ProtegePluginsLibraryByTopic

This section of our Wiki is a library of plug-ins and applications (organized by topic) 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.    (3PN)

Topics:    (3PO)

• Biomedical Informatics    (3PP)
• Project Management    (3PQ)
• Search & Navigation    (3PR)
• Visualization    (3PS)
• Import & Export    (3PT)
• Inference & Reasoning    (3PU)
• Validation    (3PV)
• Semantic Web    (3PW)
• Terminologies    (3PX)
• Software Engineering    (3PY)
• Date & Time    (3PZ)
• Code Examples    (3Q0)
• Natural Language Processing    (4H4)

Biomedical Informatics    (3Q1)

• Eligibility Screening Tab Widget: Find a set of clinical trial protocols in breast cancer for which a patient might be eligible.    (3Q2)

• UMLS Tab Widget: Search the Unified Medical Language System (UMLS) and annotate your Protégé ontology with terms, concept ids, synonyms, relations, and other information from UMLS.    (3Q3)

Project Management    (3Q4)

• Change Management: Track and annotate changes to Protege ontologies.    (5XJ)

• Project Browser Application: An application that helps manage a library of Protégé projects.    (3Q5)

• PROMPT Tab Widget: Manage multiple 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.    (3Q6)
  • Web site    (3Q7)
  • Wiki page    (3Q8)

• PromptViz Tab Widget: Create visual representations of the differences between two versions of an ontology.    (3Q9)

• Protege Web Browser Application: 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.    (3QA)

Search & Navigation    (3QD)

• InstanceTree Tab Widget: Provides a tree view of frames referenced directly or indirectly by an Instance.    (3QE)

• Search API: An API that implements a number of ways to search a Protégé knowledge base.    (3QF)

• String Search Tab Widget: Search all values of type String in a knowledge base. Search includes classes, slots, instances, slot values, and metaclasses.    (3QG)

• InstanceXL Tab Widget: Provides a spreadsheet view of classes.    (3QXX)

Visualization    (3QH)

• ezOWL Tab Widget: Visual OWL (Web Ontology Language) editor for Protégé.    (3QI)

• FCAView Tab Widget: Visualize Protégé classic or OWL ontologies using the formal concept analysis (FCA) technique.    (3QJ)

• Jambalaya Tab Widget: Visualize Protégé ontologies with SHriMP (Simple Hierarchical Multi-Perspective).    (3QK)

• OntoViz Tab Widget: Visualize Protégé ontologies with the help of Graphviz graph drawing software.    (3QL)

• OWL-S Editor Tab Widget: Load, create, manage, and visualize OWL-S services.    (3QM)

• OWLViz Tab Widget: Navigate OWL ontologies easily and switch between the asserted and inferred model after classification. Protégé colour coding and several export formats are supported.    (3QN)

• PromptViz Tab Widget: Create visual representations of the differences between two versions of an ontology.    (3QO)

• TGViz Tab Widget: Visualize Protégé ontologies using the TouchGraph library.    (3QP)

Import & Export    (3QQ)

• DAML+OIL Storage Backend: Create and edit DAML+OIL ontologies with Protégé.    (3QR)

• DataGenie Tab Widget: Read data from an arbitrary database into Protégé.    (3QS)

• Docgen (Documentation Generator): Provides a quick export of all the content of an ontology (classes, instances and documentation) in various formats (html, pdf, fo...).    (4GG)

• OKBC Tab Widget: Import and export ontologies to and from OKBC servers via the OKBC interface.    (3QT)

• OntoBase Tab Widget: Represent a relational database as an ontology and the database data as an instance tree.    (3QU)

• Oracle RDF Data Model: Manage OWL ontologies developed in Protege in the Oracle RDF store.    (4VR)

• OWL Storage Backend: Load, save, and edit Web Ontology Language (OWL) ontologies in Protégé.    (3QV)
  • Web site    (3QW)
  • Wiki page    (3QX)

• Protégé Server Application: A CORBA-Based server for Protégé.    (3QY)

• Query Export Tab Widget (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.    (3QZ)

• RDF Storage Backend: Create, import, and save RDF(S) files in Protégé.    (3R0)

• Remote KB Tab Widget: Create your own tab to browse a remote knowledge source using a standard API and user interface.    (3R1)

• TX RuleML Tab Widget: Convert Taxonimic RuleML files to corresponding taxonomic class hierarchies in Protégé and vice versa.    (3R2)

• UML Storage Backend: Store a Protege knowledge base in UML.    (5XM)

• XMI Storage Backend: Store a Protégé 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.    (3R4)

• XML Ontology Storage Backend: 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.    (3R5)

• XML Schema Storage Backend: 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.    (3R6)

• XML Tab Widget: Extract Protégé ontologies from XML files and create XML files from Protégé ontologies.    (3R7)

Inference & Reasoning    (3R8)

• Algernon Tab Widget: A rule based inference system implemented in Java and interfaced with Protégé. Performs forward and backward rule-based processing of frame-based knowledge bases.    (3R9)

• CLIPS Tab Widget: Use the CLIPS Rule Engine from within Protégé.    (3RA)

• EZPal Tab Widget: Facilitate acquisition of Protégé Axiom Language (PAL) constraints without knowing the PAL language.    (3RB)

• Flora Query Tab Widget: A query tab based on F-Logic.    (3RC)

• JadeJessProtege Application: An integration of JADE, Jess, and Protégé using the JessTab.    (3RD)

• 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.    (3RE)

• Jess Tab Widget: Allows the use of Jess and Protégé together.    (3RF)

• PDSTab: Visual integrated spatial simulation scenario development and replay environment based on Drools inference engine and Openmap geoinformation system library    (5FL)

• Prolog Tab Widget: An integration of GNU Prolog for Java: with Protégé.    (3RG)

• Protégé Axiom Language (PAL) Tab Widget: Express constraints about a knowledge base and make logical queries about the contents of a knowledge base.    (3RH)

• Protégé Script Console Tab Widget: A scripting interface to Protégé for automating modifications, consistency checking, and queries. Supports languages such as Python, Perl, Beanshell and Ruby.    (3RI)
  • Web site    (3RJ)
  • Wiki page    (3RK)

• PSM Librarian Tab Widget: Browse a Problem-Solving Methods library.    (3RL)

• SWRLTab: An extension to Protege-OWL that supports editing and execution of SWRL rules.    (6GV)

Validation    (3RM)

• Facet Constraints Identify and fix Instances that have constraint violating facets.    (3RN)

• Protégé Axiom Language (PAL): Express constraints about a knowledge base and make logical queries about the contents of a knowledge base.    (3RO)

Semantic Web    (3RP)

• Class Description Display: Allows you to invoke a dialog which contains the description of the selected class in various formats, including the OWL Abstract Syntax, and a Paraphrase/Descriptive style syntax.    (3RQ)

• DAML+OIL Storage Backend: Create and edit DAML+OIL ontologies with Protégé.    (3RR)

• ezOWL Tab Widget: Visual OWL (Web Ontology Language) editor for Protégé.    (3RS)

• iAnnotate: Annotate text or Web documents with OWL ontology concepts.    (4F9)

• OIL Classifier Tab Widget: Classify OIL ontologies with the FaCT descriptions-logic classfier.    (3RT)

• OWL Support: Load, save, and edit Web Ontology Language (OWL) ontologies in Protégé.    (3RU)
  • Web site    (3RV)
  • Wiki page    (3RW)

• Protege Wizards: Easier and faster creation of knowledge bases through wizards supporting task-oriented development.    (3RX)

• OWL-S Editor Tab Widget: Load, create, manage, and visualize OWL-S services.    (3RY)

• OWLViz: Navigate OWL ontologies easily and switch between the asserted and inferred model after classification. Protégé color coding and several export formats are supported.    (3RZ)

• Protege2Jena Import/Export: Import/export Protégé ontologies from/to Jena persistent storage.    (3S0)

• Protege2Joseki Import/Export: Import/export Protégé ontologies from/to Joseki RDF Server.    (3S1)

• RDF Storage Backend: Create, import, and save RDF(S) files in Protégé.    (3S2)

• RDF(s)-DB Storage Backend: Store and load ontology and instance data from a Sesame repository.    (3S3)

Terminologies    (3S4)

• OntoLing Tab Widget: Facilitates terminological enrichment of ontologies and includes an interface for WordNet.    (3S5)

• UMLS Tab Widget: Search the Unified Medical Language System (UMLS) and annotate your Protégé ontology with terms, concept ids, synonyms, relations, and other information from UMLS.    (3S6)

• WordNet Tab Widget: Search WordNet and annotate your Protégé ontology with terms, concept ids, synonyms, relations, and other information from WordNet.    (3S7)

Software Engineering    (3S8)

• Bean Generator Tab Widget: Generate FIPA/JADE compliant ontologies from Protégé projects.    (3S9)

• BeanShell Tab Widget: Interactively use the the Protégé Knowledge-Base API.    (3SA)

• JessAgent Tab Widget: Export Protégé ontologies to Jess in a template based representation.    (3SB)

• JSave Application: Generate Java class definition stubs for Protégé classes.    (3SC)

• Protégé Script Console Tab Widget: A scripting interface to Protégé for automating modifications, consistency checking, and queries. Supports languages such as Python, Perl, and Beanshell.    (3SD)
  • Web site    (3SE)
  • Wiki page    (3SF)

• UML Storage Backend: Store a Protege knowledge base in UML.    (3SG)

• XMI Storage Backend: Store a Protégé 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.    (3SH)

Date & Time    (3SI)

• Date Slot Widget: Automatically fills in a slot value with current date and time.    (3SJ)

Code Examples    (3SK)

• Eligibility Screening Tab Widget: Find a set of clinical trial protocols in breast cancer for which a patient might be eligible.    (3SL)

Natural Language Processing    (4H2)

• Knowtator: Knowtator is a general-purpose text annotation tool that is integrated with the Protégé knowledge representation system. Knowtator facilitates the manual creation of training and evaluation corpora for a variety of natural language processing tasks.    (4H3)