COBrA-CT: Usability Tasks

The tasks should be carried out in order. The first is to install a version of the Protege tool (developed by Stanford University) that includes the extensions developed by COBrA-CT. Please do not use a version of Protege below 3.2. The second task assumes installation has been successful. If installation is a problem, please report this to stuart@aiai.ed.ac.uk. Please answer all the questions associated with each task, and email the answers to stuart@aiai.ed.ac.uk at the end. We are interested in your experiences of installing the tools - in addition to it being necessary for the following tasks. The results will influence how the tools are packaged in future.
Before starting, please ensure you have Java 1.5 installed: At a terminal window type 'java -version' - the build should be 1.5.*. If not, you may not be able to progress futher.

Preliminary questions:

• Question i. Are you a user of DAGEdit/OBOEdit or comparable ontology tools? If so, list the tools you use and tasks you typically perform.
• Question ii. Are you a Protege user?
• Question iii. Are you familiar with the OWL ontology language? If so, what use do you make of it?
• Question iv. Which ontologies or anatomies do you use on a regular basis, if any? What are the main uses of these ontologies?

Option 1
• Download and install Protege from the Stanford site: http://protege.stanford.edu/download/download.html
• Download the OBO tools from the downloads page and install them according to the instructions on the help page
• Start Protege by double-clicking the application (on Linux, run the commandline script)

Option 2
• Download Protege version 3.2.1 from one of these local archives: download Protege (all platforms), or download Protege (Windows zip file).
• Expand and un-tar the archive (winzip, stuffit or typing 'gunzip protege321.tar.gz' and 'tar -xvf protege321.tar' will do this). You should have a new directory: Protege_3.2.1
• Start Protege (on Windows: double-click run_protege_windows.bat; on Mac OS: start a Terminal, cd to the Protege_3.2.1 directory and type ./run_protege_mac; on Linux: cd to the Protege_3.2.1 directory and type ./run_protege_linux.sh).

Download and open an OWL file
• Download and save this verson of the cellular component ontology: component.owl. It should be saved as component.owl. (Some browsers will try to add .txt which is incorrect.)
• Create a new Protege project and open the component.owl file following step 1 (only) of the instructions on the help page.
• Select the OWLClasses tab (yellow). You should see the subclass hierarchy with classes labelled by the GO IDs. Explore the hierarchy for a moment or two. You are not expected to learn all of Protege's features. Additional notes on Protege projects can be found here: Notes on opening a Protege file.
• Exit Protege
• Question 1.1 Which platform are you using (Windows, Linux, OS X)?
• Question 1.2 Did you follow option 1 or option 2, and were the installation descriptions sufficiently detailed?
• Question 1.3 Was installation successful and were you able to start the system?

• Part 1: Prepare to open an OBO file
• Download and save the OBO file containing the GO cellular component ontology: component.obo
• Start Protege as described above. (If Protege is still running from Task 1, you can just select File/New Project and move to the next step).
• Create a Protege Project, then configure the OBO tools and load the component.obo file following steps 1-3 in the help file.
• Read through the section 4 of the user guide for the OBO Explorer tab.
• Question 2.1 Are you able to load the component.obo file by following the user guide, is the guide sufficiently clear?
• Part 2: Edit the OBO file
  • Select the OBO Explorer tab. Select GO_0005575 in the class hierarchy. Note the distinction between the term name and ID. Select the Show names checkbox in the OBO Explorer tab to create a new (temporary) ID for each term. Note that you can drag the divider to expand the space for the class hierarchy.
  • Question 2.2 Does the distinction between names and IDs correspond to your expectation?
  • Try to find the class food_vacuole using the search box at the bottom of the class hierarchy display panel (bottom left).
  • Question 2.3 Does the Show names feature combined with search enable you to locate the term?
  • Having found the term food_vacuole (GO:0020020), modify the synonyms by changing the synonym scope of "food vacuole (sensu Apicomplexa)" from Exact to Narrow.
  • Question 2.4 Are you able to successfully modify the synonym?
    If you are unable to modify the synonym please consult the help file and try once more.
  • Choose a top-level term such as envelope and modify the definition (e.g. add a sentence). Select cellular_component (the term below owl:Thing) then select envelope once more.
  • Question 2.5 Were the changes you made to the definition of envelope stored by the system, and do you find this method of entering text natural?
    If you are unable store the changes please consult the help file and try once more.
  • Introduce a new term. This requires the ID prefix to be set: Check the Create IDs box on the OBO Explorer tab then Enter 'GO' as the ID prefix. Create a new subclass of cellular_component. Give the new term a Name and a Definition. Associate a DbXRef with the Definition, e.g. by using 'GOC' (GO curator) as the database name and your initials for the accession.
  • Question 2.6 Are you able to create the new term successfully?
    If you are unable enter any data please consult the help file and try once more.
  • un-check the Show names option.
  • Use the menu options File/Save Project As to save the edited file as component_2.owl for future use. Quit Protege
  • Please send your answers and the file component_2.owl to stuart@aiai.ed.ac.uk.