This section of our Wiki is a guide to plug-ins and applications (alphabetically organized within type) that are of potential interest to our user community. They were developed both here at Stanford Medical Informatics (SMI) and outside of Stanford. We encourage you to add links to your plug-ins and applications. If you have questions about specific plug-ins, please contact individual authors. (3SM)
Note: The notation "(LR)", following a package name, indicates that the package has known licensing restrictions on use, redistribution, etc. That is, it is not Open Source. (4UG)
Types: (3SN)
- APIs (7YJ)
- Applications (3SO)
- Backends (3SP)
- Import/Export (3SQ)
- Project (3SR)
- Slot Widgets (3SS)
- Tab Widgets (3ST)
APIs (7YI)
- Search API: Implements a number of ways to search a Protege knowledge base (7YK)
Applications (3SU)
- JadeJessProtege: An integration of JADE, Jess (LR), and Protégé using the JessTab. (3SV)
- Neuron Web Services: Provides a WSDL Web Services interface to the Protégé Server, enabling access to the server using SOAP/HTTP from any SOAP standard client. (4JK)
- Neuron Spreadsheet: Uses Neuron Web Services to download views of your knowledge base instance information into an Excel spreadsheet, for example for analysis. (5C3)
- Ontology Navigator: Semantic Web search engine platform and tools. Allows users to navigate their ontologies. (4M2)
- Project Browser: An application that helps manage a library of Protégé projects. (3SX)
- Protégé Server: A CORBA-Based server for Protégé. (3SY)
- Protege Web Browser: A Java-based Web application that allows users to share, browse, and do some basic editing of Protege knowledge bases via the World Wide Web. (3SZ)
Backends (3T2)
- Java Function Calls Slot Widgets and Storage Backend: A group of plug-ins that allows the description of things in flux, activities, and processes which cause a knowledge base to change over a time scale. (3T4)
- OWL: Load, save, and edit Web Ontology Language (OWL) ontologies in Protégé. (3T5)
- RDF Storage Backend: Create, import, and save RDF(S) files in Protégé. (3T8)
- XMI: Store a Protege knowledge base as XMI files. XMI is a standard format for metadata exchange supported by OMG, the group that is responsible for standards such as UML, CORBA and the Common Warehouse Metamodel. (3TB)
- XML Ontology: Store a Protégé knowledge base in XML. Classes are represented in a Schema file as types and instances are output into an XML document instance conforming to the generated schema. (3TC)
- XML Schema: Store a Protégé knowledge base in XML. The backend will generate an XML Schema file which conforms to the Protégé knowledge model and an XML file which contains classes and instances. (3TD)
Import/Export (3TE)
- Data Genie: Inports data from an arbitrary database into Protégé. (3U0)
- Docgen (Documentation Generator): provides a quick export of all the content of an ontology (classes, instances and documentation) in various formats (html, pdf, fo...). (4G4)
- OBO ImportTab: Imports OBO format files into Protégé (frames). (3UC)
- OBOConverter: Imports and converts OBO format files into Protege-OWL using the OBO to OWL mapping described at http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page (8DJ)
- Oracle RDF Data Model: Manage OWL ontologies developed in Protege in the Oracle RDF store. (4VS)
- OWL2XHTML Tab: Lightweight tabwidget plugin for exporting an OWL ontology to a single HTML file. (4LJ)
- Protege2Jena: Import/export Protégé ontologies from/to Jena persistent storage. (3TF)
- Protege2Joseki: Import/export Protégé ontologies from/to Joseki RDF Server. (3TG)
- Query Export Tab (by D. Schober and T. Tudorache): Query Protégé knowledge bases as with the QueryTab and export the results (classes, slots, instance names, or slot values) as a tab-delimited text file for further processing in spreadsheet-based tools. (3TH)
- Reporting Database (by Frank Sauer & Christopher Creel): XSL to convert the XML file that Protege can use as a back-end to a SQL statement to create a fully normalized reporting database. This is very handy for creating recurring, canned reports using technologies like Jasper Reports (8PE)
Project (3TI)
- Collaborative Protégé: Extension of Protégé that supports the collaborative ontology development process (9AR)
- Protégé Wizards: Easier and faster creation of knowledge bases through wizards supporting task-oriented development. (3TJ)
Slot Widgets (3TK)
- Bayesian Network (LR): Make approximate inferences over ontologies where classes are arranged in DAG form. (3TL)
- DateWidget: Automatically fills in a slot value with current date and time. (3TM)
- Display Indirect Instances: Automatically displays all the indirect instances of a class. (3TN)
- Enhanced Standard Widgets: Enhanced versions of most of the commonly used widgets in Protégé. (3TO)
- Java Function Calls Slot Widgets and Storage Backend: A group of plug-ins that allows the description of things in flux, activities, and processes which cause a knowledge base to change over a time scale. (3TQ)
- Measurement: Provides flexible measurement entry. (3TR)
- Power-plant Control: Edit control rules for a simple nuclear power plant simulator. (3TT)
- Swap Values: Swap slot values between slots. (3TU)
Tab Widgets (3TV)
- Algernon: A rule-based inference system implemented in Java and interfaced with Protégé. Performs forward and backward rule-based processing of frame-based knowledge bases. (3TW)
- OntologyBeanGenerator: Generate FIPA/JADE compliant ontologies from Protégé projects. (3TX)
- Change Management: Track and annotate changes to Protege ontologies. (5X1)
- CLIPSTab: Use the CLIPS Rule Engine from within Protégé. (3TZ)
- DataMaster: Import schema structure and data from relational databases into Protege. (9C9)
- Eligibility Screening: Find a set of clinical trial protocols in breast cancer for which a patient might be eligible. (3U1)
- ezOWL: Visual OWL (Web Ontology Language) editor for Protégé. (3U2)
- EZPal: Facilitate acquisition of Protégé Axiom Language (PAL) constraints without knowing the PAL language. (3U3)
- Facet Constraints: Identify and fix Instances that have constraint violating facets. (3U4)
- FCAView: Visualize Protégé classic or OWL ontologies using the formal concept analysis (FCA) technique. (3U5)
- FOAM Plugin Tab Widget: This Plugin performs mapping between two ontologies based on similaity heuristics of the individual entities (concepts, relations and instances). (733)
- Formal Concept Analysis (FCA): Demonstrate the benefit of applying FCA while building an ontology. (3U6)
- GrOWL Tab Widget: Visualize OWL ontologies using GrOWL visualization model. (9AI)
- InstanceTree: Provides a tree view of frames referenced directly or indirectly by a Protege instance. (3U8)
- InstanceXL: Provides a spreadsheet representation of classes. (3UXX)
- JBRSTab: Visual integrated spatial simulation scenario development and replay environment based on JBoss Rules inference engine and Openmap geoinformation system library (5FK)
- JessAgentTab: Export Protégé ontologies to Jess (LR) in a template-based representation. (3UA)
- Knowtator: Knowtator is a general-purpose text annotation tool that facilitates the manual creation of training and evaluation corpora for a variety of natural language processing tasks. (4H5)
- nRQL Tab Plugin: Racer Query Language interface to Protégé ontologies using Racer reasoner. (3UZ)
- OBO ImportTab: Imports OBO format files into Protégé. (3UC)
- OBOConverter: Imports and converts OBO format files into Protege-OWL using the OBO to OWL mapping described at http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page (8DJ)
- OBO Explorer: Provides an editor for OBO terms, i.e. for the synonyms, subsets, DbXRefs and other annotations that are associated with OBO terms as defined by the OBO to OWL mapping http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page (8PB)
- OIL Classifier: Classify OIL ontologies with the FaCT descriptions-logic classifier. (3UD)
- OntoBase (LR): Represent a relational database as an ontology and the database data as an instance tree. (3UF)
- OntoLing: Facilitates terminological enrichment of ontologies and includes an interface for WordNet (from 1.6 to 2.0) and DICT dictionaries. (3UG)
- OpenMAP Tab: Combine spatial simulation and the geoinformation system (GIS) functionality of OpenMAP with Protégé's knowledge representation functionality. (3UJ)
- OpenOME plug-in for Protégé: OpenOME is a toolset to support goal-oriented, agent-oriented and aspect-oriented requirements engineering. (3UK)
- OWL-S Editor: Load, create, manage, and visualize OWL-S services. (3UL)
- OWLViz: Navigate OWL ontologies easily and switch between the asserted and inferred model after classification. Protégé colour coding and several export formats are supported. (3UM)
- Prolog: An integration of GNU Prolog for Java: with Protégé. (3UN)
- Wiki '''PROMPT''': Manage multiple ontologies, create a mapping between ontologies, merge separate ontologies to create a single coherent ontology, extract a part of an ontology, and move frames from an included to an including project. (3UO)
- PromptViz (LR): Create visual representations of the differences between two versions of an ontology. (3UR)
- Protege Axiom Language (PAL): Express constraints about a knowledge base and make logical queries about the contents of a knowledge base. (3US)
- Protege Script Console Tab Widget: A scripting interface to Protege for automating modifications, consistency checking, and queries. Supports languages such as Python, Perl, Beanshell and Ruby. (84W)
- PSM Librarian: Browse a Problem-Solving Methods library. (3UW)
- Relations Tab: Browse reified relations in the same way you can browse regular relations. (3UX)
- Remote KB: Create your own tab to browse a remote knowledge source using a standard API and user interface. (3UY)
- ScriptRules: a prototype plugin for developing and executing 'scriptrules' using a graphical interface (9F1)
- String Search: Search all values of type String in a knowledge base. Search includes classes, slots, instances, slot values, and metaclasses. (3V0)
- TGVizTab: Visualize Protege ontologies using the TouchGraph library. (3V1)
- TMTab (Topic Map Tab) (LR): Build an ontology which may be exported as a topic map in XTM syntax. (3V2)
- TX RuleML: Convert Taxonomic RuleML files to corresponding taxonomic class hierarchies in Protege and vice versa. (3V3)
- UMLS Tab: Search the Unified Medical Language System and annotate your Protege ontology with terms, concept IDs, synonyms, relations, and other information from UMLS. (3V4)
- Velocity Tab : You can generate reports and other kind of file output from the OWL Model using the power of the Velocity templating engine from Apache Jakarta project (alpha code) (82X)
- WordNet Tab: Search WordNet and annotate your Protege ontology with terms, concept ids, synonyms, relations, and other information from WordNet. (3V5)