Assignment 1: QUDT

Assignment Type: 

Research Report, 3 pages max.

Assignment:

  1. Read the QUDT article and write a half-page summary.
  2. Create a Protégé ontology that models simple one-dimensional quantities covering length quantities in meters and feet as well as weight quantities in grams and ounces.
  3. Create two quantity individuals: (i) “a length of 5 meter”, and (ii) “a weight of 50 gram”.
  4. Include a screenshot of the OWL file (including the individuals) in the submission.

Remarks & tips:

  • You should use the QUDT ontology as the source of inspiration. The reason we want  you to recreate the core part of the QUDT ontology (instead of using it directly) is to help you understand what the QUDT concepts stand for.
  • We suggest you focus on the four classes Quantity, QuantityKind, QuantityValue and Unit.

Literature:

QUDT – Quantities, Units, Dimensions and Data Types in OWL and XML. R. Hodgson & P. Keller, NASA, September 2011.

Recommended reading:

Natalya F. Noy and Deborah L. McGuinness. “Ontology Development 101: A Guide to Creating Your First Ontology”. Stanford Knowledge Systems Laboratory Technical Report KSL-01-05 and Stanford Medical Informatics Technical Report SMI-2001-0880, March 2001.

Submission deadline:

Friday: 9 November, 23:59 CET 

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25 Responses to Assignment 1: QUDT

  1. Snorre Rubin says:

    Hey, does anybody have the install file for Graphviz 2.28.0 for OS X Lion? Graphviz.org seems to be down, and protege doesn’t seem to be able to run properly without Graphviz…

    • minhalee says:

      I emailed you about it. But I’m running on an older version of mac. and btw, you might run into problems with a dot file.

      • George Kyriacou says:

        hey guys . i have the installation package for Graphviz 2.28 . I am running on Snow Leopard and although i was facing some problems, i have just figured it out. visit http://www.graphviz.org/Download_macos.php and follow the instructions depending on the operating system you are running. The path for both Leopard and Snow Leopard is /usr/local/bin/dot

  2. Hello everyone! I have some questions!
    “Length” and “Weight” are Quantities, right?
    “meters” and “feet” are units, right?
    How can units be illustrated in “Protégé”? :/

  3. margreet says:

    I have the same problem also already for a long time. Couldn’t find proper way to visualize it. I still have snow leopard. Anyone suggestions?

  4. Julien L. says:

    I found a relatively easy way to get Protégé to work on my Macbook. I run Mountain Lion (Mac OS 10.8.2) which is why I could not use George’s method. Here is the details of how I got everything to work well, hoping to help some other students! 😉

    1. Install Protégé
    I used the InstallAnywhere package for Mac OS, which can be found on the following page: http://protege.stanford.edu/download/protege/4.1/installanywhere/Web_Installers/ Your computer might tell that the APP file you downloaded is broken and should be moved to trash, but this is wrong. The file is simply not signed by Apple. You can go to System Settings > Security and Privacy, and change the “Allow applications downloaded from:” value to “Anywhere” so that your Macbook will open the Protégé installation file. You could have to click on the lock at the bottom right of the Settings panel to be able to change this setting. You should also set it back to a safer value once you installed Protégé.

    2. Check the Protégé installation
    Start Protégé, and create a new Ontology. Everything should work fine, but when going to the OWLViz tab, you should get an error saying that OWLViz cannot find the DOT application. DOT is an other application than Protégé. Protégé uses DOT to draw visual representations of your Ontologie, instead of doing the drawing itself. The next step will make sure OWLViz can use DOT, you can close Protégé for now…

    3. Install the Command Line Tools
    I simply followed the Step 1 of this page to install the Command Line Tools: http://www.moncefbelyamani.com/how-to-install-xcode-homebrew-git-rvm-ruby-on-mac/ You can also follow steps 2 and 3 to get Homebrew…

    4. Install Homebrew
    I stopped at the Step 1 on the previous link, and simply went on the homepage of Homebrew: http://mxcl.github.com/homebrew/ There, you can see that by opening a terminal window and copy/pasting the following command, you will get Homebrew installed: ruby -e “$(curl -fsSkL raw.github.com/mxcl/homebrew/go)” ; and check that the installation went well with the next command: brew doctor.

    5. Install Graphviz
    Graphviz is a package containing a lot of useful drawing binaries, including DOT. Because Graphviz doesn’t give any package for Mountain Lion, we had to install Homebrew to be able to install Graphviz through Homebrew. If the command “brew doctor” gave positive results, you can now type “brew graphviz” to get Graphviz and all its dependencies installed. Thanks to the power of Homebrew, everything will be done for you.

    6. Go back to Protégé
    We can now start Protégé again, go in the preferences, and specify the right path of DOT, in the OWLViz tab. In my case, the path was “/usr/local/Cellar/graphviz/2.28.0/bin/dot” but you should check that. By going to the Finder, and choosing the menu Go > Go to folder… and typing “/usr/local”, you can try to find what the real path of your DOT binary file is. Once the right path is entered in the options, you should be able to use the OWLViz tab of Protégé without an error!

    Let me know how that worked for the Mac users 😉

    • Jilai Chen says:

      Thanks for your tutorial, it helps me to get the graphviz working. I am using the same operating system with you. The only difference is that I type “brew install graphviz” instead of yours “brew graphviz” in Step 5. Others can try both until you install the graphviz successfully.

      • Julien L. says:

        @Jilai Chen: I’m glad you tried to follow my “mini-tutorial” and was able to get Graphviz working. You are right: “brew graphviz” isn’t a valid homebrew command and people should type “brew install graphviz” !

        Now I’ve been struggling to get Protégé 4.1 to work well on my machine, and OWLViz to be also fine, I am not happy with the way it displays the OWL Ontologie… The thing is: I am quite sure I was able to recreate the Ontologie shown there: http://www.qudt.org/images/QUDT-QuantityDiagram.jpg (I created Classes, Object properties and Data properties in the same way) but I cannot get a nice visualization. I am still looking for the best way to view OWL Ontologies…

        Maybe teachers can help us find out how this kind of visualization can be obtained: http://www.qudt.org/images/QUDT-QuantityDiagram.jpg ? My next try is a previous version or Protégé (3.4.8) with the Jambalaya plugin… I will keep you all updated on that one!

        I’m also not sure about what teachers mean with “a screenshot of the OWL file”. This is very vague since I can take a screenshot of the file icon in finder, of the file contents in a text editor, or the file rendered in – I don’t know which – OWL renderer…

    • Marek Janiszewski says:

      as stated in protege wiki
      “Mac users – finding the right version of Graphviz
      The current status of Graphviz for the Mac OS is very unclear.
      The latest binaries they point to directly (the pixelglow implementation) no longer contain the dot application required by OWLViz. According to their download page this distribution is out of date and not maintained.
      Install version 2.14 from one of their alternatives and point to that instead (it gets installed in /usr/local/graphviz-2.14/). This contains the necessary binaries in the bin/ folder.
      In Preferences, the string you want is: usr/local/graphviz-2.14/bin/dot ”

      I see in the cmd line that the folder is there (usr/local/graphviz-2.14/bin/) with dot, but still setting it in protege gives an error. Now I will try to check different versions.

  5. Julien L. says:

    Next to Protégé 4.1, I also tried a previous version (3.4.8). This idea came up to me after seeing this comparison between the two versions, which shows that the 4.x versions are not more complete than the 3.x versions (yet): http://protegewiki.stanford.edu/wiki/Protege4Migration#Side_by_Side_Comparison

    In the version 3.4.8, I could go to the menu OWL > Preferences, in the “Tabs” tab and tick the “JambalayaTab” line. This opened one more tab in Protégé 3.4.8, making me able to render my classes and properties in Jambalaya… At this point, the best I could get looks like this: https://dl.dropbox.com/u/61281858/jambalaya.jpg Still far from the nice pictures of the QUDT article… 😦

    I’m reaching a state of frustration where I would expect our teachers to give us more and clearer information about what is expected and how to do it… Struggling for hours, just trying to figure out how to work, and still not getting any feeling of the course content being useful for this assignment… is really depressing!

  6. The goal is not to exactly replicate the figure in the QUDT article, but to understand the domain and the modelling assignment on a conceptual level.

    Protégé has its flaws, but it is actually one of the more developed and supported open source tools out there. At this level, you cannot expect to always work with ‘easy’ or fully developed tools such as you may be used to, as such tools are generally out of the realm of research and more meant for end-users.

    • Julien L. says:

      My issue is not so much to get how Protégé works and since I come from a nerdy geeky technical background, I even enjoy discovering new softwares (even if I myself would put Protégé in the category of bad examples I should not follow when designing software solutions, its discovery and making everything work on my system was quite fun!).

      The thing is, it is very hard for me to figure out what is expected from us (i.e. I still have not the tiniest idea of what a “screenshot of a file” could be…) and even harder to make the link between the 3 first classes of K&M and this first assignment. I might use a Mind Map to help my team work on the summary of the article, but that’s about it!

      The regret I am expressing here is simply about the fact that most of my time/energy is spent on understanding Protégé and the Assignment itself, while understanding QUDT seems quite straightforward.

      • Snorre Rubin says:

        I must admit that I feel much the same as Julien.
        I have been looking at several different protégé tutorials, and I understand some of what the program is supposed to do. Also I understand what we are supposed to do in our assignment.
        Even more to the point, I understand the point of the assignment: the central points of the QUDT system. Like Julien, I feel that I am bumping my head agains the wall in trying to get protégé to do what I want it to do. This makes me feel stupid, and it feels like a stupid waste of time, as it is no problem for me to describe the relations between the parts of the ontology that we are supposed to make, in words. But doing it in protégé is still beyond me.
        It may be that it is simply me who do not get protégé, but I would like to be able to carry on with the actual points of the assignment, and not just knock my head against this program.

  7. margreet says:

    I have been working with Protege and Topbraid during the premaster, both are absolutely not user friendly program. We had a whole course to create one ontology. Now it is expected to do so in a couple of days. The reasoner also crashes often. Indeed I agree the focus should be on the model and not getting additional software running on your laptop as Graphviz.
    So the assignment in the end is possible, but you have to be really persistent.

    • Julien L. says:

      Yes… Well I just hope we will be given a new chance to ask questions (and get real answers) during the class of tomorrow. Otherwise, I’m still very unsure about how my screenshots would look…

      • Julien L. says:

        Meh. My phone went out of battery.. and therefore the alarm as well. I hope others were able to be in class to ask all our questions 😉

  8. Richard H. says:

    Hi all,

    is there a chance to make individuals and object properties (which describe the relations) visual in protege? I get only the classes and subclasses as an image in OWLViz. I am struggling since hours with that issue.

    Thanks for any help !

  9. George Kyriacou says:

    hi all.except of the attachment of screenshot of the OWL file, do we have to explain it?? Or is it enought the screenshot along with the diagram? Also about the OWL file, you just want it in OWL or also in Turtle?

    • Kirsten says:

      For as far as I understand you have to write a research paper which incorporates the screenshot and the summary. This will give you a chance to explain you screenshot.

  10. Athanasios Tsokaktsidis says:

    There is a problem with the password for uploading the assignment in DropitTo
    Does anyone have a valid password because the one we have given in the class is not working.

  11. George Kyriacou says:

    I have noticed that the website for uploading the assignment does not work. I dont know if i am doing something wrong .. If anyone tried to upload the assignment with success please inform me. gracias

  12. aan680 says:

    The password given to us does not seem to work. I tried several variants, such as – instead of _, but did not crack the code, so our team submitted by e-mail.

  13. Julien L. says:

    Hi all! The good variant was KM_Assignment1
    I was able to upload thanks to George who had more patience than me trying all kinds of possibilities, but I hope for those who sent by mail that our teachers will be fine with it 😉

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