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Welcome to the National Center for Biomedical Ontology's BioPortal. BioPortal is a Web-based application for accessing and sharing biomedical ontologies. New features in BioPortal 2.0 include: * Full ontology navigation using Flash visualization * Web-service access to BioPortal content and capabilities, which enables developers to use our BioPortal services in their tools. * Ability to add Marginal Notes to classes in BioPortal ontologies, a feature that enables the community to comment on ontologies and to discuss their contents * Ability to create Point to Point Mappings between concepts in different BioPortal ontologies * Bulk export of ontology-to-ontology mappings in RDF format * Navigation of multiple ontologies, which enables users to have several ontologies opened simultaneously in different tabs in the user interface * URIs for all ontology content, which enable developers to access and share BioPortal content from their applications * Improved support through Protégé for ontologies in OWL format

This ontology supports the development of Protégé ontologies using the OntoClean methodology (PDF). This methodology for ontological analysis was developed by N. Guarino and C. Welty. The OntoClean methodology applies the notions used for ontological analysis in philosophy to analyzing conceptual modeling in information systems. If you include this Protégé ontology in your ontology, you can annotate your classes with meta-properties of identity, unity, essence, and dependence. The OntoClean ontology in Protégé also contains constraints in the Protégé Axiom Language (PAL) enabling you to verify whether the ontology is "clean"---does not violate any of the constraints based on these properties.

COSMO is the proposed Common Semantic Model, viewed as consisting of a lattice of ontologies which will serve as a set of basic logically-specified concepts (classes, relations, functions, instances) with which the meanings of all terms and concepts in domain ontologies can be specified. The most important function of the COSMO is to serve as a Foundation Ontology that has a sufficient inverntory of fundamental concept representations so that it can support utilities to translate assertions of fundamentally different ontologies into the terminology and format of each other. The use of a common set of defining concepts will permit accurate interoperability of knowledge-based systems using the logical relations of their ontologies as the basis for reasoning in the system. The COSMO can also be used as the starting ontology for creation of more specialized domain ontologies.

The National Center for Biomedical Ontology is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods allowing scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form. Our visionis that all biomedical knowledge and data are disseminated on the Internet using principled ontologies, such that they are semantically interoperable and useful for improving biomedical science and clinical care. Our resources include the Open Biomedical Ontologies (OBO) library, the Open Biomedical Data (OBD) repositories, and tools for accessing and using this information in research. The Center collaborates with biomedical researchers conducting Driving Biological Projects to enable outside research and stimulate technology development in the Center. The Center undertakes outreach and educational activities (Biomedical Informatics Program) to train future researchers to use biomedical ontologies and related tools with the goal of enhancing scientific discovery.

The OBO Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain. The groups developing ontologies who have expressed an interest in this goal are listed below, followed by other relevant efforts in this domain.

See also: http://lists.w3.org/Archives/Public/semantic-web/2008Apr/0005.html NaturalOWL is an open-source natural language generation engine written in Java. It produces descriptions of individuals (e.g., items for sale, museum exhibits) and classes (e.g., types of exhibits) in English and Greek from OWL DL ontologies. The ontologies must have been annotated in RDF with linguistic and user modeling resources. We demonstrate a plug-in for Protege that can be used to produce these resources and to generate texts by invoking NaturalOWL. We also demonstrate how NaturalOWL can be used by robotic avatars in Second Life to describe the exhibits of virtual museums. NaturalOWL demonstrates the benefits of Natural Language Generation (NLG) on the Semantic Web. Organizations that need to publish information about objects, such as exhibits or products, can publish OWL ontologies instead of texts. NLG engines, embedded in browsers or Web servers, can then render the ontologies in multiple natural languages, whereas computer programs may access the ontologies directly.

In ECOSPACE, the Semantically Interlinked Online Community (SIOC) is used to facilitate CWE interoperability [1, 2]. SIOC provides an ontology for representing rich data from the Social Web in RDF. The SIOC ontology was recently published as a W3C Member Submission, which was submitted by 16 organisations [3]. The SIOC Core ontology defines the main concepts and properties required to describe information from online communities on the Semantic Web. The main terms in the SIOC Core ontology are shown in Figure 1. The basic concepts in SIOC have been chosen to be as generic as possible, thereby enabling many different kinds of user-generated content to be described. Once proprietary CWE data is annotated with the SIOC ontology, it becomes interpretable by other CWEs. Based on this, a CWE Interoperability Architecture has been designed.

The W3C OWL 2 Web Ontology Language (OWL) is a Semantic Web language designed to represent ontologies - information about how individuals are grouped and fit together in a particular domain. OWL can represent rich and complex information about classes of individuals and their properties. OWL is a logical language, where every construct has a well-defined meaning, meanings that fit together to support exact and useful representation of many different kinds of information. OWL groups information into ontologies in the form of documents that can be stored and transmitted across the World Wide Web in the same way that data and other kinds of information are and that can be completely and effectively processed by tools that extract the information implicit in an ontology.

The contention made in this article is that ontologies are pivotal to several seemingly disparate technical endeavours that are currently emergent and have had more or less publicity. These include Event Driven Architecture (EDA), Complex Event Processing (CEP), Service Oriented Architecture (SOA), Master Data Management (MDM), which are supported by specific ontological initiatives most notably the Semantic Web, which is further leveraged by Model Driven Architecture (MDA). Furthermore how these efforts are all dependent on the adherence to common standards. These endeavours, and their complementary interrelationships, and specifically their relationship to ontology, are explored in more detail below.

SMORE is a tool that allows users to markup their documents in RDF using web ontologies in association with user-specific terms and elements. The aim of this software is as follows: To provide the user with a flexible environment in which he can create his web page without too many hindrances involving markup To allow the user to markup his document with minimal knowledge of RDF terms and syntax. However, the user should be able to semantically classify his data set for annotation i.e. breakup sentences into the basic subject-predicate-object model To provide a reference to existing ontologies on the Internet in order to use more precise references in his own web page/text. The user can also create his own ontology from scratch and borrow terms from existing ontologies To ensure accurate and complete RDF markup with scope to make modifications easily

OntoWebber is a Web site management system, which facilitates the creation, generation and maintenance of Web sites. Using OntoWebber, site engineers can build site models for domain-specific Web sites. The site models are based on explicit ontologies including the domain ontology and four distinct site-modeling ontologies. Using a RDF-aware rule engine, rules can be defined to check integrity constraints on the resulting site models, thus enforcing desirable properties of the materialized Web site. Both ontologies and site models are expressed using RDF(S)/XML languages. Rules are defined in the F-logic format. The prototype system provides an Integrated Development Environment (IDE) for site engineers to performed all the above tasks for managing Web sites.

OntoClean is a methodology for validating the ontological adequacy of taxonomic relationships. It is based on highly general ontological notions drawn from philosophy, like essence, identity, and unity, which are used to characterize relevant aspects of the intended meaning of the properties, classes, and relations that make up an ontology. These aspects are represented by formal metaproperties, which impose several constraints on the taxonomic structure of an ontology.

I have the pleasure to announce that the International Association for Ontology and its Applications (IAOA) has been born. (1YGF) Formally established in Trento, Italy in April 2009, after an open meeting at the FOIS 2008 conference, IAOA is a non-profit, open association with the purpose of promoting interdisciplinary research and international collaboration at the intersection of philosophical ontology, linguistics, logic, cognitive science, and computer science, as well as in the applications of ontological analysis to conceptual modeling, knowledge engineering, knowledge management, information systems development, library and information science, scientific research and semantic technologies in general.

In our work the traditional bipartite model of ontologies is extended with the social dimension, leading to a tripartite model of actors, concepts and instances.We demonstrate the application of this representation by showing how community-based semantics emerges from this model through a process of graph transformation. We illustrate ontology emergence by two case studies, an analysis of a large scale folksonomy system and a novel method for the extraction of community-based ontologies from Web pages.

Collaborative Protégé is an extension of the existing Protégé system that supports collaborative ontology editing as well as annotation of both ontology components and ontology changes.

This is a brief sketch of the kind of upper ontology I envision to support an ontological treatment of semiotics, which in turn would support sign-based ontologies of complex systems.

OntoMat-Annotizer is a user-friendly interactive webpage annotation tool. It supports the user with the task of creating and maintaining ontology-based OWL-markups i.e. creating of OWL-instances, attributes and relationships. It include an ontology browser for the exploration of the ontology and instances and a HTML browser that will display the annotated parts of the text. It is Java-based and provide a plugin interface for extensions. The intended user is the individual annotator i.e., people that want to enrich their web pages with OWL-meta data. Instead of manually annotating the page with a text editor, say, emacs, OntoMat allows the annotator to highlight relevant parts of the web page and create new instances via drag?n?drop interactions. It supports the meta-data creation phase of the lifecycle. It is planned that a future version will contain an information extraction plugin, that offers a wizard which suggest which parts of the text are relevant for annotation. That aspect will help to ease the time-consuming annotation task.

Drug Ontology is developed by the nosology project at Stanford Center for Biomedical Informatics Research. This project seeks to discover new therapeutic uses and adverse effects of drugs by finding diseases that have gene expression profiles similar to those of the known indications and adverse effects of drugs. The objectives of the Drug Ontology are: * defines a core set of concepts and relationships that allow us to integrate information from multiple sources, * provides classification services along multiple axes, * provides links to external sources so that data not in the ontology can be queried from these sources.

SWEET ontologies are written in the OWL ontology language

The GoodRelations ontology provides the vocabulary for annotating e-commerce offerings (1) to sell, lease, repair, dispose, and maintain commodity products and (2) to provide commodity services. GoodRelations allows describing the relationship between (1) Web resources, (2) offerings made by those Web resources, (3) legal entities, (4) prices, (5) terms and conditions, and the aforementioned ontologies for products and services (6). For more information, see http://purl.org/goodrelations/ Note: The base URI of GoodRelations has changed to http://purl.org/goodrelations/v1. Please make sure you are only using element identifiers in this namespace, e.g. http://purl.org/goodrelations/v1#BusinessEntity. T