3) It is more pragmatic to agriculture services. (4) This system has a wide range of users and a great potential of dissemination in agricultural extension. PQ-PickBugs is another multimedia expert system with almost same architecture as PestDiag. However, it has been developed as a plant quarantine orientated product, based partially on the knowledge that is transplanted from PQ-InforMIS and added with new information on more species that are similar morphologically with the quarantine species.

CN-VegePest, a multimedia database, consists of about 200 species as vegetable pest insects distributing in China and runs on Windows platform. This system includes information of the insects on Chinese name, English name, scientific name, vernacular name, synonym, classification status, geographical distribution, host plants, morphological characters, harmful behaviour, habits, outbreak condition and control strategy. The information is expressed, as well as shown textually, with images of morphology of eggs, larvae, pupa, and adults, images of damaged characters of crop plants caused by the pests, audio voice to introduce the pests, and video records to show life cycle in field. The software has a friendly graphic interface, easy to operate. Its functions include browse, retrieve, edit, print the above-mentioned data either as text or as images.

IPMIST Laboratory Department of Plant Protection The China Agricultural University, Beijing 100094, China,
Tel. (86 10) 6289 3015, Fax (86 10) 6289 3214, E-mail:


Information systems and data bases of the Institute of Zoology, NAS of Belarus

The work on development and creation of information systems and data bases in different fields of zoological research has been carried out in the Institute of Zoology for the last several years. The information system on the administrative plan ZOOINFO, created in the Institute, contains data bases on accomplished scientific research, bibliography of the researchers' publications, applications and recommendations of the scientific research, manning table, the Red Book of rare and endangered species of Belarusian fauna (Roshchin, Matveyenko, Blinov). This information system is maintained in the mode of permanent updating. An information system on the reserves of game animals based on the official data of the winter root counts (Roshchin, Matveyenko) has been developed and created. Great attention is being paid in the Institute to the creation of the objective-oriented data bases aimed at on-line informational support of the different directions of research. Thus, there are bases on fish radioecology (Yermolayev), species diversity of zooplancton in different types of lakes (Galkovskaya, Roshchin). There were created and partially filled data bases on entomophagous parasites, ants and soil invertebrates (Khotko, Gurin, Blinov, Matveyenko, Tereshkin). A block of data bases on near-water predators is oriented on resolving tasks related to the assessment of numbers, feeding, parasites and craniology of this systematic group (Sidorovich, Lauzhel). The work with the information system supporting the study of the vertebrates of the Polessky radio-ecological reserve is being carried out, a map-based information system has been created (Nikiforov, Roshchin). By the order of the Ministry of Natural Resources and Environmental Protection of Belarus an information and reference system "Protected natural territories of the Republic of Belarus" has been developed (Gurin, Kozulin). It is planned to integrate the majority of mentioned data bases and information systems into the "Rational nature management" information system, which is currently being created in our country.

The Institute of Zoology, National Academy of Sciences of the Republic of Belarus, 27 Academicheskaya street, Minsk 220072 Belarus, Tel. +375 (17) 284-21-92 , Fax +375 (17) 284-10-36, E-mail


Bioinformatics in Western Australia: management and dissemination of fundamental flora data sets

The Western Australian Herbarium is the primary custodian of fundamental biodiversity datasets concerning the state's flora. Since 1985 the herbarium's 450,000 voucher specimens have been databased and geocoded, and since 1990 the census of vascular plants database has grown to over 16,000 entries representing the 12,500 taxa present in WA. Constantly maintained and updated these two resources are a foundation for plant biodiversity assessment in WA and a fundamental resource in both taxon and regional conservation management. A number of descriptive datasets based on DELTA (Descriptive Language for Taxonomy) methodologies have been developed over the last five years, at both species and generic level for the whole flora and also for significant plant groups. Interactive keys have been developed and natural-language output used for a range of publications. A number of strategies have been used to integrate these various data types into a single primary source of flora information. The world wide web was chosen as the most flexible method for integration and presentation and after three years of refinement the resulting web application - FloraBase - was launched onto the Internet in late 1998 ( Data warehousing, site maintenance, component modularity, levels of access and effective collaboration are some of the management issues that must be addressed in order for such a web application to remain informative and continue to evolve.

Western Australian Herbarium, Department of Conservation and Land Management, Como, 6152, WA, Australia, Tel. +61 8 9334 0506, Fax +61 8 9334 0515, E-mail


Darwin biodiversity information in the former Soviet Union: the millenium opportunity

In the 1999 round of Darwin Initiative awards (UK Government, Department of the Environment, Transport and the Regions) Dr Dave Minter of BioNET-INTERNATIONAL and CABI Bioscience (Egham, Surrey, UK) and Dr Adrian Thomas of the Institute of Terrestrial Ecology (Bangor, Wales, UK) have been awarded funds for a three-year project in the former Soviet Union. The project has three objectives: to make a directory of FSU institutions working with biodiversity, prioritizing those working with neglected groups of organisms such as fungi, protozoa, insects, molluscs and other invertebrates; to establish a forum where future plans for biodiversity work in the FSU can be discussed; to provide computers for selected scientists within those institutions. Scientists willing to collaborate through computerization of their reserve's biological records will be prioritized. In many businesses, there is currently great concern about whether computers will handle dates in the next millenium. The present project treats this "millenium bug" as an opportunity rather than a problem. Computers discarded by organizations in the west will be collected. They will then be taken to biodiversity institutions lacking resources in the former Soviet Union, and their internal clocks will be re-set to 1980: in a remote nature reserve, who cares what a computer thinks the date is?

BioNET-INTERNATIONAL, Bakeham Lane, Egham, Surrey, TW20 9TY, UK


Electronic Metadatabase on biodiversity. Methodology and perspectives for wide use

Need for the information exchange on biodiversity lead to establishment of the Russian Conservation-Monitoring Center, which is also the Russian National Focal Point in the International Clearing House Mechanism project. The Center provides meta-information on biodiversity databases and information systems developed in different regions of Russia. Metadatabase is being created according international standards and presented in electronic form. The software used is MetaMaker, organized in accordance with the NBII Metadata Standard, FGDC. Metadatabase includes now 40 items and provides information on their citation details, content, quality and completeness of data, spatial reference and terms of access. In future the Metadatabase will be published in Internet in the form of interactive collective network resource in English and Russian.

Russian Conservation-Monitoring Center, GEF project, Moscow, 117312, Vavilova, 41, 1. Tel./Fax: 095 124 50 11, E-mail


Botany and zoology database for information exchange system: electronic catalogue "Biodiversity Databases of Russia"

Document is an information fixed on any material carrier using the semiotic principle. Computer technologies have created a new carrier type (magnetic disks) and new document types (databases and electronic publications). Development of the botanical and zoological databases leads to growing requirements to the secondary information, which can be satisfied by the electronic catalogue "Biodiversity Databases of Russia" collecting an information with the aims of 1) identification and 2) unification of the quality characters. Identification is necessary for citation of data from a DB, for references to electronic publications including the Internet ones, for the DB copyright protection. Unification is the description of DB by means of classification and typology. Here is proposed the DB typology according to the following quality characters: information source (primary, secondary); form of the data presentation; model type; information type; PC type, OS type; DB OS type and the quantitative characters: Mb volume and number of DB records. Efficient information supply may favor 1) the free integration of the biodiversity databases 2) the creation of "virtual scientific teams", such as ILDIS project "Leguminosae of the World". Descriptive key-words dictionary "Biodiversity Thesaurus" may be created by biologists working in different fields (as a part of catalogue).

Komarov Botanical Institute RAS, St. Petersburg 197376 Russia, Tel. (812) 2341237, Fax (812) 2344512,