5/6/2023 0 Comments Protege synonymYou may also start typing words from ontology name, and an auto-complete feature will display suggestions. In the BioPortal import panel, select a BioPortal ontology from the drop-down list. The BioPortal Import plugin can be invoked by selecting a class of a domain ontology in the OWL Classes Tab (that will serve as the superclass of the imported classes), and then clicking on the BioPortal Import icon as shown below: This is a screenshot showing the NCI Thesaurus loaded in Protege, and the SNOMED CT terminology browsed in the BioPortal Import Panel. import author, timestamp, source ontology and version, etc.)Ī related plugin to this one that allows users to create reference to classes in BioPortal (rather than importing them) is the BioPortal Reference Plugin. import metadata at the level of a class or the ontology (e.g.choose which (if any) property values to import for each class and assign an equivalent user property for each imported property, if desired.save the imported classes as a separate ontology and/or as a file to the local disk.import entire subtrees of classes from BioPortal ontologies.The import configuration allows the user to customize the import and it includes: The plugin is configurable and works with Protege-OWL. The user can browse the class tree of the selected BioPortal ontology right from the Protege desktop interface, and also view the properties of each class. The BioPortal Import plugin is added as a button to the OWL Classes tab of the Protege-OWL 3.x user interface. However, ontologies denoted as remote in BioPortal cannot be explored in the plugin, since BioPortal does not provide the information for these ontologies through its REST services. The plugin uses the BioPortal REST services to access and import the content of BioPortal ontologies. import them as subclasses of the selected class in the local ontology.select one or more classes to import from the BioPortal ontology,.browse through the BioPortal ontologies (except remote ones) and select which one to import classes from.The basic steps in using the plugin are to: If you are using Protege 4 to develop your ontology, you can still use this plugin by opening the OWL file in Protege 3.x, make the import, save, and then continue to develop the ontology in Protege 4. We plan to have an implementation of this plugin also in Protege 4 as part of the future work. This plugin works with the Protege 3.x releases, not Protege 4.x releases. The plugin allows a user to import classes from external ontologies and terminologies stored in the BioPortal ontology repository into the local ontology. Go to File menu -> Open from URL, and paste the link in the box.Copy the download link of the ontology from the ontology summary view in BioPortal (e.g., right-click on the link -> Copy link address).To open the BioPortal ontology in Protege 5.x, do these simple steps: Follow this GitHub issue for updates.Īs a work around for now, you may open the BioPortal ontology directly in Protege 5.x, and edit it (for example, extract branch by deleting the rest of the ontology, or by using the Refactor menu -> Copy/move/delete axioms). We plan to add this functionality to WebProtege. As of May 2014, the BioPortal Import plugin does not work anymore.īioPortal has updated its REST APIs and the plugin has not been ported to the new API, yet.
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