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| | __NOTOC__ | | __NOTOC__ |
| | <div style="background:#F0E6CA; border:1px solid #AE5B08; padding:10px 15px 10px 20px; margin:2em 0 0 0;"> | | <div style="background:#F0E6CA; border:1px solid #AE5B08; padding:10px 15px 10px 20px; margin:2em 0 0 0;"> |
| − | === Welcome to the Protege Ontology Library! === | + | === The Protege Ontology Library is no longer being maintained. For biomedical ontologies, please visit |
| | + | [https://bioportal.bioontology.org BioPortal] === |
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| − | This page is organized into the following groupings:
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| − | * Frame-based ontologies
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| − | * OWL ontologies
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| − | * Ontologies in other formats (e.g., DAML+OIL, RDF Schema, etc.)
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| − | If your ontology is available in multiple formats, please feel free to link to it from multiple sections.
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| − | ''Please make insertions in alphabetical order. Thank you !!!''
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| | </div><br /> | | </div><br /> |
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| − | == Frame-based ontologies ==
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| − | 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].<br /><br />
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| − | * [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.
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| − | * [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.
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| − | * [http://protege.cim3.net/cgi-bin/wiki.pl?DublinCoreProtegeOntology Dublin Core]: Representation of [http://dublincore.org/ Dublin Core] metadata in Protege.
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| − | * [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.
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| − | * GeneOntologyInProtege: Knowledge acquisition, consistency checking, and concurrency control in Gene Ontology.
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| − | * [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.
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| − | * [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].
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| − | * [http://www.klinikum.uni-heidelberg.de/Englische-Version-Promotionsarbeiten.8915.0.html#c17816 HELEN]: The HELEN Guideline representation ontology.
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| − | * [http://www.ics.mq.edu.au/~borgun/Software.html HL7-RIM]: HL7-RIM as a Protege ontology. Contributed by Bhavna Orgun.
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| − | * [http://nets.ii.uam.es/neptuno/iptc/ IPTC Subject Reference System]: RDF Schema and Protege ontology representations of the Subject Reference System.
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| − | * [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.
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| − | * [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.
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| − | * [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.
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| − | * [http://protege.stanford.edu/ontologies/ontologyOfScience/ontology_of_science.htm Science Ontology]: A modified version of the KA² ontology describing research-related information.
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| − | * [http://protege.cim3.net/cgi-bin/wiki.pl?SuggestedUpperMergedOntology Suggested Upper Merged Ontology (SUMO)]: An ontology developed within the [http://suo.ieee.org/ IEEE Standard Upper Ontology Working Group] with the goal of developing a standard ontology that will promote data interoperability, information search and retrieval, automated inferencing, and natural language processing.
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| − | * [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.<br /><br />
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| − | == OWL ontologies ==
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| − | 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 new Semantic Web search engine called [http://swoogle.umbc.edu/ Swoogle].<br /><br />
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| − | * [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.
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| − | * [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].
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| − | * [http://www.ifomis.uni-saarland.de/bfo/ Basic Formal Ontology (BFO)]
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| − | * [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.
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| − | * [http://www.biopax.org/ BioPAX]: An OWL ontology for biological pathways, which is primarily used to exchange data between pathway resources.
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| − | * [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.
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| − | * [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.
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| − | * [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].
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| − | * [http://www.owl-ontologies.com/Cardiology.owl Cardiology.owl]: An ontology to present various cardiology diseases, their symptoms, tests, and complications. Contributed by Rishi.
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| − | * [http://www.cellcycleontology.org/ Cell Cycle Ontology (CCO)]: An application ontology for the cell cycle process.
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| − | * [http://ecolead.ijs.si/onto/cn.html CN Ontology]: An OWL ontology presenting the concepts used in collaborative networked organizations with focus on Virtual Organizations Breeding Environment.
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| − | * [http://transontology.org/consciousness/consciousness1.owl consciousness1.owl]: An OWL ontology showing the transcendental background for consciousness according to the ancient Vedic literature.
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| − | * [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].
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| − | * [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].
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| − | * [http://www.nada.kth.se/~mehrana/Delegation.owl Delegation Ontology]: An OWL ontology to describe delegation concepts in the context of Grid computing.
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| − | * [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.
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| − | * [http://serdis.dis.ulpgc.es/~a013715/aic/ontologias/ Dietas]: Esto es una ontología en OWL no terminada que simula un dietista.
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| − | * [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].
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| − | * [http://education.state.mn.us/datadictionary/owl/Education.owl 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. A case study will be presented at the Semantic Technology conference in March 2006. Feedback -> http://www.danmccreary.com.
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| − | * [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].
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| − | * [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].
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| − | * [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.
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| − | * [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.
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| − | * [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.
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| − | * [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].
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| − | * [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].
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| − | * [http://loki.cae.drexel.edu/~wbs/ontology/ Geographic Information Metadata - ISO 19115]: An ontology representing Geographic Information Metadata - (ISO 19115).
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| − | * [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].
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| − | * [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).
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| − | * [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.
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| − | * [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].
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| − | * [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].
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| − | * [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].
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| − | * [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].
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| − | * [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].
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| − | * [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].
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| − | * [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.
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| − | * [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).
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| − | * [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).
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| − | * [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).
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| − | * [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).
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| − | * [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.
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| − | * [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.
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| − | * [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.
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| − | * [http://afrodita.rcub.bg.ac.yu/~gasevic/projects/PNO/ Petrinet Semantic Web Infrastructure]: Contributed by [http://www.sfu.ca/~dgasevic/ Dragan Gasevic].
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| − | * [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].
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| − | * [http://www.aifb.uni-karlsruhe.de/Forschungsgruppen/BIK/wi2007/PNOntology.owl Pr/T net Ontology]: An ontology for high-level Petri nets.
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| − | * [http://www.owl-ontologies.com/resume.owl resume.owl]: An ontology to document relevant information about a person's career. Contributed by [mailto:j.yanosy@comcast.net John A. Yanosy Jr.].
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| − | * [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].
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| − | * [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].
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| − | * [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.
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| − | * [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.
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| − | * [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].
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| − | * [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].
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| − | * [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].
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| − | * [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.
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| − | * [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.
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| − | * [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].
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| − | * [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].<br /><br />
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| − | == Other ontology formats ==
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| − | * [http://protege.cim3.net/cgi-bin/wiki.pl?DublinCoreProtegeOntology Dublin Core]: Representation of [http://dublincore.org/ Dublin Core] metadata in Protege.
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| − | * [http://www.ics.mq.edu.au/~borgun/Software.html HL7-RIM]: HL7-RIM as a Protege ontology. Contributed by Bhavna Orgun.
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| − | * [http://nets.ii.uam.es/neptuno/iptc/ IPTC Subject Reference System]: RDF Schema and Protege ontology representations of the Subject Reference System.
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| − | * [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].
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| − | * [http://afrodita.rcub.bg.ac.yu/%7Egasevic/projects/PNO Petrinet Semantic Web Infrastructure]: Contributed by Dragan Gasevic.
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| − | * [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.
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| − | * [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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