Mapping connections between topics covered in academic papers - does such a tool exist? I'm interested in learning about how to go about writing a paper, and obviously, an integral part of this process will be to read papers written by others, and study those. I'm curious about the idea of using software mapping tools as a means of logging connections between certain papers of interest. 

The following questions: Is there a network map of subjects and how they connect with each other? and Map (tree) of citations/references are related to my question, but I'm not sure the suggested software, Auto Desk
or Cytoscape, would be entirely appropriate for what I'm interested in doing.

Does anyone have any other suggestions?
ScienceWISE is one of the attempts:

The ScienceWISE project aims to develop a scientist-generated on-line knowledge base fully integrated into the physics ArXiv.org
The ScienceWISE system allows scientists, in the course of their daily work to

dynamically generate professional-field-specific ontologies: add concepts and logical relations between them; provide expertly-written, community-ranked definition articles and links to other existing resources;
to create an interactive semantic environment, annotating scientific research papers, uploaded to ArXiv.org, and linking them to the ScienceWISE ontology, thus expanding content of their papers with supporting material in the form of encyclopedia-like articles.


(See also info on the arXiv: http://arxiv.org/help/sciencewise)