Cytoscape WikiRFC Name : Cytoscape Themes |
Editor(s): Alex Pico| Date: October 24 2007 |
Status: Under Construction |
Proposal
While it is important that the semantics in the core of Cytoscape remain domain-agnostic, we also recognize the need to support use cases and plugins that are very domain-specific. We propose the concept of Cytoscape Themes to provide plugin developers and users with flavors of Cytoscape designed with specific research domains in mind. By providing a few basic overlays and defined standards we can greatly facilitate plugin development and improve user experience.
This proposal touches on a number of areas including domain-specific semantics, data integration and user interfaces. We propose to do the following:
Overlay domain-specific syntax onto the data model (a.k.a [http://en.wikipedia.org/wiki/Syntactic_sugar syntactic sugar]), while maintaining the agnostic core model.
- Define annotation standards per domain to facilitate the mapping of external data sources to a standard set of attributes
- Make changes to the view to reveal the appropriate semantics to the user in the form of menus, panels, labels, etc.
Overlaying domain-specific syntax onto the data model will clarify the model and help direct plugin developers who are implementing domain-specific functionality (e.g., microarray analysis). The effect of the “sweetened” syntax should trickle down to the end user by making it easier to load and map datasets and interpret domain-specific visualizations.
The first step, however, is to re-layer the core Cytoscape code and settle the API (see [:CytoscapeLayerRefactor:RFC 46] and [:PluginRefactor:RFC 47]). We should keep Cytoscape Themes in mind as one of many motivations for performing these crucial tasks.
Use Cases
Provide examples of how the products of this project will be used.
Implementation Plan
Once the core Cytoscape code has been re-layered and and API is settled, we can develop a set of modular plugins to define a given theme (see genomics example below). These plugins, and their respective APIs, can be used by developers and, in turn, be bundled with their plugins to facilitate installation and use by the end-user (see [:CytoscapePluginBundles: CytoscapePluginBundles RFC]).
The following plugins would, together, support the basic biological semantics for pathway analysis of microarray data, for example.
- 1.Overlay basic biological syntax onto the core data model. Here are a few examples:
- Define annotation standards. For example, ID mapping from various data sources:
database name (standardized like http://www.geneontology.org/cgi-bin/xrefs.cgi)
- identifier
- symbol
- full name
- aliases
- genomic location
Variations on the these functions could be mixed, matched and bundled to support various domain-specific tasks.
Project Management
Project Timeline
Provide a timeline for implementation. Insert a graphic if you can. Try this free online tool for making project timelines -> [http://www.helpuplan.com/index.asp Help-u-Plan] (create a new chart; modify; right-click to save gif; then attach to this page)
Tasks and Milestones
Outline the major milestones and tasks involved in implementation.
Milestone 1: …
- Task 1: ...
- Task 2: ...
Milestone 2: …
Project Dependencies
Outline and projects that depend on this project, link to relevant RFC's and note at what point dependent projects could be started.
Related RFCs
Link to other related RFCs
Issues
List any issues, conflict, or dependencies raised by this proposal
Comments
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