Difference between revisions of "GMOD Components"

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GMOD is a loose federation of software applications (components) aimed at providing functionality that is needed by all organism databases.  
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GMOD is a loose federation of software applications (components) aimed at providing functionality that is needed by all organism databases. The table below classifies GMOD components according to their functional categories.  
  
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* '''Comparative Genomics Visualization'''
 
* '''Comparative Genomics Visualization'''
 
** [[CMap]]
 
** [[CMap]]
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** [[GeneXplorer]]
 
** [[GeneXplorer]]
 
** [[Java TreeView]]
 
** [[Java TreeView]]
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* '''Genome Visualization & Editing'''
 
* '''Genome Visualization & Editing'''
 
** [[Apollo]]
 
** [[Apollo]]
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* '''Ontology Visualization'''
 
* '''Ontology Visualization'''
 
** [[GO_Graphic_Viewer|Go Graphic Viewer]]
 
** [[GO_Graphic_Viewer|Go Graphic Viewer]]
* '''Phenotype Visualization'''
 
 
* '''Sequence Alignment'''
 
* '''Sequence Alignment'''
 
** [[BLAST_Graphic_Viewer|Blast Graphic]]
 
** [[BLAST_Graphic_Viewer|Blast Graphic]]
* '''Strain & Library Visualization'''
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* '''Utilities'''
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* '''Community Visualization'''
** [[org.bdgp]]
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** [[Community]]
 
* '''Workflow Management'''
 
* '''Workflow Management'''
 
** [[Citrina]]
 
** [[Citrina]]
 
** [[TIGR-Workflow_/_Ergatis|Ergatis]]
 
** [[TIGR-Workflow_/_Ergatis|Ergatis]]
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* '''Phenotype Visualization'''
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* '''Strain & Library Visualization'''
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* '''Utilities'''
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** [[org.bdgp]]
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The diagram below represents a model organism database (MOD) and its typical components. The "top ten" types of functionality are represented in the top row of the diagram as a set of interfaces. The "Vis" prefix on the end of each interface is an abbreviation of "Visualization", and should be interpreted literally -- an alignment visualization interface should not merely allow users to passively view pre-existing alignments, but should also to user interaction to create and visualize alignments of their own.
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The diagram below represents a model organism database (MOD) and its typical components. The ''top ten'' types of functionality are represented in the top row of the diagram as a set of interfaces. The ''Vis'' prefix on the end of each interface is an abbreviation of ''Visualization'', and should be interpreted literally -- an alignment visualization interface should not merely allow users to passively view pre-existing alignments, but should also to user interaction to create and visualize alignments of their own.
  
  
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** solid arrows indicate a relationship between components that currently exists.
 
** solid arrows indicate a relationship between components that currently exists.
 
** dashed arrows indicate a relationship between components that does NOT currently exist.
 
** dashed arrows indicate a relationship between components that does NOT currently exist.
** dashed arrows with a solid white head indicate an interface/realization relationship between a GMOD-Web required interface and a component that provides that interface. e.g. gbrowse implements the "genomeVis" interface.
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** dashed arrows with a solid white head indicate an interface/realization relationship between a GMOD-Web required interface and a component that provides that interface. e.g. gbrowse implements the ''genomeVis'' interface.
 
* coloration
 
* coloration
 
** white: components or interfaces that currently exist and integrated into the GMOD system.
 
** white: components or interfaces that currently exist and integrated into the GMOD system.

Revision as of 15:51, 14 February 2007

GMOD is a loose federation of software applications (components) aimed at providing functionality that is needed by all organism databases. The table below classifies GMOD components according to their functional categories.









The diagram below represents a model organism database (MOD) and its typical components. The top ten types of functionality are represented in the top row of the diagram as a set of interfaces. The Vis prefix on the end of each interface is an abbreviation of Visualization, and should be interpreted literally -- an alignment visualization interface should not merely allow users to passively view pre-existing alignments, but should also to user interaction to create and visualize alignments of their own.


Roadmap.png


Symbols used in this UML diagram

  • boxes
    • tabbed white boxes are packages -- logical groups of related components
    • boxes marked with <<interface>> are abstract interfaces required by GMOD-Web. All other labeled boxes are concrete components of the GMOD system.
  • connectors
    • solid arrows indicate a relationship between components that currently exists.
    • dashed arrows indicate a relationship between components that does NOT currently exist.
    • dashed arrows with a solid white head indicate an interface/realization relationship between a GMOD-Web required interface and a component that provides that interface. e.g. gbrowse implements the genomeVis interface.
  • coloration
    • white: components or interfaces that currently exist and integrated into the GMOD system.
    • green: components or interfaces that currently exist and are integrated into the GMOD system.
    • pink: components or interfaces that currently exist, but the feasibility of integrating their functionality into the GMOD system is unknown.
    • red: components that do not currently exist, but may need to be implemented.
    • orange: a common set of templates to provide a consistent look and feel for all GMOD systems. The "common gene page" concept is in this group.
    • cyan: components that are specific to each MOD, and are not deployable as part of a GMOD system.

GMOD components fulfilling the requirements of an interface are linked to the interface, as well as to the Chado schema modules if they are known to interact with Chado. The requirements of an interface, as well as the components that implement a given interface are described in the documents linked at the end of this document.