Protege Wiki - User contributions [en]

Protege4Migration

2011-07-09T15:22:41Z

Joyservice:

<div class="orangeBox">
<span class="orangeBoxTitle">Choosing between versions of Protege</span><br /><br />
This page contains a high level outline of the major differences in features between Protege 3.4 and Protege 4.0.
</div><br />

__TOC__

== Overview ==
There are a number of differences between Protege 3.4 and 4.0. This page is designed to highlight some of the major factors that may influence which of the two systems would be most appropriate for your project at present. It will also serve as a useful reference point for identifying major features that need priority migration from 3.4 to 4.0. This list is by no means exhaustive and is only intended as an overview.

== Recommendations ==

=== Frames ===

For working with '''frames-based ontologies''' there is only one choice - Protege 3.4 is built on a very mature and stable codebase. Frames support is not currently available in P4.x.

=== OWL (and RDF) ===

For working with '''OWL''', there are several factors that may influence your decision on whether to use 3.4 or 4.x.

==== Developers ====

For coders writing '''purely OWL applications''', we recommend 4.x. For applications where you cannot cleanly break away from '''RDF''' you should consider 3.4.

Protege 4.x uses the open source, Java-based [http://owlapi.sourceforge.net/ OWL API] that is proving popular with many developers around the world. This makes writing or migrating to and from other systems more straightforward, and a larger developer community means more assistance and a more robust codebase. In addition, the OWL API supports much of the upcoming OWL 2.0 recommendation.

However, for developers that require access to the RDF model at the level of a triple store, the [http://protege.stanford.edu/plugins/owl/api/index.html Protege-OWL API] from Stanford is an option. This API was built on top of the older frames-based system, i.e., RDF and OWL constructs are layered over Protege's frame objects. This is much harder to develop with as all levels of abstraction are visible at the API level, but allows for more control over the relationship between the different models.

==== Users ====

For ontology developers the choice is harder as the tasks that any given user/application needs to perform can be very different. For users creating purely '''OWL''' ontologies or
needing OWL2.0 features we would recommend P4.x. For users wanting access to '''RDF''' or that require particular tools that have not yet been converted, P3.x is currently still the choice.

Ultimately, P3.x is coming to a stable state such that the features of the platform are well known and the behaviour is predictable. There are many plugins available that aid particular tasks
that are not currently available for P4.x. So for example, those wanting SWRL support will find the framework in P3.x much more substantial than in P4.x. Equally, users that need access
to RDF(S) level constructs will need to use P3.x.

P4.x is much more lightweight, being a wholly OWL editing environment currently, and is therefore optimised considerably for dealing with even modestly large OWL ontologies in memory.
The number of groups producing additional tools for visualisation, mining etc is growing. The framework uses more standard mechanisms for customisation and can therefore be more easily tuned to a particular group's workflow. P4.x will also support all OWL2.0 features, such as QCRs, role chains, additional property characteristics etc, many of which are already implemented.

== Side by Side Comparison ==
{| cellpadding="3" cellspacing="3" style="border:1px dashed #BC8F8F;"
! align="left" width="50%" | Protege 3.x
! align="left" width="50%" | Protege 4.0
|-
| style="border-bottom:1px dashed #BC8F8F;" | [[Image:p3.3.png|frame|left|Protege 3 Screenshot]]
| style="border-bottom:1px dashed #BC8F8F;" | [[Image:p4.0.png|frame|left|Protege 4 Screenshot]]
|-
| '''Frames Support''' || '''Frames Support'''
|-
| valign="top" style="border-bottom:1px dashed #BC8F8F;" | Frames editing supported via the [http://protege.stanford.edu/overview/protege-frames.html Protege-Frames editor]
| valign="top" style="border-bottom:1px dashed #BC8F8F;" | None (Protege-Frames editor has not been migrated yet)<br /><br />
|-
| '''OWL Support''' || '''OWL Support'''
|-
| '''[http://www.w3.org/2004/OWL/ OWL 1.0]''' language support
| '''[http://www.w3.org/2007/OWL/wiki/OWL_Working_Group OWL 2.0]''' language support
|-
| OWL and RDF(S) support
| Pure OWL framework
|-
| valign="top" | OWL and RDF(S) files are accessible via the [http://protege.stanford.edu/plugins/owl/api/index.html Protege-OWL API]. This API layered OWL and RDF support over the existing Frames API.
| valign="top" | OWL files are accessible via the [http://owlapi.sourceforge.net/ OWL API], which was developed at the [[The University Of Manchester]] (''not the Protege-OWL API, which was used in the 3.x series''). This is a very clean API that closely follows the OWL specification and the parser is optimized to be faster and use less memory.
|-
| SPARQL support
| No SPARQL support yet
|-
| SWRL support through the SWRLTab
| SWRL support through a basic editor and pellet for reasoning
|-
| Support for meta-modeling (allowing OWL Full)
| No OWL Full
|-
| valign="top" | Reasoner support through HTTP DIG interface allows connection to any DIG compliant reasoner, as well as direct connection to the Pellet reasoner
| valign="top" | Direct connection to FaCT++, Pellet and other DL reasoners for optimum speed of classification
|-
| valign="top" | Configuration settings stored in Protege Project files (.pprj)
| valign="top" | Configuration settings global (No project files). Preferences persist across installations of Protege
|-
| valign="top" style="border-bottom:1px dashed #BC8F8F;" | OWL imports [http://protege.stanford.edu/doc/owl/owl-imports.html handled through a repository mechanism]
| valign="top" style="border-bottom:1px dashed #BC8F8F;" | Imports resolution from a common folder, user repositories or the web<br /><br />
|-
| '''Plugins''' || '''Plugins'''
|-
| valign="top" | Plugin framework developed at Stanford for tab widgets, slot widgets, back-ends, projects, importing, and exporting
| valign="top" | Plugin framework has been switched to the more industry standard technology, [http://www.osgi.org/osgi_technology/index.asp?section=2 OSGi], which allows for any type of plugin extension
|-
| valign="top" style="border-bottom:1px dashed #BC8F8F;" | Large set of plugins available, developed both in-house and externally by the Protege community
| valign="top" style="border-bottom:1px dashed #BC8F8F;" | Large set of plugins available, developed both in-house and externally by the Protege community<br /><br />
|-
| '''User Interface''' || '''User Interface'''
|-
| valign="top" | Tab and slot widgets make much of user interface configurable
| valign="top" | Plugins define all user interface elements including tabs, views, and menus making everything configurable
|-
| Support fill-in-the-blank style of setting property values in individuals
| Property values of individuals are added as axioms
|-
| valign="top" style="border-bottom:1px dashed #BC8F8F;" | Access is provided to the meta model and can be used to configure the user interface
| valign="top" style="border-bottom:1px dashed #BC8F8F;" | Menu and drag and drop user interface elements
|-

<br /><br />
|-
| '''Multi-user Support''' || '''Multi-user Support'''
|-
| valign="top" style="border-bottom:1px dashed #BC8F8F;" | Multiple users can edit the same ontology using the [[Protege_Client-Server_Tutorial|client-server version of Protege]]
| valign="top" style="border-bottom:1px dashed #BC8F8F;" | None ([[Protege_Client-Server|Protege Client-Server]] has not been migrated yet)<br /><br />
|-
| '''Database Storage Model''' || '''Database Storage Model'''
|-
| valign="top" | Ability to store ontologies in a database provided by the [http://protege.stanford.edu/doc/design/jdbc_backend.html|Protege JDBC database back-end]
| valign="top" | None (database back-end has not been migrated yet)<br /><br />
|}
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Protege Ontology Library

2011-07-09T15:21:51Z

Joyservice: /* Other ontology formats */

__NOTOC__
<div style="background:#F0E6CA; border:1px solid #AE5B08; padding:10px 15px 10px 20px; margin:2em 0 0 0;">
=== Welcome to the Protege Ontology Library! ===

This page is organized into the following groupings:

* [[#OWL_ontologies|OWL ontologies]]
* [[#Frame-based_ontologies|Frame-based ontologies]]
* [[#Other_ontology_formats|Ontologies in other formats (e.g., DAML+OIL, RDF Schema, etc.)]]

If your ontology is available in multiple formats, please feel free to link to it from multiple sections.

''Please make insertions in alphabetical order. Thank you !!!''
</div><br />

== OWL ontologies ==

Information on how to open OWL files from the [http://protege.stanford.edu/overview/protege-owl.html Protege-OWL editor] is available on the main Protege Web site. See the [http://protege.stanford.edu/doc/owl/getting-started.html#creating_loading Creating and Loading Projects] section of the [http://protege.stanford.edu/doc/owl/getting-started.html Getting Started with Protege-OWL] Web page. Other ways to search for OWL ontologies include using Google: http://www.google.com/search?q=filetype:owl+owl, or the Semantic Web search engine [http://swoogle.umbc.edu/ Swoogle].

* [http://www.aimatshape.net/resources/aas-ontologies AIM@SHAPE Ontologies]: Ontologies pertaining to digital shapes. Source: [http://www.aimatshape.net/ AIM@SHAPE NoE] - Advanced and Innovative Models And Tools for the development of Semantic-based systems for Handling, Acquiring, and Processing knowledge Embedded in multidimensional digital objects.

* [http://www.co-ode.org/ontologies/amino-acid/2005/10/11/amino-acid.owl amino-acid.owl]: A small OWL ontology of amino acids and their properties. Source: [http://www.co-ode.org/ontologies/amino-acid/2005/10/11/ Amino Acid Ontology Web site].

* [http://www.ifomis.uni-saarland.de/bfo/ Basic Formal Ontology (BFO)]

* [http://transontology.org/bhakti_gaudiya/bhakti.owl bhakti.owl]: An OWL ontology for the transcendental states of consciousness experienced by practitioners of bhakti-yoga, a form of Vedic consciousness engineering.

* [http://dumontierlab.com/?page=ontologies Biochemical Ontologies]: Over 30 ontologies for knowledge representation and reasoning across scientific domains. Ontologies are normalized into non-disjoint primitive skeletons and complex class expressions for DL reasoning. Ontologies describe atoms, bonds, molecules, macromolecules and the processes they participate in.

* [http://www.biopax.org/ BioPAX]: An OWL ontology for biological pathways, which is primarily used to exchange data between pathway resources.

* [http://www.nbirn.net/birnlex/ BIRNLex]: An ontology created by and for the [http://www.nbirn.net/ Biomedical Informatics Research Network (BIRN)] in order to provide a shared semantic framework in which to annotate BIRN data related to multi-resolutional, cross-species studies of neurodegenerative disease. BIRNLex follows the OBO Foundry best practices and makes use of other OWL-based OBO ontologies.

* [http://www.dataindia.org/ontologies/OntoBlackPepper.owl Black Pepper Ontology]: A black pepper ontology created for [http://www.dataindia.org DataIndia.ORG] to provide support for farm automation and agro-processing. Joint project between [http://www.amaljyothi.com/ AMAL JYOTHI College of Engineering] and [http://www.drmgrdu.ac.in Dr. M.G.R. University].

* [http://acl.icnet.uk/~mw BreastCancerOntology]: An OWL ontology for describing some features of Breast Cancer; Basic model is stable, but still being fleshed out.

* [http://protege.cim3.net/file/pub/ontologies/camera/camera.owl camera.owl]: An OWL ontology about the individual parts of a photo camera. Source: [http://www.xfront.com/ XFront OWL Tutorial].

* [http://www.bltk.ru/OWL/camera2.owl camera2.owl]: An improved OWL camera ontology based on above one from Roger L. Costello. Contributed by [mailto:igor_bessmertny@hotmail.com Igor Bessmertnyy].

* [http://www.cellcycleontology.org/ Cell Cycle Ontology (CCO)]: An application ontology for the cell cycle process.

* [http://users.ecs.soton.ac.uk/cm7e09/files/cinemaChain.owl Cinema Chain Ontology]: An ontology for modelling cinemas that have screenings of films. Contributed by [http://ecs.soton.ac.uk/~cm7e09 Connor McCabe]

* [http://kt.ijs.si/software/CNOntology/cno.html CN Ontology]: An OWL ontology presenting the concepts used in collaborative networked organizations with focus on Virtual Organizations Breeding Environment.

* [http://www8.informatik.uni-erlangen.de/IMMD8/Services/cidoc-crm/index.html CIDOC CRM Erlangen Implementation]: An OWL DL ontology implementing the [http://cidoc.ics.forth.gr/ CIDOC CRM] (ISO 21127:2006).

* [http://kaiko.getalp.org/kaiko/ontology/colors.owl Colors] : Color list (690 elements) with standard color representation values (RGB, HSV, etc.) in OWL format. Built from the list found in [http://en.wikipedia.org/wiki/List_of_colors Wikipedia] on the 6th of june 2010. Available under the Creative Commons Attribution-ShareAlike License.

* [http://transontology.org/consciousness/consciousness1.owl consciousness1.owl]: An OWL ontology showing the transcendental background for consciousness according to the ancient Vedic literature.

* [http://on.cs.unibas.ch/owl/1.0/Context.owl Context.owl]: An OWL ontology presenting a generic context model that can be used for describing the structure and elements of context aware systems. It is developed in the context of [http://dbis.cs.unibas.ch/projects/ongoing-projects/loca/dbis_project_view LoCa], a Swiss National Research Project. Contributed by [http://dbis.cs.unibas.ch/team/thorsten-moller/dbis_staff_view Thorsten Möller].

* [http://www.bpiresearch.com/BPMO/2004/03/03/cdl/Countries countries.owl]: The ISO 3166 Code List of countries. Contributed by [http://www.jenzundpartner.de/index.htm Dieter E. Jenz].

* [https://mywebspace.wisc.edu/jpthielman/web/DaycareOntology.htm Daycare.swrl.owl]: A demo ontology about a childcare center showing the use of SWRL for reasoning. Contributed by [mailto:peace@wisc.edu Jane Peace].

* [http://www.nada.kth.se/~mehrana/Delegation.owl Delegation Ontology]: An OWL ontology to describe delegation concepts in the context of Grid computing.

* [http://www.ecs.soton.ac.uk/~aoj04r/resist.owl Dependable Systems Ontology]: Ontology about resilient and dependable systems including threats, failures, faults and errors as used in the [http://www.resist-noe.eu ReSIST] project.

* [http://serdis.dis.ulpgc.es/~a013715/aic/ontologias/ Dietas]: Esto es una ontología en OWL no terminada que simula un dietista.

* [http://dolce.semanticweb.org/ DOLCE]: The Dolce foundational ontology and its extensions provide a domain-independent framework to build ontologies on the basis of highly-reusable patterns. Contributed by [mailto:aldo.gangemi@istc.cnr.it Aldo Gangemi].

* [http://www.danmccreary.com/presentations/semweb2006/ K-12 Education Ontology]: Ontology for the Minnesota Department of Education based on the National Information Exchange Model (NIEM) structures and ISO/IEC 11179 standards. This domain includes information about K-12 students, teachers, schools, districts, enrollments, assessments, USDA food and nutrition programs, and on-line courses. Includes approximately 400 data elements. The OWL file is an report of the metadata registry. Paper and Slide Materials included from the 2006 Semantic Technology conference. Feedback -> [mailto:dan@danmccreary.com Dan McCreary]

* [http://trajano.us.es/%7Eisabel/EHR/ EHROntology]: An Electronic Health Records ontology based on openEHR work. Contributed by [http://trajano.us.es/%7Eisabel Isabel Roman Martinez].

* [http://www.iis.nsk.su/persons/ponom/ontologies/ Einstein's riddle]: Have you ever tried to solve the famous Einstein's logic puzzle? It is claimed that only 2% of the world's population can solve it! A Description Logic reasoner can do it for you just in one click. Here you find a formulation of the puzzle in ALCOIF description logic. It contains the original formulation of the puzzle from [http://en.wikipedia.org/wiki/Zebra_puzzle http://en.wikipedia.org/wiki/Zebra_puzzle]. For convenience, all key axioms in the ontology are provided with annotation, a corresponding condition of the puzzle. Just classify this ontology in Protege and get a solution by clicking on individuals! Contributed by [http://www.iis.nsk.su/persons/ponom/ Denis Ponomaryov].

* [http://edesign.ecs.umass.edu/index.php?n=Research.Ontologies Engineering Design Ontologies]: A suite of ontologies developed at the University of Massachusetts Amherst for representing different aspects of the product development process.

* [http://www.csm.ornl.gov/~7lp/esg-owl/ESG1.1.owl ESG]: An ontology describing very large simulation datasets and related information for climate sciences such as those found in the [http://www.earthsystemgrid.org/ Earth System Grid] project. Contributed by [http://www.csm.ornl.gov/~7lp Line Pouchard].

* [http://protege.cim3.net/file/pub/ontologies/family.swrl.owl/family.swrl.owl family.swrl.owl]: A SWRL/OWL demo ontology about family relationships . Contributed by Christine Golbreich.

* [http://www.osera.gov/owl/2004/11/fea/FEA.owl Federal Enterprise Architecture Reference Model Ontology (FEA-RMO)]: Representation of Federal Enterprise Architecture in OWL.

* [http://www.fadyart.com/ontologies/data/Finance.owl Finance]: an ontology on financial instruments, involved parties, processes and procedures in securtities handling. Contributed by [http://www.fadyart.com/financeOntologyEN.htm Eddy Vanderlinden].

* [http://loki.cae.drexel.edu/~wbs/ontology/fgdc-csdgm.htm fgdc-csdgm.owl]: Ontology for Content Standard for Digital Geospatial Metadata (CSDGM) of Federal Geographic Data Committee (FGDC). Contributed by Akm Saiful Islam, Bora Beran, Volkan Yargici, and Michael Piasecki.

* [http://www.l3s.de/%7Edolog/fsm/index.html fsm.owl]: A simple ontology for finite state machines. Contributed by [http://www.learninglab.de/~dolog/index2.html Peter Dolog].

* [http://xmlns.com/foaf/spec/index.rdf FOAF Ontology]: An ontology describes people, the links between them and the things they create and do. Contributed by [http://xmlns.com/foaf/spec/ Dan Brickley and Libby Miller].

* [http://protege.cim3.net/file/pub/ontologies/generations/generations.owl generations.owl]: An ontology about family relationships that demonstrates classification. Contributed by [http://www.cs.man.ac.uk/~horridgm Matthew Horridge].

* [http://loki.cae.drexel.edu/~wbs/ontology/ Geographic Information Metadata - ISO 19115]: An ontology representing Geographic Information Metadata - (ISO 19115).

* [http://i2geo.net/ontologies/current/GeoSkills.owl GeoSkills]: an ontology representing the mathematics competencies, topics, and educational levels for schools of Europe. See the page [http://i2geo.net/xwiki/bin/view/About/GeoSkills about GeoSkills].

* [http://loki.cae.drexel.edu/%7Ehow/HydrologicUnits/hu hu.owl]: A hierarchic division of hydrologic units. Contributed by [http://loki.cae.drexel.edu/%7Ehow/Hydrologic_Units_ontology.html Luis Bermudez].

* [http://individual.utoronto.ca/hesham/DetailedResearch.htm Infrastructure Product Ontology]: An OWL ontology for utility infrastructure products, their attributes, mechanisms, and measures. Products span all five sectors of utilities (Water, Wastewater, Gas, Electricity, and Telecom).

* [http://loki.cae.drexel.edu/%7Ewbs/ontology/list.htm iso-metadata.owl]: Several ISO Geographic Information Ontologies developed with the Protege-OWL editor. Contributed by Akm Saiful Islam, Bora Beran, Luis Bermudez, Stephane Fellah & Michael Piasecki.

* [http://protege.cim3.net/file/pub/ontologies/ka/ka.owl ka.owl]: Defines concepts from academic research. Contributed by [http://www.cs.man.ac.uk/%7Ehorrocks/ Ian Horrocks].

* [http://protege.cim3.net/file/pub/ontologies/koala/koala.owl koala.owl]: A simple ontology about humans and marsupials. Contributed by [http://www.knublauch.com/ Holger Knublauch].

* [http://lifeeventontology.googlepages.com/leo.owl leo.owl]: A simple ontology about life events within e-Government. Contributed by [http://domen.cukjati.googlepages.com/home Domen Cukjati].

* [http://www.estrellaproject.org/lkif-core LKIF Core]: A core ontology of basic legal concepts. Contributed by [http://www.leibnizcenter.org/users/rinke Rinke Hoekstra].

* [http://protegewiki.stanford.edu/images/d/de/Monetary_ontology_0.1d.zip Monetary_ontology_0.1d.zip]: A zipped Protégé project of an ontology for currency creation and use. Also contains an "owl". The objective is an active description of all forms of "money" from barter to clearing systems, from precious metal coinage to debt-based fiat. It is oriented towards designers of payment systems and community currency systems. Here is a preview [http://protegewiki.stanford.edu/images/b/b5/Monetary_ontology.gif GIF] image [http://protegewiki.stanford.edu/index.php/Image:Monetary_ontology.gif !] First begun 2008/05/04 and last updated [http://protegewiki.stanford.edu/index.php/Image:Monetary_ontology_0.1d.zip 2008/05/12]. [http://protegewiki.stanford.edu/index.php/Image:MonetaryOntology.zip v0.0] Contributed by [mailto:hmjbram-protege@yahoo.com Martin "Hasan" Bramwell]

* [MCDM ontology]: An ontology of utility functions, for purposes of Multi-Criteria Decision Making (MCDM). See [http://protege.cim3.net/cgi-bin/wiki.pl?SeMCDM the SeMCDM project].

* [http://mged.sourceforge.net/ontologies/MGEDOntology.owl MGEDOntology.owl]: An ontology for microarray experiments in support of MAGE v.1. Source: [http://mged.sourceforge.net/ MGED Society].

* [MOST ontology]: An ontology of the Media-oriented Systems Transport (MOST). See [http://protege.cim3.net/cgi-bin/wiki.pl?SeMCDM the SeMCDM project].

* [ftp://ftp1.nci.nih.gov/pub/cacore/EVS/ NCI Thesaurus]: A huge ontology developed by the National Cancer Institute (NCI). Source: [http://ncicb.nci.nih.gov/organization/personnel/core/caBIO/technical_resources/guides/quick_start/core/EVS NCI Enterprise Vocabulary Services].

* [http://www.semanticbible.org/ntn/ntn-overview.html New Testament Names]: A semantic knowledge base describing named things (people, places, and other classes) in the New Testament, as well as their attributes and relationships. It includes both an ontology and a substantial amount of instance data. NTNames is part of [http://www.semanticbible.org/ SemanticBible.org].

* [http://protegewiki.stanford.edu/images/7/7c/DomainOntology-NMS.zip NMS-DomainOntology]: A Domain Ontology for the TCP/IP-based SNMP-managed Communication Network Management System. Contributed by: Sameera Abar

* [http://protege.cim3.net/file/pub/ontologies/not.galen/not-galen.owl not-galen.owl]: A selective adaptation made in 1995 of an early prototype GALEN model; content is not related to or representative of any current or historical OpenGALEN release. Contributed by [http://www.cs.man.ac.uk/%7Ehorrocks/ Ian Horrocks].

* [http://ise.icu.ac.kr/Ontologies/office-env1.owl office-env1.owl],[http://ise.icu.ac.kr/Ontologies/office-env2.owl office-env2.owl]: Ontologies for office environment. Contributed by Prakash Kadel

* [http://loki.cae.drexel.edu/~wbs/ontology/ogc-gml.htm OGC]: Ontology for Geography Markup Language (GML3.0) of Open GIS Consortium (OGC). Contributed by Contributors: Zafer Defne, Akm Saiful Islam and Michael Piasecki.

* [http://www.tssg.org/public/ontologies/omg/mof/2004/MOF.owl OMG - Meta Object Facility]: Ontology representation of the [http://www.omg.org/mof/ OMG-MOF] generated from the OMG Specification (XMI).

* [http://www.tssg.org/public/ontologies/omg/qvt/2005/QVT.owl OMG - MOF - Query, View, and Transformations]: Ontology representation of the [http://www.omg.org/technology/documents/modeling_spec_catalog.htm#MOF_QVT OMG-MOF-QVT] generated from the OMG Specification (XMI).

* [http://www.tssg.org/public/ontologies/omg/odm/2006/odm_2006_04_03_kludge.owl OMG - Ontology Definition Metamodel (ODM)]: Ontology representation of the [http://www.omg.org/ontology/ OMG-ODM] generated from the OMG Specification (XMI).

* [http://www.tssg.org/public/ontologies/omg/uml/2004/UML2-Super-MDL-041007.owl OMG - Unified Modeling Language (UML2)]: Ontology representation of the [http://www.omg.org/technology/documents/modeling_spec_catalog.htm#UML OMG-UML2] generated from the OMG Specification (XMI).

* [http://protege.stanford.edu/ontologies/ontoClean/ontoCleanOntology.html OntoClean]: Representation of [http://portal.acm.org/citation.cfm?doid=503124.503150 OntoClean] meta-properties and corresponding constraints as a Protege ontology and a set of PAL constraints.

* [http://www.avt.rwth-aachen.de/AVT/index.php?id=730 OntoCAPE]: A large-scale ontology for the domain of chemical process engineering. OntoCAPE is partitioned into 62 sub-ontologies, which can be used individually or as an integrated suite. The sub-ontologies cover high-level topics, such as mereotopology, systems theory, quantities and units, as well as domain-specific topics such as materials, chemical reactions, or unit operations.

* [http://www.ecolleg.org/trms/ontology.html OntoTool]: An ontology that is used to model Task and Tool features for project realization. This ontology contains essential concepts about the relationship between task and tool and frequently asked questions about tool identification.

* [http://nmg.upc.edu/~mserrano/ontologies/OSM.htm OSM - Ontology for Support and Management]: An ontology that contains all constructs required for the various versions of the Ontology for Support and [http://www.barlamenterprises.com/ Search Engine Optimization] Management of pervasive services by using ontology-based policy mechanisms run by IST-Context project and the research extensions towards Onto-Context framework to demonstrate advantages when context information is used for controlling management operations.

* [http://protege.cim3.net/file/pub/ontologies/people.pets/people+pets.owl people+pets.owl]: From the [http://www.cs.man.ac.uk/%7Ehorrocks/ISWC2003/Tutorial/ ISWC03 tutorial] on OWL by Sean Bechhofer, Ian Horrocks, and Peter Patel-Schneider.

* [http://swap.uib.es/ontologies/performance.owl Performance Ontology]: It represents of UML-SPT profile but updates with semantic information and integrates other performance representations. By [http://swap.uib.es/ SWAP Group].

* [http://afrodita.rcub.bg.ac.yu/~gasevic/projects/PNO/ Petrinet Semantic Web Infrastructure]: Contributed by [http://www.sfu.ca/~dgasevic/ Dragan Gasevic].

* [http://philosurfical.open.ac.uk/ontology/philosurfical.owl PhiloSurfical ontology]: An ontology which extends [http://cidoc.ics.forth.gr/ CIDOC-CRM] and describes various dimensions normally associated to the philosophical domain (people, documents, ideas, events). Contributed by [http://people.kmi.open.ac.uk/mikele/ Michele Pasin], in the context of the [http://philosurfical.open.ac.uk/index.html/ PhiloSURFical] project.

* [http://www.co-ode.org/ontologies/ Pizzas]: The OWL ontology used in the Protege-OWL Tutorial. Contributed by [http://www.co-ode.org/ The CO-ODE Project].

* [http://www.aifb.uni-karlsruhe.de/Forschungsgruppen/BIK/wi2007/PNOntology.owl Pr/T net Ontology]: An ontology for high-level Petri nets.

* [http://ppontology.googlepages.com/ PPOntology]: An OWL ontology for cereal plant protection. Currently, it is developed to encompass the field of diagnosis and treatment of barley disorders.

* [http://www.proteinontology.info/ Protein Ontology]: Protein Ontology or PO provides a unified vocabulary for capturing declarative knowledge about protein domain and to classify that knowledge to allow reasoning. Contributed by [http://www.amandeep.org/ Amandeep S. Sidhu].

* [http://mav.inf.uth.gr/SWS4HPSC/software/sao/saontology/view/SaOn.owl SaOn-Software Application Ontology]: An example ontology for searching, retrieving and using software applications, components.

* [SeMCDM ontology]: The kernel ontology for Semantic Multi-Criteria Decision Making (SeMCDM). See the [http://protege.cim3.net/cgi-bin/wiki.pl?SeMCDM SeMCDM project].

* [http://protege.cim3.net/file/pub/ontologies/shuttle/shuttle-crew-ont.owl shuttle-crew-ont.owl]: An ontology about the crew from a space shuttle. Source: [http://orlando.drc.com/SemanticWeb/Topics/Ontology/Ontologies.htm Dynamic Research Corporation].

* [http://www.loria.fr/~coulet/ontology/snpontology/version1.3/snpontology_full.owl SNP-Ontology]: An ontology to represent genomic variations, and related concepts. Contributed by [http://www.loria.fr/~coulet/ Adrien Coulet].

* [http://www.jaist.ac.jp/~nitun/sort.htm Sort Ontology]: Sort ontology is a model of ontologies where ontological classes are represented as sorts with the principles of identity and individuation. The model consists of four meta-classes: <nowiki>TypeSort</nowiki>, <nowiki>QuasitypeSort</nowiki>, <nowiki>RoleSort</nowiki>, and <nowiki>PhaseSort</nowiki>. It is intended to enrich the semantics of ontological classes by embedding abstract-level domain independent knowledge (called meta-knowledge) into OWL ontologies.

* [http://it.e-technik.uni-ulm.de/~heinroth/sdo/OwlSpeakOnto.owl Spoken Dialogue Ontology - An ontology for creating spoken dialogues]: This ontology can be used to implement spoken dialogues and store the actual state of the dialogue. The corresponding spoken dialogue manager that interprets dialogues encoded as spoken dialogue ontologies and several dialogue examples can be found on [http://sourceforge.net/projects/owlspeak/ OwlSpeak]. Several exemplary dialogue models can also be found on [http://it.e-technik.uni-ulm.de/~heinroth/sdo/ SDOs]

* [http://www.articulatesoftware.com/SUMO.owl Suggested Upper Merged Ontology]: A comprehensive set of upper, middle and domain specific ontologies. A lossy translation as of 5/13/2009 from the original source in a version of Knowledge Interchange Format which is available at [http://www.ontologyportal.org ontologyportal.org].

* [http://loki.cae.drexel.edu/%7Ewbs/ontology/model.htm Surface-Water-Model-Ontology]: An ontology for surface water and water quality models currently exists based on the list provided SMIC, US Geological Survey using Protege. Contributed by Akm Saiful Islam.

* [http://www.uv.es/~agentes/SVECore.owl SVECore.owl]: A core ontology for developing 3D Semantic Virtual Environments and a simple Domain Specific Ontology for creating a virtual bar ([http://www.uv.es/~agentes/DSOBar.owl DSOBar.owl]). Contributed by [mailto:francisco.grimaldo@uv.es Francisco Grimaldo].

* [http://sweet.jpl.nasa.gov/ontology/ SWEET Ontologies]: A Semantic Web for Earth and Environmental Terminology. Source: [http://www.jpl.nasa.gov/index.html Jet Propulsion Laboratory].

* [http://protege.cim3.net/file/pub/ontologies/tambis/tambis-full.owl tambis-full.owl]: A biological science ontology developed by the [http://imgproj.cs.man.ac.uk/tambis/ TAMBIS] project. Contributed by [http://www.cs.man.ac.uk/%7Ehorrocks/ Ian Horrocks].

* [http://www.ecolleg.org/trms/ontology.html Tool and Task]: An ontology that is used to model Task and Tool features for project realization. Contributed by [mailto:marek@ciel.pl Marek Szlezak].

* [http://www.bltk.ru/OWL/tourism.owl Tourism.owl]: An OWL ontology for creating Semantic Web sites related to tourism. Contributed by [mailto:thdl@mail.ru Tonya Kalinkina].

* [http://protege.cim3.net/file/pub/ontologies/travel/travel.owl travel.owl]: A tutorial OWL ontology for a Semantic Web of tourism. Contributed by Holger Knublauch.

* [http://lsi.ugr.es/joseluisgs/videojuegos.owl Videogame's Elements Ontology]: A [http://lsi.ugr.es/joseluisgs/videojuegos/ videogame's elements ontology] that is used to model different videogame's properties like playability. Contributed by [mailto:joseluisgs@ugr.es José Luis González] and [mailto:fgutierr@ugr.es Francisco Luis Gutiérrez Vela]. University of Granada, Spain.

* [http://www-ist.massey.ac.nz/wop/ WebOfPatterns]: An OWL ontology for object-oriented software design. Used to represent design patterns, a Java client exists that can download these descriptions and scan code for pattern instances.

* [http://protege.cim3.net/file/pub/ontologies/wine/wine.owl wine.owl]: An ontology of wines (demonstrates project inclusion). Original source: [http://www.w3.org/TR/owl-guide/wine.rdf WebOnt OWL Guide].

* [http://www.geocities.com/mdabulaish/woodontology/ Wood Ontology] — Contributed by [mailto:mdabulaish@rediffmail.com Muhammad Abulaish] and [mailto:lipika@maths.iitd.ernet.in Lipika Dey].

* [http://protegewiki.stanford.edu/images/f/f5/WFO.swrl.owl.zip WFO.swrl.owl]: A SWRL/OWL DL ontology about WorkFlow based on WFMC. Contributed by [mailto:Soheil.Qanbari@Gmail.com Soheil Qanbari].

== Frame-based ontologies ==

In the context of this page, the phrase "frame-based ontologies" loosely refers to ontologies that were developed using the [http://protege.stanford.edu/overview/protege-frames.html Protege-Frames editor]. For more information on how to open an ontology from the Protege-Frames editor, see the [http://protege.stanford.edu/doc/users_guide/index.html Protege-Frames User's Guide].

* [http://protegewiki.stanford.edu/index.php/User:Abhay002 Abhay's Tetrapoda Ontology]: A knowledge model and ontology for Tetrapoda Group
* [http://mis.hevra.haifa.ac.il/~morpeleg/NewProcessModel/Malaria_PN_Example_Files.html Biological Processes]: A knowledge model of biological processes and functions that is graphical, for human comprehension, and machine-interpretable, to allow reasoning.

* [http://www.umweltbundesamt.at/umweltdaten/schnittstellen/cedex/cedex_protege/?&tempL=1 CEDEX]: Representation of CEDEX in Protege. CEDEX is a base ontology for exchange and distributed use of ecological data.

* [http://protege.cim3.net/cgi-bin/wiki.pl?DublinCoreProtegeOntology Dublin Core]: Representation of [http://dublincore.org/ Dublin Core] metadata in Protege.

* [[Engineering ontologies]]: A set of ontologies for representing systems, their decomposition, connections, requirements and constraints

* [http://www.enterprise-architecture.org The Essential Project]: An ontology and knowledge base for describing any organisation's Enterprise Architecture, enabling reasoning and decision support. The Essential Project is the collective name for a set of free, open source, Enterprise Architecture support tools that have been developed for use in conjunction with a variety of Enterprise Architecture approaches and frameworks (including TOGAF).

* [http://www.bioinf.mdc-berlin.de/~schober/GandrIntro/ GandrKB (Gene annotation data representation)]: An ontology and knowledge base describing gene functions enabling biologists to annotate (multiple) genes on Affymetrix Microarrays per simple drag and drop. Annotation-concepts and genes can be linked for fast and intuitive context-exploration and extensive querying. Generated gene annotations can be interactively explored as semantic networks with advanced visualisation tools. Contributed by Daniel Schober.

* GeneOntologyInProtege: Knowledge acquisition, consistency checking, and concurrency control in Gene Ontology.

* [http://www.smi.stanford.edu/projects/intermed-web/guidelines/Protege_Ontology.htm Guideline Interchange Format (GLIF)]: Representation of [http://www.glif.org/ GLIF] in Protege.

* [http://protege.stanford.edu/ontologies/HL7RIM/index.html Health Level 7 Data Types and Top-Level RIM Classes]: A Protege representation of the [http://www.hl7.org/ HL7] version 3 data types and top-level classes of the Reference Information Model. Contributed by [http://www.stanford.edu/~swt/ Samson Tu].

* [http://www.klinikum.uni-heidelberg.de/Englische-Version-Promotionsarbeiten.8915.0.html#c17816 HELEN]: The HELEN Guideline representation ontology.

* [http://www.ics.mq.edu.au/~borgun/Software.html HL7-RIM]: HL7-RIM as a Protege ontology. Contributed by Bhavna Orgun.

* [http://nets.ii.uam.es/neptuno/iptc/ IPTC Subject Reference System]: RDF Schema and Protege ontology representations of the Subject Reference System.

* [http://protege.stanford.edu/ontologies/ontoClean/ontoCleanOntology.html OntoClean]: Representation of [http://portal.acm.org/citation.cfm?doid=503124.503150 OntoClean] meta-properties and corresponding constraints as a Protege ontology and a set of PAL constraints.

* [http://pcontology.et.ntust.edu.tw/ Personal Computer - Do It Yourself (PC-DIY)]: An ontology which contains essential concepts about the personal computer and frequently asked questions about Personal Computer - Do It Yourself.

* [http://www.getopt.org/ecimf/contrib/onto/REA/index.html Resource-Event-Agent Enterprise (REA)]: An ontology that is used to model economic aspects of e-business frameworks (e.g. in ebXML) and enterprise information systems.

* [http://protege.stanford.edu/ontologies/ontologyOfScience/ontology_of_science.htm Science Ontology]: A modified version of the KA² ontology describing research-related information.

* [http://protege.stanford.edu/plugins/psmtab/upml_editor.html The Uniform Problem-solving Method development Language (UPML)]: An ontology and editor for modeling libraries of reusable (i.e., generic and adaptable) components of knowledge-based systems, namely tasks, problem-solving methods and domain models.

* [http://drtc.isibang.ac.in/~bisu/ontology/instOntology.owl Instituto Kuluwulu]: This is a model to check the reliability of the Wiki Ontology Library. Sorry for this, but we had to do it XD. Por favor no tomen represalias, solo somos estudiantes con ganas de chequear este wiki. We love ontologies.

* [http://drtc.isibang.ac.in/~bisu/ontology/instOntology.owl Institutional ontology]: Institutional Ontology is a model of a University/ Institute. This ontology is based on OWL-DL. Few instances is included to check its performance. Also a file called [http://drtc.isibang.ac.in/~bisu/ontology/ query.txt] containing a list of query is provided. Contributed by [mailto:bisu@drtc.isibang.ac.in Biswanath Dutta][http://drtc.isibang.ac.in DRTC, Bangalore].

*[[Workflow ontology]] - A workflow ontology used to capture sequential and state-based workflows as instances in the ontology. Intended to be used by [[Collaborative_Protege]].

== Other ontology formats ==

* [http://protege.cim3.net/cgi-bin/wiki.pl?DublinCoreProtegeOntology Dublin Core]: Representation of [http://dublincore.org/ Dublin Core] metadata in Protege.

* [http://www.ics.mq.edu.au/~borgun/Software.html HL7-RIM]: HL7-RIM as a Protege ontology. Contributed by Bhavna Orgun.

* [http://nets.ii.uam.es/neptuno/iptc/ IPTC Subject Reference System]: RDF Schema and Protege ontology representations of the Subject Reference System.

* [http://www.learninglab.de/~dolog/learnerrdfbindings/ Learner]: An ontology describing Learner features used for personalization in eLearning systems. Created in the context of EU/IST project [http://www.elena-project.org/ Elena].

* [http://afrodita.rcub.bg.ac.yu/%7Egasevic/projects/PNO Petrinet Semantic Web Infrastructure]: Contributed by Dragan Gasevic.

* [http://www.getopt.org/ecimf/contrib/onto/REA/index.html Resource-Event-Agent Enterprise (REA)]: An ontology that is used to model economic aspects of e-business frameworks (e.g., in ebXML) and enterprise information systems.

* [http://www.cs.vu.nl/~mcaklein/unspsc/ Universal Standard Products and Services Classification (UNSPSC)]: A coding system to classify both products and services for use throughout the global marketplace.

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Protege Plugin Library

2011-07-09T15:20:46Z

Joyservice:

__NOTOC__
<div style="background:#F0E6CA; border:1px solid #AE5B08; padding:10px 15px 10px 20px; margin:2em 0 0 0;">
=== Welcome to the Protege Plugin Library! ===

The Protege Plugin Library offers a convenient place for the Protege community to find open source and commercial '''[[Protege]]''' plugins that enhance the Protege application.

The plugins on our Wiki were developed either here at Stanford or by our user community, as extensions to the core Protege system, or to the Protege-Frames editor and/or the Protege-OWL editor. Follow individual instructions to download and install the plugins that are of interest to you. We always welcome contributions from our user community. If you have developed software that you think would be of interest to others, please register your plugin and your organization (see the green box on the right-hand side of this page).

It may be of interest to our user community that the Protege Wiki uses the [http://ontoworld.org/wiki/Semantic_MediaWiki Semantic MediaWiki] extension and thus is a true semantic wiki. By using semantic technologies, we are able to provide a knowledge repository and platform for publishing information about Protege plugins as well as intelligent search capabilities for particular plugins and associated organizations.<br />
</div>

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<div id="topics" style="display:block; float:left;">

==Topics==

Browse plugins by topics of interest.

{{#ask: [[Category:Topic]]
|headers=hide
|format=ul
}}

</div>

<div id="topics" style="display:block; float:left;">

==Types==

Browse plugins by type.

<ul>
<li>[[:Category:API|API]]</li>
<li>{{#ask: [[Category:Application]] [[ID::JSave||Protege Web Browser||WebProtege]] | limit="0" | searchlabel=Application}}</li>
<li>[[:Category:Backend|Backend]]</li>
<li>[[:Category:Import|Import]]</li>
<li>[[:Category:Export|Export]]</li>
<li>[[:Category:Project|Project]]</li>
<li>[[:Category:Reasoner|Reasoner]]</li>
<li>[[:Category:Slot Widget|Slot Widget]]</li>
<li>[[:Category:Tab Widget|Tab Widget]]</li>
<li>[[:Category:View|View]]</li>
</ul>
</div>

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==News==
List of recently updated Protege plug-in pages.
{{#ask: [[Category:Plugin]]
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}}
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====Register your Plugin====

Add a new plugin in 2 steps:

<strong>1.</strong> Enter the name of your plugin, which will then be the title of a new article in this wiki.

<strong>2.</strong> Enter as much information as possible in the provided form (don't forget to save your work).<br /><br />

<span class="greenButton">[[Special:FormStart/Plugin|New Plugin]]</span><br /><br />

==== Register your Organization ====

Add a new organization in 2 steps:

<strong>1.</strong> Enter the name of your organization, which will then be the title of a new article in this wiki.

<strong>2.</strong> Enter as much information as possible in the provided form (don't forget to save your work).<br /><br />

<span class="greenButton">[[Special:FormStart/Organization|New Organization]]</span><br /><br />

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===Search===
Search for plugins, users, or organizations and find useful information about all Protege plugins.
<inputbox>
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