JP2003167882A - Pathway information display device, pathway information display method, program and recording medium - Google Patents

Abstract

<P>PROBLEM TO BE SOLVED: To provide a pathway information display device capable of automatically plotting a graph on a complicated pathway and a medium-scale or large- scale pathway. <P>SOLUTION: This pathway information display device 100 and an external system 200 for providing an external database and a homology retrieving external program on pathway information including a gene control pathway, a metabolism pathway and an information transmitting pathway are connected so as to be communicable via a network 300. <P>COPYRIGHT: (C)2003,JPO

Description

Detailed Description of the Invention

[0001]

BACKGROUND OF THE INVENTION 1. Field of the Invention The present invention relates to a pathway information display device, a pathway information display method, a program and a recording medium, and more particularly to a pathway information display device, a pathway information display method and a program for automatically drawing a binary relational model. And a recording medium.

[0002]

2. Description of the Related Art Conventionally, in the field of bioinformatics, a method of graphically modeling metabolic circuits, pathways for signal transmission, and gene control pathways has been used. For example, P. Karp and S.K. M. Pa
ley, “Automated drawing of
metabolic paths "(in Th
ird International Confere
nce on Bioinformatics and
Genome Research (H. Lim, C.I.
Cantor, and R.M. Robbins, ed
s. (1994), a technique of modeling a metabolic pathway in a graph and drawing it is disclosed.

Also, Tomihiro Koike a
nd Andrew Rzhetsky, “A gr
apic editor for analysis
gsignal-transduction path
ways ”(GENE 259, pp. 235-24)
4, 2000), a technique of modeling a signal transmission pathway by a graph and drawing / editing is disclosed.

In addition, Moritz Y. Becker
and Isabel Rojas. "A gra
ph layout algorithm for d
Rawing Metabolic Pathway
s "(Bioinformatics, Vol. 1
7, No 5, pp. 461-467, 2001), a technique of modeling a metabolic pathway in a graph and drawing it is disclosed.

[0005]

However, the conventional method of modeling a pathway of metabolism or the like by a graph can automatically draw a relatively simple and small pathway, but a complicated pathway or A medium-scale or large-scale pathway has a problem in that it cannot be automatically drawn because it takes a long time to calculate.

Further, the pathway graph automatically drawn by the conventional method has a problem in that the description areas of the nodes and edges themselves and their labels are often overlapped with each other, which is very difficult to see.

Various tools have been developed for users to manually draw pathway information in a graph.
When creating complex pathways or medium- or large-scale pathways, perform clustering appropriately for the relationships between nodes (that is, draw nodes that are closely related to each other) and do not overlap nodes. Since it is necessary to draw evenly, it is necessary to have a skillful technique for the tool, and even if the tool is used, it takes a lot of time and labor, and thus there is a problem that the creation is difficult.

As described above, conventional pathway graph drawing systems and the like in the field of bioinformatics have various problems, and as a result, they are inconvenient for both users and drawing people, and The usage efficiency was poor.

The problems to be solved by the conventional techniques and inventions described so far are not limited to bioinformatics systems that draw pathway information such as gene control pathways, metabolic pathways, and signal transduction pathways. It can be similarly considered in all the systems that graph the pathway information of.

The present invention has been made in view of the above problems, and a pathway information display device, a pathway information display method, a program, and a program capable of automatically drawing a graph for a complex pathway or a medium-scale or large-scale pathway. Also, it is intended to provide a recording medium.

[0011]

In order to achieve such an object, the pathway information display device according to claim 1,
Pathway information 2 consisting of nodes and edges
A binary relation model creating means for creating a term relation model, a repulsive force calculating means for calculating a repulsive force generated between the nodes within a certain distance, and an attractive force generated between the nodes connected by the edges. An attractive force calculation unit, a repulsive field calculation unit that sets a repulsive field to a predetermined peripheral area of the node to calculate the repulsive force and the attractive force, and the repulsive force calculated by the repulsive force calculation unit and the attractive force calculation Based on the attractive force calculated by the means, the repulsive field calculated by the repulsive field calculating means, and the attractive force of the repulsive field, the coordinate position of the node is determined by a spring layout, and the node and the edge are drawn by a graph. And a graph drawing unit for displaying the pathway information in the form of a binary relational model.

According to this apparatus, a binary relational model of pathway information composed of nodes and edges is created. Here, the pathway information includes information about gene regulation pathways, metabolic pathways, signal transduction pathways, etc. By mapping the main information to a binary relation, complicated pathway information is simplified and modeled,
You will be able to express it comprehensively. Then, the repulsive force generated between the nodes within a certain distance is calculated, and the attractive force generated between the nodes connected by the edge is calculated,
By determining the coordinate position of the node based on the repulsive force and the attractive force by the spring layout and drawing the nodes and edges in a graph, even if it is medium or large scale pathway information or complicated pathway information, it can be done within a certain time. It will be possible to automatically draw a graph that is somewhat readable. Here, if the layout is performed only by the force based on the repulsive force and the attractive force between the nodes, the nodes may be too close to each other and the node or the edge itself or the label thereof may be difficult to see. Therefore, in the present invention, a repulsive field is set for a predetermined peripheral area of each node to prevent the nodes from being too close to each other. That is, the present invention sets a repulsive field to a predetermined peripheral region of a node, calculates repulsive force and attractive force, and calculates the coordinate position of the node based on the calculated repulsive force, attractive force, repulsive field repulsive force and attractive force. It is decided by the spring layout, and the nodes and edges are drawn in a graph, and the pathway information is displayed in a graph with a binary relational model, so that the nodes and edges themselves and their labels are prevented from overlapping and the readability of the graph is further improved. Like

The pathway information display device according to a second aspect of the present invention is the pathway information display device according to the first aspect, wherein the repulsive field calculation means weakens the attractive force to the peripheral region of the node. And / or
It is characterized in that the repulsive force and the attractive force of the repulsive field are calculated by increasing the repulsive force between the nodes located in the peripheral region of the node.

This shows one example of the repulsive field calculation more specifically. According to this device, by weakening attractive force (including not generating attractive force) to the peripheral region of the node, and / or increasing repulsive force between the nodes located in the peripheral region of the node. The repulsive field is calculated, and based on these forces, the spring layout is performed so that the total force (for example, the energy value that is the sum of the absolute values of the combined vector of all edges) realizes the minimum energy state of the system. The coordinate position of the node is determined, and the node and the edge are graph-drawn.

The pathway information display device according to a third aspect of the present invention is the pathway information display device according to the first or second aspect, wherein it is determined whether the coordinate position of the node is within a predetermined drawing area. It is further characterized by further comprising a boundary determining means for moving the coordinate position of the node to the boundary of the drawing area when it is out of the drawing area.

According to this apparatus, it is determined whether the coordinate position of the node is within a predetermined drawing area, and if it is out of the drawing area, the coordinate position of the node is moved to the boundary of the drawing area. The pathway information can always be drawn in the drawing area.

The pathway information display device according to claim 4 is the pathway information display device according to any one of claims 1 to 3, wherein the repulsive field of the node is narrowed within a predetermined time. In addition, control is performed to increase the attractive force between the nodes, and after the time has elapsed, the repulsive field of the nodes is widened, the attractive force between the nodes is weakened, and the repulsive force between the nodes is increased. By further controlling the graph drawing so that the related nodes are brought closer to each other during the above time and the approaching nodes are dispersed after the above time has passed. Is characterized by.

According to this device, the repulsive field of the nodes is controlled to be narrowed within a predetermined time and the attractive force between the nodes is strengthened, and after a lapse of time, the repulsive field of the nodes is widened and the repulsive field of the nodes is widened. By controlling so that the repulsive force between the nodes is weakened and the repulsive force between the nodes is strengthened, the graphs are drawn so that the related nodes move closer to each other in time and the approaching nodes disperse after the lapse of time. Can be controlled.

The pathway information display device according to a fifth aspect is the pathway information display device according to the fourth aspect, wherein an absolute value of a composite vector is obtained based on the node and the edge drawn by the graph drawing means. The apparatus further comprises energy calculating means for calculating energy by obtaining the sum of the values, until the energy calculated by the energy calculating means becomes smaller than a predetermined value, or until the energy becomes the minimum. It is characterized in that the dynamic parameter control means is repeatedly performed.

According to this apparatus, the energy is calculated by obtaining the total sum of the absolute values of the composite vector based on the drawn nodes and edges, or until the calculated energy becomes smaller than a predetermined value, or By repeatedly performing dynamic parameter control until the energy becomes the minimum, it is possible to obtain an arrangement that realizes a system having a somewhat small energy state or a minimum energy state.

The pathway information display device according to claim 6 is the pathway information display device according to any one of claims 1 to 5, wherein the connection destination of the edge of the node is another edge. In some cases, provisional node setting means for setting a provisional node on the other edge is further provided, and the graph drawing means draws the provisional node portion as a bending point.

According to this apparatus, when the connection destination of the edge of the node is another edge, a temporary node is set on the other edge and the temporary node portion is drawn as a bending point. Readability can be improved when connected to another edge.

The present invention also relates to a pathway information display method, and the pathway information display method according to claim 7 is a binary relational model for creating a binary relational model of pathway information composed of nodes and edges. A model creating step, a repulsive force calculating step for calculating a repulsive force generated between the nodes within a certain distance, an attractive force calculating step for calculating an attractive force generated between the nodes connected by the edge, and the node in advance. A repulsive field calculation step for calculating the repulsive force and the attractive force by setting a repulsive field for the defined peripheral area, the repulsive force calculated by the repulsive force calculating step, the attractive force calculated by the attractive force calculating step, and The coordinate position of the node based on the repulsive force and the attractive force of the repulsive field calculated in the repulsive field calculating step. The determined by the spring layout, and a graph drawing step for graphing the nodes and the edge, the pathway information, characterized in that the graph display in the binary relation model.

According to this method, a binary relational model of pathway information composed of nodes and edges is created. Here, the pathway information includes information about gene regulation pathways, metabolic pathways, signal transduction pathways, etc. By mapping the main information to a binary relation, complicated pathway information is simplified and modeled,
You will be able to express it comprehensively. Then, the repulsive force generated between the nodes within a certain distance is calculated, and the attractive force generated between the nodes connected by the edge is calculated,
By determining the coordinate position of the node based on the repulsive force and the attractive force by the spring layout and drawing the nodes and edges in a graph, even if it is medium or large scale pathway information or complicated pathway information, it can be done within a certain time. It will be possible to automatically draw a graph that is somewhat readable. Here, if the layout is performed only by the force based on the repulsive force and the attractive force between the nodes, the nodes may be too close to each other and the node or the edge itself or the label thereof may be difficult to see. Therefore, in the present invention, a repulsive field is set for a predetermined peripheral area of each node to prevent the nodes from being too close to each other. That is, the present invention sets a repulsive field to a predetermined peripheral region of a node, calculates repulsive force and attractive force, and calculates the coordinate position of the node based on the calculated repulsive force, attractive force, repulsive field repulsive force and attractive force. It is decided by the spring layout, and the nodes and edges are drawn in a graph, and the pathway information is displayed in a graph with a binary relational model, so that the nodes and edges themselves and their labels are prevented from overlapping and the readability of the graph is further improved. Like

The pathway information display method according to claim 8 is the pathway information display method according to claim 7, wherein the repulsive field calculation step weakens the attractive force to the peripheral region of the node. And / or by increasing the repulsive force between the nodes located in the peripheral region of the node, the repulsive force and the attractive force of the repulsive field are calculated.

This shows one example of the repulsive field calculation more specifically. According to this method, by weakening attractive force (including not generating attractive force) to the peripheral region of the node, and / or increasing repulsive force between nodes located in the peripheral region of the node. The repulsive field is calculated, and based on these forces, the spring layout is performed so that the total force (for example, the energy value that is the sum of the absolute values of the combined vector of all edges) realizes the minimum energy state of the system. The coordinate position of the node is determined, and the node and the edge are graph-drawn.

The pathway information display method according to claim 9 is the pathway information display method according to claim 7 or 8, wherein it is determined whether the coordinate position of the node is within a predetermined drawing area, It is characterized by further including a boundary determination step of moving the coordinate position of the node to the boundary of the drawing area when it deviates from the drawing area.

According to this method, it is determined whether the coordinate position of the node is within a predetermined drawing area, and if it is out of the drawing area, the coordinate position of the node is moved to the boundary of the drawing area. The pathway information can always be drawn in the drawing area.

The pathway information display method according to claim 10 is the pathway information display method according to any one of claims 7 to 9, wherein the repulsive field of the node is narrowed within a predetermined time. In addition, control is performed to increase the attractive force between the nodes, and after the time has elapsed, the repulsive field of the nodes is widened, the attractive force between the nodes is weakened, and the repulsive force between the nodes is increased. Control to control the graph drawing so that the related nodes are brought closer to each other during the above time and the approaching nodes are dispersed after the above time has passed. Characterize.

According to this method, the repulsive field of the nodes is controlled to be narrowed within a predetermined time and the attractive force between the nodes is strengthened, and after a lapse of time, the repulsive field of the nodes is widened and the repulsive field of the nodes is increased. By controlling so that the repulsive force between the nodes is weakened and the repulsive force between the nodes is strengthened, the graphs are drawn so that the related nodes move closer to each other in time and the approaching nodes disperse after the lapse of time. Can be controlled.

The pathway information display method according to claim 11 is the pathway information display method according to claim 10, wherein the absolute value of the composite vector is based on the node and the edge drawn in the graph drawing step. The method further includes an energy calculating step of calculating energy by obtaining the sum of the values, until the energy calculated in the energy calculating step becomes smaller than a predetermined value or until the energy becomes minimum. The feature is that the dynamic parameter control step is repeated.

According to this method, the energy is calculated by obtaining the sum of the absolute values of the composite vector based on the drawn nodes and edges, and until the calculated energy becomes smaller than a predetermined value, or By repeatedly performing dynamic parameter control until the energy becomes the minimum, it is possible to obtain an arrangement that realizes a system having a somewhat small energy state or a minimum energy state.

A pathway information display method according to a twelfth aspect is the pathway information display method according to any one of the seventh to eleventh aspects, wherein the connection destination of the edge of the node is another edge. In some cases, the method further includes a temporary node setting step of setting a temporary node on the other edge, and the graph drawing step is characterized by drawing the temporary node portion as a bending point.

According to this method, when the connection destination of the edge of the node is another edge, a temporary node is set on the other edge and the temporary node portion is drawn as a bending point. Readability can be improved when connected to another edge.

Further, the present invention relates to a program, and the program according to claim 13 comprises a binary relation model creating step of creating a binary relation model of pathway information constituted by nodes and edges, and a fixed step. A repulsive force calculation step for calculating a repulsive force generated between the nodes within a distance, an attractive force calculation step for calculating an attractive force generated between the nodes connected by the edges, and a predetermined peripheral area of the node A repulsive field calculation step of setting a repulsive field and calculating the repulsive force and the attractive force, and the repulsive force calculated by the repulsive force calculating step,
The coordinate position of the node is determined by a spring layout based on the attractive force calculated in the attractive force calculation step, the repulsive force of the repulsive field calculated in the repulsive field calculation step, and the attractive force, and the node and the edge are determined. And a graph drawing step for drawing the graph, and the pathway information is displayed as a graph by the binary relational model.

According to this program, a binary relational model of pathway information composed of nodes and edges is created. Here, the pathway information includes information about gene regulatory pathways, metabolic pathways, signal transduction pathways, etc. By mapping the main information into a binary relation, complicated pathway information is simplified and modeled, Be able to express. Then, the repulsive force generated between the nodes within a certain distance is calculated, the attractive force generated between the nodes connected by the edge is calculated, and the coordinate position of the node is determined by the spring layout based on the repulsive force and the attractive force, By drawing the nodes and edges as a graph, it becomes possible to automatically draw a somewhat readable graph within a certain time even for medium- or large-scale pathway information or complicated pathway information. Here, if the layout is performed only by the force based on the repulsive force and the attractive force between the nodes, the nodes may be too close to each other and the node or the edge itself or the label thereof may be difficult to see. Therefore, in the present invention, a repulsive field is set for a predetermined peripheral area of each node to prevent the nodes from being too close to each other. That is, the present invention sets a repulsive field to a predetermined peripheral region of a node, calculates repulsive force and attractive force, and calculates the coordinate position of the node based on the calculated repulsive force, attractive force, repulsive field repulsive force and attractive force. It is decided by the spring layout, and the nodes and edges are drawn in a graph, and the pathway information is displayed in a graph with a binary relational model, so that the nodes and edges themselves and their labels are prevented from overlapping and the readability of the graph is further improved. Like

The program according to claim 14 is
The program according to claim 13, wherein the repulsive field calculation step weakens the attractive force to the peripheral area of the node and / or between the nodes located in the peripheral area of the node. It is characterized in that the repulsive force and the attractive force of the repulsive field are calculated by increasing the repulsive force of.

This shows one example of the repulsive field calculation more specifically. According to this program, by weakening attractive force (including not generating attractive force) to the peripheral region of the node, and / or increasing repulsive force between nodes located in the peripheral region of the node. The repulsive field is calculated, and based on these forces, the spring layout is performed so that the total force (for example, the energy value that is the sum of the absolute values of the combined vector of all edges) realizes the minimum energy state of the system. The coordinate position of the node is determined, and the node and the edge are graph-drawn.

Further, the program according to claim 15 is
The program according to claim 13 or 14, wherein it is determined whether the coordinate position of the node is within a predetermined drawing area, and if it is out of the drawing area, the coordinate position of the node is moved to the boundary of the drawing area. The method further includes a boundary determination step of

According to this program, it is determined whether the coordinate position of the node is within a predetermined drawing area, and if it is out of the drawing area, the coordinate position of the node is moved to the boundary of the drawing area. The pathway information can always be drawn in the drawing area.

Further, the program according to claim 16 is
The program according to any one of claims 13 to 15, wherein the repulsive field of the nodes is narrowed and the attractive force between the nodes is strengthened within a predetermined time, and the time elapses. After that, by spreading the repulsive field of the nodes, weakening the attractive force between the nodes, and controlling the repulsive force between the nodes to be stronger, the related nodes will approach each other within the time, It is characterized by further including a dynamic parameter control step for controlling the graph drawing so that the approaching nodes are dispersed after the lapse of the above time.

According to this program, the repulsive field of the nodes is controlled to be narrowed and the attractive force between the nodes is strengthened within a predetermined time, and the repulsive field of the node is widened after a lapse of time, and By controlling so that the repulsive force between the nodes is weakened and the repulsive force between the nodes is strengthened, the graphs are drawn so that the related nodes move closer to each other in time and the approaching nodes disperse after the lapse of time. Can be controlled.

The program according to claim 17 is
17. The program according to claim 16, further comprising an energy calculating step of calculating energy by calculating a sum of absolute values of combined vectors based on the nodes and the edges drawn in the graph drawing step, It is characterized in that the dynamic parameter control step is repeated until the energy calculated in the calculation step becomes smaller than a predetermined value or until the energy becomes minimum.

According to this program, the energy is calculated by obtaining the sum of the absolute values of the composite vector based on the drawn nodes and edges, until the calculated energy becomes smaller than a predetermined value, or By repeatedly performing dynamic parameter control until the energy becomes the minimum, it is possible to obtain an arrangement that realizes a system having a somewhat small energy state or a minimum energy state.

The program according to claim 18 is
In the program according to any one of claims 13 to 17, when the connection destination of the edge of the node is another edge, a temporary node setting step of setting a temporary node on the other edge Further, the graph drawing step is characterized in that the temporary node portion is drawn as a bending point.

According to this program, when the connection destination of the edge of the node is another edge, a temporary node is set on the other edge and the temporary node portion is drawn as a bending point. Readability can be improved when connected to another edge.

The present invention also relates to a recording medium, and the recording medium according to claim 19 is characterized in that the program according to any one of claims 13 to 18 is recorded.

According to this recording medium, the program recorded in the recording medium is read and executed by the computer, and the program described in any one of claims 13 to 18 is used by the computer. It can be realized, and the same effect as each of these methods can be obtained.

[0049]

BEST MODE FOR CARRYING OUT THE INVENTION Embodiments of a pathway information display device, a pathway information display method, a program, and a recording medium according to the present invention will be described in detail below with reference to the drawings. The present invention is not limited to this embodiment. In particular, in the following embodiments, the present invention will be described as an example in which it is applied to a bioinformatics system that performs graph drawing of pathway information such as gene control pathway, metabolic pathway, and signal transduction pathway, but is not limited to this case. , Can be similarly applied to a system for drawing pathway information in all fields.

[Outline of the Present Invention] The outline of the basic principle of the present invention will be described below, and then the configuration and processing of the present invention will be described in detail. FIG. 1 is a conceptual diagram showing the outline of the basic principle of the present invention.

In the present invention, first, a binary relational model of pathway information composed of nodes and edges is created to construct a binary relational model database. Here, the "node" represents a substance or a phenomenon. Also,
“Edge” expresses various relationships between nodes, and has a node serving as a start point and a node or edge serving as an end point, and represents a binary relation from a start point to an end point. For example, nodes represent substances such as genes, proteins, amino acids, enzymes, coenzymes, and phenomena such as enzymatic reactions and metabolic reactions, and edges represent relationships between starting points and ending points such as generation, inhibition, and binding. . Normally, nodes and edges are represented by different shapes depending on the type.

Next, spring layout is executed for each node (A to U in FIG. 1) and edge (e ₁ to e ₁₅ ) defined in the binary relational model database to draw a graph. Here, "spring layout" is called a force-directed arrangement in the drawing method of general undirected graphs, where nodes are replaced by rings and edges by springs, and the spring force (repulsive force and attractive force) applied to the ring. Is a configuration that realizes the minimum energy state of the system. That is, according to the present invention, the repulsive force and the attractive force between the nodes are calculated according to the distance between the nodes, the coordinate position of the node is determined based on the force, and the node and the edge are graph-drawn. Here, the "repulsive force" is a force generated between all the node groups existing within a certain distance, and the repulsive force disperses the nodes and removes the overlap. "Attractive force" is the force that acts between nodes connected by edges,
Since the nodes edge-connected by the attractive force approach each other, the related nodes can approach each other, making it easy to distinguish them from unrelated nodes.

If the spring layout is performed only by the force based on the repulsive force and the attractive force between the nodes, the nodes may be too close to each other and the nodes or edges themselves or their labels may be difficult to see. Therefore, in the present invention, a "repulsive field" is defined for a predetermined peripheral area of each node,
It prevents the nodes from getting too close. That is,
The present invention weakens an attractive force (including not generating an attractive force) with respect to a peripheral region of a node, and / or
The repulsive field is calculated by increasing the repulsive force between the nodes located in the peripheral region of the node, and based on these forces, the spring layout is used to calculate the total force (for example, the sum of the absolute values of the combined vectors of all edges). The energy coordinates of all nodes are determined so that the minimum energy state of the system is realized, and the nodes and edges are plotted in a graph.

Further, according to the present invention, it is determined whether the coordinate position of the node is within a predetermined drawing area, and if it is out of the drawing area, the coordinate position of the node is moved to the boundary of the drawing area. The pathway information can always be drawn in the drawing area. By setting the drawing area in advance in this way, it is possible to set a limit on the action distance of the repulsive force, and it is possible to avoid the phenomenon of keeping away forever, which is often the case in a normal spring layout. Also,
When node movement is suppressed at the window boundary, the phenomenon that many nodes are accumulated at the boundary is avoided.

Further, according to the present invention, the repulsive field of the node is controlled to be narrowed within a predetermined time and the attractive force between the nodes is strengthened, and after a lapse of time, the repulsive field of the node is widened.
By controlling so that the attractive force between the nodes is weakened and the repulsive force between the nodes is strengthened, the related nodes will be brought closer to each other within a certain period of time, and the approaching nodes will be dispersed after a certain period of time. Graphs can be drawn by dynamically controlling parameters (dynamic parameter control processing).
Then, the energy is calculated by obtaining the total sum of the absolute values of the combined vector based on the nodes and the edges, and the energy is iterated until the energy becomes smaller than a predetermined value or the energy becomes the minimum. By executing the dynamic parameter control process, related nodes can approach each other in a short time and perform appropriate clustering within a predetermined time even for large-scale pathway information or complicated pathway information. You can Also, many of the edge intersections are eliminated, reducing the chance of energy falling into a local minimum placement. In addition, the readability of complicated pathway information can be improved after the elapse of a predetermined time.

[System Configuration] First, the configuration of this system will be described. FIG. 2 is a block diagram showing an example of the configuration of the present system to which the present invention is applied, and conceptually shows only the portion related to the present invention in the configuration. The present system schematically includes a pathway information display device 100.
And an external system 200 that provides an external database for pathway information including gene control pathways, metabolic pathways, information transmission pathways, etc., and an external program for homology search, etc., are communicatively connected via a network 300. Has been done.

In FIG. 2, the network 300 has a function of mutually connecting the pathway information display device 100 and the external system 200, and is, for example, the Internet.

In FIG. 2, the external system 200 is connected to the pathway information display device 10 via the network 300.
It has a function of being connected to 0 and providing a user with an external database for pathway information and the like and a website for executing external programs such as homology search and motif search.

Here, the external system 200 may be configured as a WEB server, an ASP server, or the like, and its hardware configuration is configured by an information processing device such as a workstation or a personal computer that is generally commercially available and its auxiliary device. You may. Further, each function of the external system 200 is realized by a CPU, a disk device, a memory device, an input device, an output device, a communication control device, and the like in the hardware configuration of the external system 200 and a program for controlling them.

In FIG. 2, the pathway information display device 10
0 is a control unit 102 such as a CPU that generally controls the entire pathway information display device 100, and a communication control connected to a communication device (not shown) such as a router connected to a communication line or the like. Interface unit 104, input device 1
12, an input / output control interface unit 108 connected to the output device 114, a clock generation unit 110 that generates a system clock, and a storage unit that stores various databases and tables (binary relation model database 106a and graph data 106b). 106, and these units are communicably connected via an arbitrary communication path. Furthermore, the pathway information display device 100 is communicatively connected to the network 300 via a communication device such as a router and a wired or wireless communication line such as a dedicated line.

Various databases and tables (binary relation model database 106a) stored in the storage unit 106
The graph data 106b) is a storage means such as a fixed disk device, and stores various programs, tables, files, databases, web page files, etc. used for various processes.

Of these constituent elements of the storage unit 106,
The binary relation model database 106a is a database that stores a binary relation model of pathway information. For example, a binary relational model regarding pathway information stored in an external database such as KEGG is created and stored in the binary relational model database 106a. here,
FIG. 3 is a conceptual diagram of the binary relation model. In the example shown in FIG. 3, nodes A to D are connected by edges e ₁ to e ₃ . In this way, the pathway information can be defined by the binary relational model composed of nodes and edges.

FIG. 4 is a diagram showing an example of information stored in the binary relation model database 106a. The information stored in the binary relational model database 106a is, as shown in FIG. 4, connection source information including the name and coordinates of the connection source node and connection destination information including the name and coordinates of the connection destination node. , Edge information including edge name and length (distance), relationship between connected nodes (generation,
Related information indicating suppression, promotion, etc.) is associated with each other. Further, the graph data 106b is a graph data storage means for storing the data of the drawn graph.

In FIG. 2, the communication control interface unit 104 controls communication between the pathway information display device 100 and the network 300 (or communication device such as router). That is, the communication control interface unit 104 has a function of communicating data with other terminals via a communication line.

Further, in FIG. 2, the input / output control interface section 108 includes an input device 112 and an output device 114.
Control. Here, as the output device 114, a speaker can be used in addition to a monitor (including a home-use television) (hereinafter, the output device is described as a monitor). Further, as the input device 112, a keyboard, a mouse, a microphone or the like can be used. The monitor also realizes the pointing device function in cooperation with the mouse.

Further, in FIG. 2, the control unit 102 controls the O
A control program such as an S (Operating System), a program that defines various processing procedures, and an internal memory for storing required data, and information processing for executing various processes by these programs and the like. I do. Conceptually, the control unit 102 is a binomial relation model creation unit 102a, attractive force calculation unit 102b, repulsive force calculation unit 102c, repulsive field calculation unit 102d, boundary determination unit 1
02e, dynamic parameter control unit 102f, graph drawing unit 1
02g, an energy calculation unit 102h, and a temporary node processing unit 102i.

Of these, the binary relation model creating unit 102a
Is a binary relation model creating means for creating a binary relation model of pathway information composed of nodes and edges. The attractive force calculation unit 102b is an attractive force calculation unit that calculates an attractive force generated between nodes connected by edges. Further, the repulsive force calculation unit 102c is a repulsive force calculation unit that calculates a repulsive force generated between nodes within a certain distance. The repulsion field calculation unit 102d is a repulsion field calculation unit that sets a repulsion field in a predetermined peripheral region of the node and calculates repulsive force and attractive force.

The boundary determining unit 102e determines whether the coordinate position of the node is within a predetermined drawing area, and if it is outside the drawing area, moves the coordinate position of the node to the boundary of the drawing area. It is a boundary determination means. Also,
The dynamic parameter control unit 102f controls so that the repulsive field of the nodes is narrowed and the attractive force between the nodes is strengthened within a predetermined time, and after a lapse of time, the repulsive field of the node is widened and the repulsive field of the nodes is widened. By controlling so that the attractive force is weakened and the repulsive force between the nodes is strengthened, the graph drawing is controlled so that the related nodes are brought closer to each other in time and the approaching nodes are dispersed after the lapse of time. It is a means for controlling dynamic parameters.

Further, the graph drawing unit 102g uses the repulsive force calculated by the repulsive force calculating means, the attractive force calculated by the attractive force calculating means, and the repulsive force repulsive force and attractive force calculated by the repulsive field calculating means to coordinate positions of the nodes. Is a graph drawing means that draws a graph of nodes and edges by deciding by the spring layout. The energy calculation unit 102h is an energy calculation unit that calculates energy by calculating the sum of absolute values of the combined vector based on the nodes and edges drawn by the graph drawing unit.

The temporary node processing unit 102i is a temporary node setting means for setting a temporary node on another edge when the connection destination of the edge of the node is another edge. The details of the processing performed by these units will be described later.

[Processing of System] Next, an example of the processing of the present apparatus configured as described above in the present embodiment will be described in detail below with reference to FIGS.

[Main Processing] First, details of the main processing will be described with reference to FIG. FIG. 5 is a flow chart showing an example of the main processing of this system in this embodiment.

The pathway information display device 100 creates a binary relationship model from the pathway information by the processing of the binary relationship model creation unit 102a and stores it in the binary relationship model database 106a (step SA-1). That is, the binary relation model creation unit 102a uses the conventional KEGG
The user is allowed to select desired pathway information from the pathway information stored in the database, and the binary relational model of the pathway information shown in FIG. 3 is automatically converted into the format shown in FIG. 4 to create the binary relational model. Then, the binary relational model database 106a is stored. The binomial relation model creation unit 102a displays a binomial relation model creation screen as shown in FIG. 9 on the output device 114, and prompts the user to input node and edge information to create the binomial relation model. May be created.

Here, FIG. 9 is a diagram showing an example of a binary relation model creation screen displayed on the output device 114 of the pathway information display device 100. As shown in FIG.
The screen for creating the term relation model is displayed in the input area M for the pathway name
A-1, a connection source information input area MA-2, a connection destination information input area MA-3, and an edge information input area MA-
4 and. When the user inputs desired information into these input areas via the input device 112, 2
The term relation model creation unit 102a stores the input information in a predetermined storage area of the binomial relation model database 106a.

Then, the control unit 102 executes the spring layout process described later based on the binary relation model database 106a (step SA-2). This completes the main processing.

[Spring Layout Processing] Next, details of the spring layout processing will be described with reference to FIG. FIG. 6 is a flowchart showing an example of the spring layout process of this system in this embodiment.

First, the control unit 102 includes the clock generation unit 1
A system clock is received from 10 to activate a control timer (step SB-1), and it is monitored whether a predetermined time t1 has elapsed (step SB-2). Here, time t1
May be determined in advance based on the complexity of the graph (determined from the number of nodes and edges, etc.), the energy value of the initial graph, and the like.

If t1 time has not elapsed in step SB-2, the approach parameter is set in the dynamic parameter (step SB-3), while if t1 time has elapsed, the distributed parameter is set in the dynamic parameter. (Step SB-4).

Then, the repulsive force calculation unit 102c calculates and sets the repulsive force between all the node groups within a certain distance (step SB-5). That is, the repulsive force calculation unit 102c outputs 2
The shorter the distance between two nodes, the stronger the repulsive force is set between the nodes.

Then, the attractive force calculation unit 102b calculates and sets the attractive force between the nodes connected to the edge (step SB-6). That is, the attractive force calculation unit 102b sets a stronger attractive force as the distance between the two nodes increases.

Next, the repulsive field calculation unit 102d sets the repulsive field in the peripheral region of the node to calculate the repulsive force and the attractive force, and secures the character region of the label such as the node (step SB-7). That is, the repulsion field calculation unit 102d weakens the attractive force (including not generating the attractive force) to the peripheral region of the node and / or strengthens the repulsive force between the nodes located in the peripheral region of the node. The repulsive force and attractive force of the repulsive field are calculated.

For example, the repulsive field is set to 20% of the node size similar area from the center of the node, the attractive force is set to 95% of the distance, and the repulsive force is set to 200% of the external system. 40 from node center to node size
The repulsive force and the attractive force of the repulsive field are calculated by setting the 0% similarity region, the attractive force to 5% of the distance, and the repulsive force to 800%.

Then, the dynamic parameter control unit 102f
The dynamic parameter control process shown in FIG. 7 is executed (step SB-8).

Here, FIG. 7 is a flow chart showing an example of the dynamic parameter control processing in this embodiment of the present invention. In FIG. 7, the dynamic parameter control unit 102f
Determines the set dynamic parameter (step SC-
1) In the case of the approach parameter, control is performed so as to narrow the repulsive field and strengthen the attractive force (step SC-2), while in the case of the distributed parameter, widen the repulsive field, weaken the attractive force, and weaken the repulsive force. Control (step SC-3). That is, in the case of the approach parameter, the related nodes on the graph approach each other, and in the case of the distributed parameter, the related nodes disperse in the graph.

Returning to FIG. 6 again, the graph drawing unit 102g
Determines the coordinate position of a node by spring layout based on the repulsive force, the attractive force, the repulsive force of the repulsive field, and the attractive force, and draws a graph of the node and the edge. That is, the graph drawing unit 102g repeats the step of the spring layout in which the node is slightly moved in accordance with the combined vector of all the acting forces (the movement will continue as long as the force exists). In this method, the force is defined as a function of the arrangement state and time, and the force becomes smaller when the movement is performed in the direction of the force. Therefore, as the steps are repeated, the total sum of the absolute values of the forces of the entire arrangement (which is called "energy") decreases. That is, the repulsive forces cause the nodes to separate from each other so that they do not overlap with each other.
Also, due to the attractive force, the nodes connected by the edges come closer to each other, and the attractive force becomes zero when they come closer to each other by a certain distance or more. In addition, the repulsive field action allows the nodes having a large overlap to be specially separated.

The spring layout will be described below with reference to specific examples. First, the following processing is executed for all node sets (ni, nj) in the binary relational model. (1) When the distance d between ni and nj exceeds a certain distance, the process proceeds to the next node set processing. (2) Move ni in the anti-nj direction and nj in the anti-ni direction by a distance proportional to the force (A) and inversely proportional to the square of d. (3) When the position of ni or nj after the movement is out of the drawing area, the boundary is determined to be moved to the further boundary by the processing of the boundary determining unit 102e.

Next, the following processing is executed for all the relations r in the binary relation model. (1) The start point node of r is ns, and the end point node is ne. The distance between ns and ne is d. (2) If d is within a predetermined distance, the process proceeds to the next relationship. (3) Move ns in the ne direction and ne in the ns direction by a distance proportional to the force (B) and the distance d.

Next, the graph drawing unit 102g outputs the drawn graph to the output device 114 (step SB-
9).

Here, data in the middle of drawing may be stored in the graph data 106b, and each control unit (102a-10a).
2h) may appropriately refer to or store the data in the middle of drawing stored in the graph data 106a.

Next, when the user looks at the output graph and gives an instruction to end using the input device 112, or when the total energy calculated by the energy calculation unit 102h is smaller than a predetermined threshold value, If is the minimum, the spring layout process ends (step SB-10). On the other hand, in other cases,
Return to step SB-2.

[Temporary Node Processing] Next, details of the temporary node processing will be described with reference to FIG. FIG. 8 is a flowchart showing an example of the temporary node processing of the present system in this embodiment.

First, when the connection destination of the edge (e2) is the edge (e1) in the creation of the binary relation model,
The temporary node processing unit 102i connects a temporary node (node t) having an appropriate shape. That is, the temporary node processing unit 102
i places a temporary node (node t) at the center of the connection destination edge (e1) (step SD-1), and a temporary edge (node B) to the node (node B) to which the connection destination edge (e1) was connected. e3 and e4) are wired and the original edge (e1) is deleted (step SD-2).

Next, the provisional node is regarded as a normal node, and the arrangement is calculated by the above-mentioned method (spring layout).
Is performed (step SD-3).

Then, the temporary node processing unit 102i draws the original edge (e1) so that the central portion of the temporary node becomes the bending point, and deletes the temporary node and the temporary edge (step SD-4). This completes the temporary node processing.

[Other Embodiments] Now, the embodiments of the present invention have been described so far. However, the present invention is not limited to the above-mentioned embodiments, and has the technical idea described in the claims. It may be implemented in various different embodiments within the scope.

Further, of the processes described in the embodiment, all or part of the processes described as being automatically performed may be manually performed, or described as being performed manually. All or part of the processing can be automatically performed by a known method. In addition, the processing procedure, control procedure, and
For specific names, information including parameters such as various registration data and search conditions, screen examples, database configuration,
It can be changed arbitrarily unless otherwise specified.

Further, regarding the pathway information display device 100, the constituent elements shown in the drawings are functionally conceptual and do not necessarily have to be physically configured as shown. For example, with regard to the processing functions provided in each server of the pathway information display device 100, particularly the respective processing functions performed by the control unit, all or any part of the processing functions may be replaced by the CPU.
(Central Processing Unit)
Also, it can be realized by a program that is interpreted and executed by the CPU, or can be realized as hardware by a wired logic. The program is recorded in a recording medium described later, and can be mechanically read by the pathway information display device 100 as needed.

Various databases and the like (binary relation model database 106a and graph data 106b) stored in the storage unit 106 include memory devices such as RAM and ROM, fixed disk devices such as hard disks, storages such as flexible disks and optical disks. It is a means and stores various programs, tables, files, databases, web page files, etc. used for various processes and website provision.

Further, the pathway information display device 100 is
Software (programs, data, etc.) for connecting a peripheral device such as a printer, a monitor, or an image scanner to an information processing device such as a known information processing terminal such as a personal computer or a workstation, and realizing the method of the present invention in the information processing device. May be implemented by implementing (including).

Further, the specific form of distribution / integration of the pathway information display device 100 is not limited to that shown in the figure, and all or part of it may be functionally or physically arranged in arbitrary units according to various loads. Can be distributed and integrated into For example, each database may be independently configured as an independent database device, and a part of the processing may be performed by a CGI (Common Gateway Intete).
rface) may be used.

Further, the program according to the present invention can be stored in a computer-readable recording medium. Here, the "recording medium" means a flexible disk, a magneto-optical disk, a ROM, an EPROM, an EEPR.
Any "portable physical medium" such as OM, CD-ROM, MO, DVD, etc., any "fixed physical medium" such as ROM, RAM, HD, etc. built into various computer systems, or LAN, A "communication medium" that holds a program in a short term, such as a communication line or a carrier wave when transmitting the program through a network typified by WAN and the Internet, is included.

The "program" is a data processing method described in any language or description method, and may take any form such as source code or binary code. In addition,
The "program" is not necessarily limited to a single configuration, but may be configured as a plurality of modules or libraries distributed, or an OS (Operating System).
It also includes a program that cooperates with a separate program represented by m) to achieve its function. Note that a specific configuration for reading a recording medium in each device described in the embodiments,
Well-known configurations and procedures can be used for the reading procedure, the installation procedure after the reading, and the like.

Further, the network 300 has a function of connecting the pathway information display device 100 and the external system 200 to each other. For example, the Internet, an intranet, a LAN (including both wired / wireless) and V
AN, personal computer communication network, public telephone network (both analog and digital), leased line network (both analog and digital), CATV network, IMT2000
System, GSM system or PDC / PDC-P system or other mobile circuit switching network / mobile packet switching network, radio calling network,
Local wireless network such as Bluetooth, PHS network, C
It may include any one of satellite communication networks such as S, BS or ISDB. That is, the present system can send and receive various data via any network whether wired or wireless.

[0104]

As described in detail above, according to the present invention, a binary relational model of pathway information composed of nodes and edges is created. Here, pathway information includes information about gene regulatory pathways, metabolic pathways, signal transduction pathways, etc. By mapping the main information into a binary relation, complicated pathway information is simplified and modeled, Be able to express. Then, the repulsive force generated between the nodes within a certain distance is calculated, the attractive force generated between the nodes connected by the edge is calculated, and the coordinate position of the node is determined by the spring layout based on the repulsive force and the attractive force,
By drawing nodes and edges as graphs, it becomes possible to automatically draw a somewhat readable graph within a certain time even for medium- or large-scale pathway information or complicated pathway information.

Here, if the layout is performed only by the force based on the repulsive force and the attractive force between the nodes, the nodes may be too close to each other and the node or the edge itself or the label thereof may be difficult to see. Therefore, in the present invention, a repulsive field is set for a predetermined peripheral area of each node to prevent the nodes from being too close to each other. That is, the present invention sets a repulsive field to a predetermined peripheral region of a node, calculates repulsive force and attractive force, and calculates the coordinate position of the node based on the calculated repulsive force, attractive force, repulsive field repulsive force and attractive force. It is decided by the spring layout, and the nodes and edges are drawn in a graph, and the pathway information is displayed in a graph with a binary relational model, so that the nodes and edges themselves and their labels are prevented from overlapping and the readability of the graph is further improved. Like

Further, according to the present invention, the attractive force is weakened (including not generating the attractive force) to the peripheral region of the node and / or between the nodes located in the peripheral region of the node. The repulsive field is calculated by increasing the repulsive force, and based on these forces, the spring layout determines the total force (for example, the energy value that is the sum of the absolute values of the combined vector of all edges) as the minimum energy state of the system It is possible to provide a pathway information display device, a pathway information display method, a program, and a recording medium in which the coordinate positions of all nodes are determined so as to be realized and the nodes and edges are graph-drawn.

Further, according to the present invention, it is determined whether the coordinate position of the node is within a predetermined drawing area, and if it is out of the drawing area, the coordinate position of the node is moved to the boundary of the drawing area. Therefore, the pathway information display device that can always draw the pathway information in the drawing area,
A pathway information display method, a program, and a recording medium can be provided.

Further, according to the present invention, the repulsive field of the node is controlled to be narrowed within a predetermined time and the attractive force between the nodes is strengthened, and after a lapse of time, the repulsive field of the node is widened. By controlling so that the attractive force between nodes is weakened and the repulsive force between nodes is strengthened, the related nodes will move closer in time, and after a lapse of time, the approaching nodes will disperse. A pathway information display device capable of controlling drawing, a pathway information display method,
A program and a recording medium can be provided.

Further, according to the present invention, the energy is calculated by obtaining the sum of the absolute values of the combined vector based on the drawn nodes and edges, and until the calculated energy becomes smaller than a predetermined value, Alternatively, a pathway information display device and a pathway information display method can be obtained by repeatedly performing dynamic parameter control until the energy is minimized to obtain an arrangement that realizes a system having a somewhat small energy state or a minimum energy state. , A program, and a recording medium can be provided.

Further, according to the present invention, when the connection destination of the edge of the node is another edge, a temporary node is set on the other edge and the temporary node portion is drawn as a bending point. It is possible to provide a pathway information display device, a pathway information display method, a program, and a recording medium that can improve readability when an edge is connected to another edge.

[Brief description of drawings]

FIG. 1 is a conceptual diagram showing an outline of a basic principle of the present invention.

FIG. 2 is a block diagram showing an example of the configuration of the present system to which the present invention is applied.

FIG. 3 is a conceptual diagram of a binary relation model.

FIG. 4 is a diagram showing an example of information stored in a binary relation model database 106a.

FIG. 5 is a flowchart showing an example of main processing of the present system in the present embodiment.

FIG. 6 is a flowchart showing an example of a spring layout process of this system in this embodiment.

FIG. 7 is a flowchart showing an example of a dynamic parameter control process according to this embodiment of the present invention.

FIG. 8 is a flowchart showing an example of temporary node processing of the present system in the present embodiment.

FIG. 9 is an output device 11 of the pathway information display device 100.
6 is a diagram showing an example of a binary relation model creation screen displayed in FIG.

[Explanation of symbols]

100 pathway information display device 102 control unit 102a Binary relation model creation unit 102b Gravity calculation unit 102c Repulsive force calculation unit 102d Repulsion field calculation unit 102e boundary determination unit 102f dynamic parameter control unit 102g Graph drawing part 102h Energy calculation unit 102i temporary node processing unit 104 Communication control interface section 106 storage 106a Binomial relation model database 106b Graph data 108 Input / output control interface section 110 clock generator 112 Input device 114 output device 200 External system 300 networks

Claims (19)

[Claims] 1. A binary relational model creating means for creating a binary relational model of pathway information composed of nodes and edges, and a repulsive force calculating means for computing a repulsive force generated between the nodes within a certain distance. , An attractive force calculation means for calculating an attractive force generated between the nodes connected by the edge, and a repulsive field calculation for setting the repulsive field with respect to a predetermined peripheral region of the node to calculate the repulsive force and the attractive force. Means and the repulsive force calculated by the repulsive force calculating means, the attractive force calculated by the attractive force calculating means, the repulsive force of the repulsive field calculated by the repulsive field calculating means, and the coordinates of the node based on the attractive force A graph drawing means for drawing a graph of the node and the edge, the position of which is determined by a spring layout; Pathway information display apparatus characterized by a graphical representation in the binary relation model. 2. The repulsive field calculation means weakens the attractive force to the peripheral area of the node and / or strengthens the repulsive force between the nodes located in the peripheral area of the node. The pathway information display device according to claim 1, wherein the repulsive force and the attractive force of the repulsive field are calculated thereby. 3. A boundary determining means for determining whether the coordinate position of the node is within a predetermined drawing area, and moving the coordinate position of the node to the boundary of the drawing area when the coordinate position is out of the drawing area. The pathway information display device according to claim 1, further comprising: 4. The repulsive field of the node is controlled to be narrowed and the attractive force between the nodes is strengthened within a predetermined time, and the repulsive field of the node is widened after the lapse of the time. , By controlling so that the attractive force between the nodes is weakened and the repulsive force between the nodes is strengthened, the related nodes keep approaching each other within the time, and the approaching nodes disperse after the time elapses. 4. The pathway information display device according to claim 1, further comprising: a dynamic parameter control unit that controls the graph drawing in a progressive manner. 5. The energy calculation means further comprises energy calculation means for calculating energy by obtaining a sum of absolute values of combined vectors based on the nodes and the edges drawn by the graph drawing means. 5. The dynamic parameter control means is repeatedly executed until the energy calculated by the above becomes smaller than a predetermined value or until the energy becomes minimum.
The pathway information display device described in. 6. When the connection destination of the edge of the node is another edge, a provisional node setting means for setting a provisional node on the another edge is further provided, and the graph drawing means The pathway information display device according to claim 1, wherein the temporary node portion is drawn as a bending point. 7. A binary relational model creating step of creating a binary relational model of pathway information composed of nodes and edges, and a repulsive force calculating step of calculating a repulsive force generated between the nodes within a certain distance. , An attractive force calculation step for calculating an attractive force generated between the nodes connected by the edges, and a repulsive field calculation for setting the repulsive field with respect to a predetermined peripheral region of the node to calculate the repulsive force and the attractive force. Steps, the repulsive force calculated by the repulsive force calculation step, the attractive force calculated by the attractive force calculation step, the repulsive force of the repulsive field calculated by the repulsive field calculation step, and the coordinates of the node based on the attractive force The position is determined by the spring layout, and the graph drawing step that graphs the node and the edge is performed. When, wherein the pathway information display method of the pathway information, characterized in that the graph display in the binary relation model. 8. The repulsive field calculation step weakens the attractive force with respect to the peripheral region of the node and / or strengthens the repulsive force between the nodes located in the peripheral region of the node. The pathway information display method according to claim 7, wherein the repulsive force and the attractive force of the repulsive field are calculated by the calculation. 9. A boundary determining step of determining whether the coordinate position of the node is within a predetermined drawing area, and moving the coordinate position of the node to the boundary of the drawing area if the coordinate position is out of the drawing area. The pathway information display method according to claim 7, further comprising: 10. The repulsive field of the node is controlled to be narrowed and the attractive force between the nodes is strengthened within a predetermined time, and the repulsive field of the node is widened after the lapse of the time. , By reducing the attractive force between the nodes, and by increasing the repulsive force between the nodes,
The method further comprises a dynamic parameter control step of controlling graph drawing such that related nodes are brought closer to each other within the time period and the approached nodes are dispersed after the time period has passed. 7. The pathway information display method described in any one of 7 to 9. 11. An energy calculating step of calculating energy by calculating a sum of absolute values of a combined vector based on the node and the edge drawn in the graph drawing step, the energy calculating step further comprising: 11. The pathway information display method according to claim 10, wherein the dynamic parameter control step is repeatedly performed until the calculated energy becomes smaller than a predetermined value or the energy becomes minimum. . 12. When the connection destination of the edge of the node is another edge, the method further includes a temporary node setting step of setting a temporary node on the other edge, and the graph drawing step includes: The temporary node portion is drawn as a bending point, and the drawing is performed.
11. The pathway information display method according to any one of 1 to 11. 13. A binary relational model creating step of creating a binary relational model of pathway information composed of nodes and edges, and a repulsive force calculating step of calculating a repulsive force generated between the nodes within a certain distance. , An attractive force calculation step for calculating an attractive force generated between the nodes connected by the edges, and a repulsive field calculation for setting the repulsive field with respect to a predetermined peripheral region of the node to calculate the repulsive force and the attractive force. Steps, the repulsive force calculated by the repulsive force calculation step, the attractive force calculated by the attractive force calculation step, the repulsive force of the repulsive field calculated by the repulsive field calculation step, and the coordinates of the node based on the attractive force The position is determined by the spring layout, and the graph drawing step that graphs the node and the edge is performed. Includes a flop, a program that the pathway information, characterized in that to execute the pathway information display method for the graph display in the binary relation model in a computer. 14. The repulsive field calculation step weakens the attractive force with respect to the peripheral region of the node and / or strengthens the repulsive force between the nodes located in the peripheral region of the node. 14. The program according to claim 13, wherein the repulsive force and the attractive force of the repulsive field are calculated thereby. 15. A boundary determining step of determining whether the coordinate position of the node is within a predetermined drawing area, and moving the coordinate position of the node to the boundary of the drawing area if the coordinate position is out of the drawing area. The program according to claim 13 or 14, further comprising: 16. The repulsive field of the node is controlled to be narrowed and the attractive force between the nodes is strengthened within a predetermined time, and the repulsive field of the node is widened after the time has elapsed. , By reducing the attractive force between the nodes, and by increasing the repulsive force between the nodes,
The method further comprises a dynamic parameter control step of controlling graph drawing such that related nodes are brought closer to each other within the time period and the approached nodes are dispersed after the time period has passed. The program according to any one of 13 to 15. 17. An energy calculating step of calculating energy by obtaining a sum of absolute values of a combined vector based on the node and the edge drawn in the graph drawing step, further comprising: 17. The program according to claim 16, wherein the dynamic parameter control step is repeated until the calculated energy becomes smaller than a predetermined value or the energy becomes minimum. 18. When the connection destination of the edge of the node is another edge, the method further includes a provisional node setting step of setting a provisional node on the another edge, and the graph drawing step includes: The temporary node portion is drawn as a bending point, and the drawing is performed.
The program according to any one of 3 to 17. 19. A computer-readable recording medium on which the program according to any one of claims 13 to 18 is recorded.