Use Case Name : ../EditAnnotation

For Feature : MIMEditor

Editors: DavidKane

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A user wants to add or edit annotations to a feature in a map.

Step-by-Step User Action

  1. User selects feature in the map
  2. User specifies that the feature’s annotations should be edited
  3. User adds a pubmed id, or other reference as evidence for the presence of the feature in the map
  4. User repeats step 3, until all literature citations have been added
  5. User optionally adds additional textual explanation for the annotation

Visual Aides

Requirements for Cytoscape



Annotations are very important for the credibility of maps that seek wide usage. However, the process of adding annotations should not be tightly coupled to the process of creating and editing the map. So the process of adding annotations needs to be able to happen afterwards.

Other Examples


Shared ../MimEditorUseCaseComments

AllanKuchinsky - 2007-01-19 02:59:30

1. At the user interface level, would it be useful to be able to drag/drop a literature reference, file reference, etc. onto a Cytoscape node/feature and have that reference incorporated into the node's/feature's annotations? For example, drags a URL from web browser and drops it onto a Cytoscape node.

2. At the model level, we might want to define a Cytoscape construct to specifically support a collection of citations/references and their associated metadata. For example, something along the lines of the text source object in the Agilent Literature Search tool.

3. To support collaborative use of the maps, we could store a user id and timestamp with the annotation.

AllanKuchinsky - 2007-01-22 05:36:56

arbitrary graphical annotations functionality, for support of use cases such as GenMAPP and MiMs, is a major priority for Cytoscape versions 2.5 and 2.6. RFCs are forthcoming.

MiritAladjem - 2007-02-01 09:30:51

Molecular_Interaction_Maps/EditAnnotation (last edited 2009-02-12 01:03:15 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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