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Advanced Annotation Search
A search function to find entities based on annotation data.
BioPortal Reference Plugin
The BioPortal Reference Plugin allows the user to insert into the ontology references to external ontologies and terminologies stored in BioPortal.

The ClojureTab uses the Clojure programming language for simple programming in the Protege environment, on-the-fly debugging, and storing programs in Protege projects. Contains: 1. Integrated development environment for Clojure language ( 2. Protege API for Clojure language 3. Rule engine and Expert system shell rete4frames ( 4. Algorithms visual development environment

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Instance Selection
This plug-in adds both navigation and export features to Protege-Frames. It provides a tree view of the knowledge base as well as allows the selection of instances for data preparation and consequent export in several data mining workbench formats such as Weka and text.
Provides a tree view of frames referenced directly or indirectly by a Protege instance.
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A query tool for repositories of ontologies. The tool allows to define a repository, either local or remote -via URIs. The tool makes it possible for users to define a query and execute it against the predefined repository
OWL2Query is a conjunctive query and metaquery engine (for SPARQL-DL and negation as failure), and visualization plug-in. It facilitates creation of queries using SPARQL or intuitive graph-based syntax, and evaluates them using any OWL API-compliant reasoner.
This plugin goal is to help ontologists searching for relevant vocabularies in the Linked Open Data (LOV) catalogue, for easing the development of ontologies by reusing existing vocabularies at low fine grained level. The tool helps to improve the modeling and reuse of ontologies used in the LOD cloud.
Queries and Export Tab
This plug-in allows you to query knowledge-bases and export the results. An export button was added to the query-results window to allow for tabular export of selectable slot values of all found result-instances.
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Provides support for composing and executing SPARQL queries from within Protege's user interface.
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SWRL-IQ (Semantic Web Rule Language Inference and Query tool) is a plugin for Protege 3.4.x that allows users to edit, save, and submit queries to an underlying inference engine based on XSB Prolog.
[[Image:|thumb|170px|center]] Search API
Augmented search API that implements a number of ways to search an in-memory frame-based Protege knowledge base.
Snow Owl
Snow Owl is a free SNOMED CT browser and authoring tool integrating Protégé.
String Search Tab
Search all values of type String in a knowledge base. Search includes classes, slots, instances, slot values, and metaclasses.
[[Image:|thumb|170px|center]] Watson Search Preview
This plug-in shows a preview of a search in Watson. Whenever a class is selected, the Watson Search Plugin searches for that term and provides the top results. This is more a proof of concept or an example than a real plugin. If you are searching for something more powerful, see

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