I had an excellent Biology Professor at Huntington University (www.huntington.edu) that taught me about "concept mapping". As much as I enjoyed the class for its subject matter, I really appreciated his "concept mapping" style notes, that he used during the lecture. On a casual glance it might look pretty intimidating, hard to read (looked like chicken scratches--especially from the back of the classroom), but oddly enough, it made sense to me.
It looked a bit like the following:
In addition to defining many different words that pertain to the world of biology, I found it very helpful to understand the relationships between these defined words. Maybe you could talk about this as the "ontology" of these words. If you define "ontology" as the interaction between entities within a specific domain (in this case biology), I think it works.
While this was helpful to me, it had its limitations. This wasn't your classic outline that moved from right to left and down the page. This "map" from a theoretical standpoint had "flexibility" built-in, but in the real world this free flowing idea map became a problem when you hit the edge of the paper (or the chalkboard, as was sometimes the case).
Another shortcoming, when you looked at the "map" for a while you would begin to understand new connections, but making edits could be a challenge. Your best option was to draw a connecting line between the entities that where you had discovered another relationship.
The good news is--some things have changed in the last 15 years. It turns out that the world is a bit more digital now than it was before. Paper and chalkboards/whiteboards are still important, but the digital world brings with it some new options.
What used to be called "Concept Mapping" is more well known today as "Mind Mapping". And there a plethora of mind mapping software based tools available. You can find a comprehensive list of these at: http://www.mind-mapping.org/. I really can't speak to these other tools, but I can tell you that I appreciate the features I have found in a mind mapping tool called "Mind Manager" (www.mindjet.com).
One big problem solved! My virtual paper has no edges and ideas can be moved around easily.
