BIOINFORMATICS APPLICATIONS NOTE
Vol. 15 nos 7/8 1999 Pages 713-714
Interactive data input into the GeneNet database Fedor A. Kolpakov and Elena A. Ananko Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, Siberian Branch of Russian Academy of Sciences, 633090, Lavrentieva 10, Novosibirsk, Russia Received on November 30, 1998; revised on March 31, 1999; accepted on April 14, 1999
Abstract Summary: The GeneNet database has been developed for a formalized hierarchical description of the gene networks. To provide rapid data accumulation in the database, the Java graphical interface for data input through the Internet by independent experts equipped with convenient visual tools is developed. Availability: http://wwwmgs.bionet.nsc.ru/systems/MGL/ GeneNet/ Contact:
[email protected] Introduction The gene networks providing the regulation of physiological processes are the basic features of organisms. Information regarding the regulation of gene expression and signal transduction pathways is rapidly increasing. An object-oriented database GeneNet (Kolpakov et al., 1998) was developed for accumulating these data. A chemical formalism and object-oriented approach (Booch, 1991) were employed as a basis for describing the gene network structure and events occurring in it (Kolpakov et al., 1998). Thus, any event is described as follows:
where A are the entities entering the reaction; B, the entities affecting the course of the reaction; and C, the products of the reaction. Based on this model, all the gene network components are divided into Entities (any material objects) and Relationships between the gene network components. Two types of relationships between the entities are considered: (1) reaction (indicated by the double arrow), that is, formation of a new entity or acquisition of a new property by the entity, and (2) regulatory event (single arrow), that is, the effect of an entity on a certain reaction. The entities are subdivided into 6 classes: (1) Cell; (2) Protein or protein complex; (3) Gene; (4) RNA; (5) nonproteinaceous regulatory Substance; and (6) State of the gene network. Instances of each class are described in a separate table in the GeneNet database (Kolpakov et al., 1998). E Oxford University Press 1999
All components on the diagram are ordered hierarchically into compartments (for example, cell nucleus, cytoplasm, intercellular space). The GeneNet Java graphical user interface provides an automated generation of the gene network diagrams and allows visualization and exploration of the database through the Internet (http://wwwmgs.bionet.nsc.ru/systems/Mgl/GeneNet/). To provide rapid data accumulation in the database, the interface was supplemented with tools for data input by independent experts through the Internet. Otherwise, as a rule, within a single laboratory researchers investigate in detail only a few components of a gene network. Therefore, the developed system should allow joint efforts of many researches from different laboratories on coordinated formalized description of gene networks.
System for data input The system for data input and editing consists of a specialized server for data storage, and a Java applet running on the user computer. The Java applet provides the user with a graphical interface for data input and visual tools for creating and editing gene network diagrams. At the start of the working session, the system requests an expert name and password that has been assigned during registration (http://wwwmgs.bionet.nsc.ru/systems/Mgl/GeneNet/registration.html). Next, the expert selects a gene network diagram for editing from the list or constructs the new one. In Figure 1, a graphical interface for gene network diagram creating and editing is shown. The component toolbar is located at the top. After choosing the type of component (cell, compartment, gene, RNA, protein, substance, state) a user should locate it in a definite compartment on the diagram and then associate the component with its description in the database. For this purpose the user should select the component identifier from the list or create a new description if necessary. For each type of component there is a special form allowing component description editing or creation. To describe relationships between components, the button representing an arrow should be pressed. Then the input and output components should be chosen on the diagram by clicking the mouse. When the working session is finished, the data are stored on the server. Detailed help on the graphical user inter-
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Fig. 1. The GeneNet data input graphical user interface. The component toolbar is at the top, in the center is the diagram of the gene network of antiviral response on the cell level, on the left (top) is the panel for association of the component with its description in the database, and on the left (down) is the description of one of the gene network components.
face is located at http://wwwmgs.bionet.nsc.ru/systems/ Mgl/GeneNet/GUI.html. The system provides coordinated work of several experts on shared data. At every moment, only one expert can edit an entry. To speed up the data exchange between the client and the server, a data caching is actively applied: all the data loaded during the working session are stored in the memory of the expert’s local computer. When the expert starts the entry editing, the system checks whether this entry was modified or whether the other expert edits it. The system also enables us to inform experts about the changes in their data automatically be e-mail. For this purpose, each entry contains the list of experts who has developed the entry. Descriptions of many gene network components contain the references to the entries from the other GeneNet tables. A graphical user interface for data input provides the reference creation only by choosing an entry identifier from the corresponding list. On the other hand entry identifier chang-
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ing or deletion are forbidden. By these means, the reference integrity is guaranteed.
Acknowledgements The study was supported by the Russian Foundation for Basic Research (grants 98-04-49479, 97-04-49740, 97-07-90309, 99-07-90203). The authors are grateful to N. A. Kolchanov for scientific guidance, E. V. Ignatieva and O. A. Podkolodnaya for helpful advice and comments, S. L. Kivileva for technical assistance and G. V. Orlova for translating the manuscript into English.
References Booch,G. (1991) Object Oriented Design with Applications. The Benjamin/Cummings Publishing Company Inc. Kolpakov,F.A., Ananko,E.A., Kolesov,G.B. and Kolchanov,N.A. (1998) GeneNet: a database for gene networks and its automated visualization. Bioinformatics, 14, 529–537.
