BIRNLex Help

Browsing the BIRNLex OWLDoc view

BIRNLex may be browsed by selecting on the term name from the side menu. A page displaying the term will appear in the main window:

Importing ontologies in Protégé

Follow the guide given at the Protégé describing how to do this correctly in Protégé-OWL. The following points are extremely important to remember:

1. If you add a local OWL file to your Ontology Repository via the OWL ==> Ontology Repository... menu command, be certain to follow the rules for correctly ordering the ontologies in your repository. For instance, if you've created an OWL ontology importing a specific version of an external ontology you have on your local hard drive - e.g., a local version of OBI, PaTO, FMA/CARO - be certain the entry for that local ontology appears higher in the list than any reference you may have to a web-accessible release of that ontology. This way, when Protégé processes the owl:imports statement in your ontology, it will gather the classes to import from the local copy, as opposed to from the web release which may not be the same as your local copy.
2. Should you do this work on one machine, then move the ontologies and Protégé *.ppj project file to another machine, unless the external ontology will be placed at exactly the same path on the new machine, you must again go in to the OWL ==> Ontology Repository... dialog and add this local ontology correctly to your repository.

Displaying the 'preferred label' when viewing OWL classes in Protégé

In order to substitute the preferred label - e.g., 'occurant' as opposed to 'OBI:OBI_1' - follow these instructions to the letter:

• I) Open your BIRNLex OWL file in Protégé v3.2beta.
• II) Select Project ==> Configure...
  • a) click the Options tab
  • b) check the Display Hidden Frames checkbox
  • c) click the OK button
• III) Click back to the OWLClasses tab
• IV) You'll see many new types displayed in the Asserted Hierarchy panel.
  • a) drill into rdfs:Class
  • b) click on the child class owl:Class
• V) Click on the Forms tab
  • a) In the display slot menu select rdfs:label
• VI) Select Project ==> Configure...
  • a) click the "Options" tab
  • b) uncheck the Display Hidden Frames checkbox
  • c) click the OK button
• VII) Click back to the OWLClasses tab

The rdfs:label class property will now be used as the display label for all classes. In order for this to work on all your classes - both those native to the OWL file you are editing, as well as those being imported from ontologies in your Ontology Repository, all the ontologies must use the same class property to store their prefered class label. Our current recommended type to use for this property is the prefLabel type from the Simple Knowledge Organization System (SKOS). Unfortunately, this is not yet a standard practice in the biomedical ontology curation community.