NETWORK MODEL INTEGRATION DEVICE, NETWORK MODEL INTEGRATION SYSTEM, NETWORK MODEL INTEGRATION METHOD, AND COMPUTER PROGRAM PRODUCT

• US 20130185644A1
• Filed: 03/31/2011
• Published: 07/18/2013
• Est. Priority Date: 10/01/2010
• Status: Active Grant

• Current Assignee: Okinawa Institute of Science and Technology Graduate University, The Systems Biology Institute
• Original Assignee: Okinawa Institute of Science and Technology Graduate University, The Systems Biology Institute
• Inventors: Kitano, Hiroaki, Matsuoka, Yukiko, Ghosh, Samik
• Granted Patent: US 9,137,122 B2
• Time in Patent Office: Days
• US Class Current: 715/736
• CPC Class Codes: G06F 16/9024 Graphs; Linked lists G06F16/9027 takes precedence
• CPC Class Codes: G16B 45/00 ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
• CPC Class Codes: G16B 5/00 ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: H04L 41/22 comprising specially adapted graphical user interfaces [GUI]

Abstract

The present invention involves retrieving edges that do not constitute a designated network model which is a network model designated by a user and are linked to nodes that constitute the designated network model, displaying retrieval results that include the retrieved edges and network model IDs corresponding to the edges in a selectable manner, and generating an integrated network model in which, when the retrieval results are selected by the user, the edges that are included in the selected retrieval results and the nodes that do not constitute the designated network model and are linked to the edges, are integrated into the designated network model.

Claims

1. A network model integration device comprising:

an input unit, a display unit, a storage unit, and a control unit, wherein

the storage unit includes;

a network model storage unit that stores a network model that includes nodes that represent constituent elements of a biological object and edges that represent interactions between the constituent elements and a network model ID that identifies the network model in association, and

the control unit includes;

a retrieving unit that, when the network model is designated by a user via the input unit, retrieves the edges that are stored in the network model storage unit, do not constitute a designated network model which is the network model, and are linked to the nodes that constitute the designated network model; and

a retrieval result displaying unit that displays retrieval results including the edges retrieved by the retrieving unit and the network model ID that identifies the network model including the edges stored in the network model storage unit on the display unit in a selectable manner;

an integrating unit that, when the retrieval results displayed on the display unit by the retrieval result displaying unit are selected by the user via the input unit, generates an integrated network model which is the network model in which the edges included in the selected retrieval results and the nodes that do not constitute the designated network model and are linked to the edges are integrated into the designated network model; and

a network model storing unit that acquires the network model ID that identifies the integrated network model generated by the integrating unit and stores the integrated network model and the network model ID in the network model storage unit in association.

2. The network model integration device according to claim 1, wherein

the designated network model is the network model stored in the network model storage unit, an existing network model that is not stored in the network model storage unit, or a new network model.

3. The network model integration device according to claim 2, wherein

when the existing network model or the new network model is input by the user via the input unit, the network model storing unit further acquires the network model ID that identifies the designated network model and stores the designated network model and the network model ID in the network model storage unit in association.

4. The network model integration device according to claim 1,

wherein

when an ID selection instruction is input by the user via the input unit, the network model storing unit acquires the network model ID that identifies the designated network model, included in the integrated network model or a new network model ID as a network model ID that identifies the integrated network model based on the ID selection instruction and stores the integrated network model and the network model ID in the network model storage unit in association.

5. The network model integration device according to claim 1,

wherein

the storage unit further includes:

a pathway storage unit that stores pathways of the constituent elements;

a literature information storage unit that stores literature information on literatures related to the constituent elements and the interactions;

a news storage unit that stores news provided by a news delivery service; and

a text mining storage unit that stores text information on the constituent elements and the interactions that are extracted from the literature information using text mining,

the retrieving unit further retrieves the edges that do not constitute the designated network model and are linked to the nodes that constitute the designated network model from any one or all of the pathways stored in the pathway storage unit, the literature information stored in the literature information storage unit, the news stored in the news storage unit, and the text information stored in the text mining storage unit and acquires the network model ID that identifies the network model that includes the edges.

6. The network model integration device according to claim 1, wherein

the retrieving unit retrieves the edges that are designated in advance by the user via the input unit.

7. The network model integration device according to claim 1,

wherein

the retrieval result displaying unit further displays the retrieval results including the nodes that do not constitute the designated network model and are linked to the edges retrieved by the retrieving unit and the network model ID that identifies the network model that includes the nodes stored in the network model storage unit on the display unit in a selectable manner.

8. The network model integration device according to claim 1,

wherein

the retrieval result displaying unit performs any one or both of a process of displaying the retrieval results on the display unit in a selectable manner in a list form and a process of displaying the retrieval results on the display unit so as to be superimposed on the network model.

9. The network model integration device according to claim 1,

wherein

the control unit further includes:

a configuration notifying unit that, when the edges stored in the network model storage unit are retrieved by the retrieving unit, notifies the user, who has provided the network model, of any one or both of the nodes and edges that are included in the designated network model and are not included in the network model stored in the network model storage unit, identified by the network model ID corresponding to the edges.

10. The network model integration device according to claim 1,

wherein

the control unit further includes:

a configuration notifying unit that, when the integrated network model is generated by the integrating unit, notifies the user, who has provided, the network model, of any one or both of the nodes and edges that are included in the integrated network model and are not included in the network model stored in the network model storage unit, identified by the network model ID corresponding to the edges that are included in the retrieval results that are selected by the user via the input unit.

11. The network model integration device according to claim 1,

wherein

the network model storage unit further stores notes for a portion or all of the network models, the nodes, or the edges in association with the portion or all of the network models, the nodes, or the edges, and

the control unit further includes:

a note storing unit that, when the notes are input by the user via the input unit with respect to the portion or all of the network models, the nodes included in the network model, or the edges included in the network model, stored in the network model storage unit, stores the notes in the network model storage unit in association with the portion or all of the network models, the nodes, or the edges; and

a note notifying unit that notifies the user, who has provided the network model corresponding to the notes, the network model that includes the nodes corresponding to the notes, or the network model that includes the edges corresponding to the notes, stored in the network model storage unit, of the notes stored in the network model storage unit.

12. The network model integration device according to claim 1,

wherein

the network model storage unit further stores evaluation values on the retrieval results in association with the edges included in the retrieval results, and

the control unit further includes:

an evaluation value storing unit that, when evaluation values on the retrieval results are input by the user via the input unit, stores the evaluation values in the network model storage unit in association with the edges included in the retrieval results.

13. The network model integration device according to claim 12,

wherein

the evaluation values are input when the retrieval results displayed on the display unit by the retrieval result displaying unit are selected.

14. The network model integration device according to claim 12, wherein

the retrieval result displaying unit further displays the evaluation values that are stored in the network model storage unit and correspond to the edges retrieved by the retrieving unit on the display unit.

15. The network model integration device according to claim 5, wherein

the control unit further includes:

a keyword acquiring unit that, when a portion or all of the network models, the nodes, or the edges are selected by the user via the input unit, acquires keywords related to the portion or all of the network models, the nodes, or the edges;

a literature information retrieving unit that retrieves the literature information on the literatures that are issued within a predetermined period and are stored in the literature information storage unit using the keywords acquired by the keyword acquiring unit at intervals that are set by the user via the input unit; and

a literature information displaying unit that performs any one or both of a process of displaying the literature information retrieved by the literature information retrieving unit on the display unit in a list form and a process of displaying the literature information on the display unit so as to be superimposed on the network model stored in the network model storage unit.

16. The network model integration device according to claim 15, wherein

the control unit further includes:

a literature information notifying unit that notifies the user of the literature information retrieved by the literature information retrieving unit.

17. The network model integration device according to claim 15, wherein

the literature information displaying unit performs any one or both of the process of displaying the literature information on the display unit in the list form and the process of displaying the literature information on the display unit so as to be superimposed on the network model based on display preference conditions that are set by the user via the input unit.

18. The network model integration device according to claim 17, wherein

the display preference conditions are literature names, literature issuing organization names, or book titles.

19. The network model integration device according to claim 1,

wherein

the storage unit further includes:

an advertisement information storage unit that stores advertisement information on the constituent elements or the interactions, and

the control unit further includes;

an advertisement information acquiring unit that, when a portion or all of the network models, the nodes, or the edges are selected by the user via the input unit, acquires the advertisement information that is stored in the advertisement information storage unit and is related to the constituent elements or the interactions that are based on the portion or all of the network models, the nodes, or the edges; and

an advertisement information displaying unit that displays the advertisement information acquired by the advertisement information acquiring unit on the display unit.

20. The network model integration device according to claim 19, wherein

the advertisement information acquiring unit further acquires the advertisement information that is stored in the advertisement information storage unit and is related to neighboring constituent elements that interact with the constituent elements that are based on the portion or all of the network models, the nodes, or the edges.

21. The network model integration device according to claim 1, wherein

the storage unit further includes:

an advertisement information storage unit that stores advertisement information related to the constituent elements or the interactions, and

the control unit further includes;

a network model displaying unit that displays the network model on the display unit;

an advertisement information acquiring unit that recognizes a portion of the network model that is displayed at a center of a screen for the longest period within a predetermined period by the network model displaying unit and acquires the advertisement information that is stored in the advertisement information storage unit and is related to any one or both of the constituent elements based on the nodes and the interactions based on the edges, included in the portion of the network model; and

an advertisement information displaying unit that displays the advertisement information acquired by the advertisement information acquiring unit on the display unit.

22. The network model integration device according to claim 5, wherein

the control unit further includes:

a literature model acquiring unit that acquires the network model from the literature information in which the edges are retrieved by the retrieving unit using natural language analysis and acquires a network model ID that identifies the network model, and

the network model storing unit further stores the network model acquired by the literature model acquiring unit and the network model ID in the network model storage unit in association.

23. The network model integration device including a control unit and a storage unit and a terminal device including an input unit, a display unit, and a control unit that are connected to each other in a communicable manner, wherein

the storage unit of the network model integration device includes:

a network model storage unit that stores a network model that includes nodes that represent constituent elements of a biological object and edges that represent interactions between the constituent elements and a network model ID that identifies the network model in association,

the control unit of the network model integration device includes;

a retrieving unit that retrieves the edges that are stored in the network model storage unit, do not constitute a designated network model which is the network model that is transmitted from the terminal device and is designated by a user of the terminal device via the input unit, and are linked to the nodes that constitute the designated network model and transmits retrieval results including the retrieved edges and the network model ID that identifies the network model that includes the edges stored in the network model storage unit to the terminal device;

an integrating unit that generates an integrated network model which is the network model in which the edges included in the retrieval results that are transmitted from the terminal device and are selected by the user via the input unit and the nodes that do not constitute the designated network model and are linked to the edges are integrated into the designated network model; and

a network model storing unit that acquires the network model ID that identifies the integrated network model generated by the integrating unit and stores the integrated network model and the network model ID in the network model storage unit in association, and

the control unit of the terminal device includes;

a retrieval result displaying unit that displays the retrieval results transmitted from the network model integration device on the display unit in a selectable manner and transmits the retrieval results selected by the user via the input unit to the terminal device.

24. A network model integration method executed by a network model integration device including an input unit, a display unit, a storage unit, and a control unit, wherein

the storage unit includes:

a network model storage unit that stores a network model that includes nodes that represent constituent elements of a biological object and edges that represent interactions between the constituent elements and a network model ID that identifies the network model in association,

the method executed by the control unit comprising;

a retrieving step of retrieving the edges that are stored in the network model storage unit, do not constitute a designated network model which is the network model, and are linked to the nodes that constitute the designated network model, when the network model is designated by a user via the input unit; and

a retrieval result displaying step of displaying retrieval results including the edges retrieved at the retrieving step and the network model ID that identifies the network model including the edges stored in the network model storage unit on the display unit in a selectable manner;

an integrating step of generating an integrated network model which is the network model in which the edges included in the selected retrieval results and the nodes that do not constitute the designated network model and are linked to the edges are integrated into the designated network model, when the retrieval results displayed on the display unit at the retrieval result displaying step are selected by the user via the input unit; and

a network model storing step of acquiring the network model ID that identifies the integrated network model generated at the integrating step and storing the integrated network model and the network model ID in the network model storage unit in association.

25. A network model integration method that is performed in a network model integration system including a network model integration device including a control unit and a storage unit and a terminal device including an input unit, a display unit, and a control unit that are connected to each other in a communicable manner, wherein

the storage unit of the network model integration device includes:

a network model storage unit that stores a network model that includes nodes that represent constituent elements of a biological object and edges that represent interactions between the constituent elements and a network model ID that identifies the network model in association,

the method comprising;

a retrieving step of retrieving the edges that are stored in the network model storage unit, do not constitute a designated network model which is the network model that is transmitted from the terminal device and is designated by a user of the terminal device via the input unit, and are linked to the nodes that constitute the designated network model and transmits retrieval results including the retrieved edges and the network model ID that identifies the network model that includes the edges stored in the network model storage unit to the terminal device that is performed by the control unit of the network model integration device;

a retrieval result displaying step of displaying the retrieval results transmitted from the network model integration device on the display unit in a selectable manner and transmits the retrieval results selected by the user via the input unit to the terminal device that is performed by the control unit of the terminal apparatus;

an integrating step of generates an integrated network model which is the network model in which the edges included in the retrieval results that are transmitted from the terminal device and are selected by the user via the input unit and the nodes that do not constitute the designated network model and are linked to the edges are integrated into the designated network model that is performed by the control unit of the network model integration device; and

a network model storing step of acquires the network model ID that identifies the integrated network model generated at the integrating step and storing the integrated network model and the network model ID in the network model storage unit in association that is performed by the control unit of the network model integration device.

26. A computer program product having a non-transitory computer readable mediums including programmed instructions for a network model integration method executed by a network model integration device including an input unit, a display unit, a storage unit, and a control unit, wherein

the storage unit includes:

a network model storage unit that stores a network model that includes nodes that represent constituent elements of a biological object and edges that represent interactions between the constituent elements and a network model ID that identifies the network model in association, wherein

the instructions, when executed by the control unit, cause the control unit to execute;

a retrieving step of retrieving the edges that are stored in the network model storage unit, do not constitute a designated network model which is the network model, and are linked to the nodes that constitute the designated network model, when the network model is designated by a user via the input unit; and

a retrieval result displaying step of displaying retrieval results including the edges retrieved at the retrieving step and the network model ID that identifies the network model including the edges stored in the network model storage unit on the display unit in a selectable manner;

an integrating step of generating an integrated network model which is the network model in which the edges included in the selected retrieval results and the nodes that do not constitute the designated network model and are linked to the edges are integrated into the designated network model, when the retrieval results displayed on the display unit at the retrieval result displaying step are selected by the user via the input unit; and

a network model storing step of acquiring the network model ID that identifies the integrated network model generated at the integrating step and stores the integrated network model and the network model ID in the network model storage unit in association.

27. A computer program product having a non-transitory computer readable mediums including programmed instructions for a network model integration method executed by a network model integration device including a control unit and a storage unit that is connected to a terminal device including an input unit in a communicable manner, wherein

the storage unit includes:

a network model storage unit that stores a network model that includes nodes that represent constituent elements of a biological object and edges that represent interactions between the constituent elements and a network model ID that identifies the network model in association, wherein

the instructions, when executed by the control unit, cause the control unit to execute;

a retrieving step of retrieving the edges that are stored in the network model storage unit, do not constitute a designated network model which is the network model that is transmitted from the terminal device and is designated by a user of the terminal device via the input unit, and are linked to the nodes that constitute the designated network model and transmits retrieval results including the retrieved edges and the network model ID that identifies the network model that includes the edges stored in the network model storage unit to the terminal device;

an integrating step of generates an integrated network model which is the network model in which the edges included in the retrieval results that are transmitted from the terminal device and are selected by the user via the input unit and the nodes that do not constitute the designated network model and are linked to the edges are integrated into the designated network model; and

a network model storing step of acquires the network model ID that identifies the integrated network model generated at the integrating step and stores the integrated network model and the network model ID in the network model storage unit in association.