RFC Name : CyNode identifier

Editor(s): Ben Gross

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About this document

This is an official Request for Comment (RFC) for CyNode Identification

For details on RFCs in general, check out the Wikipedia Entry: Request for Comments (RFCs)


This RFC is still under construction and open for public comment. (01/17/06 -Ben)

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Still under discussion:

Biological Questions / Use Cases

A use case previously tied to this issue, but is actually a NodeView issue:

General Notes

In this RFC, the term "label" or "node label" has been used in place of the more historic term "name" or "node name".


Cytoscape need to have:


Cytoscape subsystems and their node identifier semantics

Open Issues

SIF File Format:



Backward Compatibility


Current Implementation Notes 2.2 (how a node gets created)


Implementation Plan - Phase 1

Remove existing references to CANONICAL_NAME, COMMON_NAME, and ALIASES. This involved removing references to the Semantics class in the following classes:

In addition, an "ID" identifier was added to:

* src/cytoscape/visual/calculators/AbstractCalculator.java

to allow such things as a controlling attribute name to be set within a Mapping Class. In addition, the following classes were modified so that this new ID identifier would be added to the attribute bundle for each node and edge:

Per Cytoscape conference calls, the vismapper code was going to be affected by this refactoring. It turns out the Gene Ontology/BioData Server - Gene Ontology Wizard is also affected by this refactoring. At least the following file makes references to canonical name:

src/cytoscape/data/annotation/AnnotationGui.java - no sure what this does

Implementation Plan - Phase 2

CyNode_Identification (last edited 2009-02-12 01:03:31 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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