25 Apr 08

CmapTools for concept mapping and OWL authoring

Working with the free software that's nothing less than legal mind expansion!

I’d be among the first to admit that, despite being a stickler for standards, sometimes I like to do things my own way.

For use cases, I should be using UML but I take one look at the diagrams and I run for my life.

For preparing ontologies, I should be writing OWL, but I end up writing my own XML variant with (shhh!) no schema. This is (almost) inexcusable, so I’ve decided to try to jump on this particular train and start using a bit of software to get me started.

Introducing Cmap Tools COE OWL

I wanted to have my cake and eat it. I wanted the graphical modelling capabilities of Visio plus the OWL export and minus the Office 2007 interface. Enter Cmap Tools COE OWL: a JAVA-based concept mapping tool with OWL export.

And what better way to introduce an concept mapping product than to display a concept map in place of a homepage? Well, a normal web page would probably have been better in terms of usability but it was a good idea anyway!

Cmap Tools Homepage

Note that Cmap Tools COE OWL is a distinct variation of the standard CmapTools.

According Cmap Tools’ custodian, the Institute for Human and Machine Cognition, the software “empowers users to construct, navigate, share and criticize knowledge models represented as concept maps”.

It’s available in great-tasting flavours Windows, Mac OS-X, Linux, Solaris and the One Laptop Per Child machine XO. It’s also free for individual, non-commercial use.

Working with the software

At such a keen price, I decided to try it out! I installed version 4.11.01

I don’t personally know any Java developers, but my experience of Java software has often been that the user interface was an afterthought – it seems to be a feature of the platform!

Lest I protest too much, Cmap Tools turns out to be a pleasant exception to the rule.

Cmap Tools screenshot

The UI is relatively straightforward, echoing the product’s overall simplicity. A separate initial window entitled Views is for file management and collaboration. From there, we can start work on a new project.

Most of the donkey work gets done via standard drag-and-drop functionality, enabling rapid drawing from a standing start with no prior experience of the software.

Growing the concept map is dead easy. Users need simply select the parent of the intended new node and drag from the top of the label. Dragging from the top does feel slightly counter-intuitive if one intends to branch below the parent, but that’s a tiny (and probably entirely personal) niggle.

Cmap Tools Nodes

As the ontology spreads, there’s an absolutely essential Autolayout feature that helps the user to bring under control any concept map that starts to look like Phil Spector on a bad day in court.

If, like me, the user likes to see a simplified view of the strict hierarchical order of their taxonomies and ontologies, then to the right under Cmap Outline, he/she will find a more traditional tree layout. What I think is a minor shame here is that the list cannot be edited from Cmap Outline. The same can be achieved in the forms-based adjacent tabs.


Now for the all-important test: how’s the OWL output?

From my very first attempt, I find that the XML result isn’t exactly as expected. I need to go back to the software and try to be more explicit in the relationships between objects before eventually I achieve more predictable output.



Cmap Tools is a great bit of software for simple rendering of taxonomies and ontologies in the form of concept maps.

It’s not a serious development tool but as an all-rounder starter kit that’s safe to put in front of clients (with a commercial licence of course), it’s usable enough to invite the uninitiated to participate.

I’ve also recently started to look at Protégé, maintained by Stanford University’s National Center for Biomedical Ontology. This is the serious tool which, along with the Protégé-Owl extension, takes advanced OWL-based ontology editing and visualisation to another level.



  1. Gravatar Tom Eskridge says:

    I’m glad you like the CmapTools software. You might be interested to know that there is an extension of CmapTools called “COE: Collaborative Ontology Editor” that makes importing and exporting ontologies much easier. CmapTools itself will export to XML, but not to OWL. COE will read, edit, and export OWL in a graphical fashion. You can download it at http://coe.ihmc.us


  2. Gravatar Mike Padgett says:

    Oops, I have to admit my error: the version tested for the article was indeed the COE OWL version of CmapTools, not the standard CmapTools release, and I’ve updated accordingly.

    Since I wrote this article, I have continued happily to use CmapTools, managing to achieve relatively complex results with it. However, for me it really comes into its own as an ontology editor.

    A colleague walked by the other day and, being unfamiliar with CmapTools, he asked whether it would generate object-based code like Rational Rose. I wish, I replied, but there’s an idea for all you developers out there!

  3. Gravatar Web Tourist says:

    I’ve read a few articles on your site, to help me get started, and I’ve just downloaded CmapTools v4.18. I’ll let you know how it goes…

  4. Gravatar Valerie says:

    I am using Protege to create my ontologies but don’t find it very friendly when trying to view them. So I export to OWL format and then view in CMap COE. Works very well, EXCEPT, if I import an ontology into my project on Protege. Then when I get to CMap to view (by importing the OWL file), the file comes up empty. Any clues re why this would be happening??

    • Gravatar Mike Padgett says:

      Hi Valerie, I think you’re right about Protege. It is indeed quite limited in that way. Since I wrote the article, I haven’t used Protege very much because I find that I don’t need to in my field of work. Plus the simplicity of CMapTools means that clients on the business side feel very comfortable working with it.

      As to the issue you’re having, the most obvious possibility is that there’s something in the actual markup of the ontology that CMapTools doesn’t like. Perhaps a slight difference in the way the XML is written means that it can’t be parsed correctly and CMapTools isn’t reporting the problem?

  5. Gravatar Lucilia says:

    I have been trying to transform my CMaps into Ontologies by using Cmap COE but the version I downloaded doesnot show the Public Ontologies box. I followed all directions to have it added, but I keep on getting the same message: try later. the server may be off line (or something like that). Anyone that could help me by getting my maps and exporting them into OWL?

  6. Gravatar t says:


    CMaps are just drawings. If you open a plain CMap in COE and export it to an OWL/XML file, COE will try. All legal nodes and arcs are exported, the illegal rest is dropped.

    You could optimize / clean-up the CMap opened in COE by manually substituting illegal constructs with CMap Ontology templates. They are available from the Public CMap Ontologies Server that, unfortunately, you can’t connect to.

    The servers are alhena.ihmc.us and homan.ihmc.us. They can be pinged.
    I can’t connect to them either, but it used to work about a year ago.

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