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Getting Started with the NIF Ontologies

Information is available about the current state of the NIF Import Tree

Download Protege

Download Notepad++

Notepad++ URL: http://notepad-plus.sourceforge.net/uk/site.htm

  • A preferred way of editing the actual text of the owl file.

Fix memory issue in Protege

If you do not do this, Protege runs out of memory and will not be able to load NIF (there are many many terms in NIF).

  • For Windows users: Go to the Protege directory and find the protege.lax file. Open it in Notepad (important that you use Notepad) and find the property "lax.nl.option.java.heap.size.max" and add a zero to the end of the number and save the file.
  • For Mac users: Go to Protege directory and open the protege start up script 'run_protege.sh' in a text editor. Then, look for the parameter under JVM Option called MAXIMUM_MEMORY. The parameter is usually set to -Xmx100m by default. Change the parameter to some larger value such as -Xmx1024m or better -Xmx2048m depending on your RAM size. Save the 'run_protege.sh' script and run it via shell.

For more complete information, view documentation here: http://protegewiki.stanford.edu/index.php/Setting_Heap_Size

Instructions for loading NIF ontology

  1. Open Protege (http://protege.stanford.edu/)
  2. Select New Project
  3. Click the checkbox for "Create from existing source" and highlight "OWL/RDF Files"
  4. NIFSTD URL on our server: http://purl.org/nif/ontology/nif.owl
  5. You can keep clicking "Next" or just click "Finish" It will take awhile.

Also, if you don't want to look at the ontologies in Protege, you can either look at them in Notepad++ or in your internet browser.

Loading Specific NIF Module(s)

The current NIF owl modules with their PURLs are listed below.

 

  1. Open Protege and select New Project
  2. Click the checkbox for "Create from existing source" and highlight "OWL/RDF Files"
  3. In Metadata tab locate the ontology browser on the left and click the first button on the top (mouse over the button says "Import Ontology...")
  4. Select "Import an ontology from the web by specifying the http:// ... URL"
  5. Enter the URL of the NIF module you wish to view
  6. Repeat step 4 to 6 if you want to view additional module(s) together
In order to view the rdfs:label of classes and properties (aka, the recognizable names and not the IDs):
  1. Select File-->Preferences..--> Renderer
  2. Under 'Entity rendering', select 'Render by annotation property' (e.g., rdfs:label, skos:prefLabel)

Now you will be able to view all the preferred labels for both classes and properties.

In order to search the classes through their synonymous terms (or other annotation properties):
  1. Under OWL menu, navigate to 'Preferences'
  2. Select 'Searching' tab and click on 'Add property..' button (a button with '+' symbol)
  3. Select obo_annot:synonym, obo_annot:acronym etc. from the 'Add search properties' listbox and click close

Now you will be able to search the classes through synonyms, acronyms, and/or other annotation properties in Protege.

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