Integration of the Gene Ontology into an object-oriented architecture

doi:10.1186/1471-2105-6-113

BMC Bioinformatics
Volume 6

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Research article

Integration of the Gene Ontology into an object-oriented architecture

Daniel Shegogue¹ and W Jim Zheng¹^,2

¹Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, 135 Cannon Street, Charleston, SC 29425 USA

²Bioinformatics Core Facility, Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas St, Charleston, SC 29425 USA

author email corresponding author email

BMC Bioinformatics 2005, 6:113doi:10.1186/1471-2105-6-113


Published:	10 May 2005

Additional files

Additional File 1:

Class-responsibility-collaboration card for TGF-beta 1. Attributes, collaborators and responsibilities of the specified protein are given. The attributes section allows the ordered listing of information not easily captured by the UML notation. The collaborator section lists the cellular components that interact with TGF-beta 1. The responsibilities section specifies the consequence of TGF-beta 1 interacting with its collaborator. This card allows TGF-beta 1 to be decomposed into an object containing attributes, operations and interactions.

Format: PDF Size: 78KB Download file

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Additional File 2:

Class-responsibility-collaboration card for TGF-beta receptor II. Attributes, collaborators and responsibilities of the specified protein are given. The attributes section allows the ordered listing of information not easily captured by the UML notation. The collaborator section lists the cellular components that interact with TGF-beta receptor II. The responsibilities section specifies the consequence of TGF-beta receptor II interacting with its collaborator. This card allows TGF-beta receptor II to be decomposed into an object containing attributes, operations and interactions.

Format: PDF Size: 79KB Download file

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Additional File 3:

Class-responsibility-collaboration card for TGF-beta receptor I. Attributes, collaborators and responsibilities of the specified protein are given. The attributes section allows the ordered listing of information not easily captured by the UML notation. The collaborator section lists the cellular components that interact with TGF-beta receptor I. The responsibilities section specifies the consequence of TGF-beta receptor I interacting with its collaborator. This card allows TGF-beta receptor I to be decomposed into an object containing attributes, operations and interactions.

Format: PDF Size: 80KB Download file

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Additional File 4:

Class-responsibility-collaboration card for SMAD2. Attributes, collaborators and responsibilities of the specified protein are given. The attributes section allows the ordered listing of information not easily captured by the UML notation. The collaborator section lists the cellular components that interact with SMAD2. The responsibilities section specifies the consequence of SMAD2 interacting with its collaborator. This card allows SMAD2 to be decomposed into an object containing attributes, operations and interactions.

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Additional File 5:

Use case describing the events leading to TGF-beta receptor complex assembly. This use case defines the boundaries of the system model. Here, the main success and alternative scenarios leading to the assembly of the TGF-beta receptor complex are described.

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Additional File 6:

Conceptual diagram of the TGF-beta receptor complex, and the proteins that associate with this complex. Gene products have been decomposed into objects. Object attributes and operations are hidden to reduce complexity. Gene products that comprise the receptor complex are shown in blue with their associated relationships in green. As the boundaries of the use case do not include them, other associated proteins that comprise the TGF-beta signaling pathway are not emphasized in further diagrams.

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Additional File 7:

State diagrams for the TGF-beta receptor complex components. State diagrams describe the possible states in which a bioentity can exist. Concurrent states are separated by vertical dashed lines. A) State diagram for TGF-beta. B) State diagram for TGF-beta receptor II. C) State diagram for TGF-beta receptor I. D) State diagram for SMAD2.

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Additional File 8:

An example of a class diagram with expanded function names showing the interactions between the components of the TGF-beta receptor complex (GO:0007181) (grayed). Cellular components containing these gene products are also shown. GO function terms are shown with their corresponding GO ids. This format demonstrates a more user-friendly interface for reading the diagrams, whereas figure 4 is more suitable as a computer readable format.

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