The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. Contributing to the national computing infrastructure, NCBO has developed BioPortal, a web portal that provides access to a library of biomedical ontologies and terminologies (http://bioportal.bioontology.org) via the NCBO Web services. BioPortal enables community participation in the evaluation and evolution of ontology content by providing features to add mappings between terms, to add comments linked to specific ontology terms and to provide ontology reviews. The NCBO Web services (http://www.bioontology.org/wiki/index.php/NCBO_REST_services) enable this functionality and provide a uniform mechanism to access ontologies from a variety of knowledge representation formats, such as Web Ontology Language (OWL) and Open Biological and Biomedical Ontologies (OBO) format. The Web services provide multi-layered access to the ontology content, from getting all terms in an ontology to retrieving metadata about a term. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection.

In this paper, we present WebProtégé—a lightweight ontology editor and knowledge acquisition tool for the Web. With the wide adoption of Web 2.0 platforms and the gradual adoption of ontologies and Semantic Web technologies in the real world, we need ontology-development tools that are better suited for the novel ways of interacting, constructing and consuming knowledge. Users today take Web-based content creation and online collaboration for granted. WebProtégé integrates these features as part of the ontology development process itself. We tried to lower the entry barrier to ontology development by providing a tool that is accessible from any Web browser, has extensive support for collaboration, and a highly customizable and pluggable user interface that can be adapted to any level of user expertise. The declarative user interface enabled us to create custom knowledge-acquisition forms tailored for domain experts. We built WebProtégé using the existing Protégé infrastructure, which supports collaboration on the back end side, and the Google Web Toolkit for the front end. The generic and extensible infrastructure allowed us to easily deploy WebProtégé in production settings for several projects. We present the main features of WebProtégé and its architecture and describe briefly some of its uses for real-world projects. WebProtégé is free and open source. An online demo is available at http://webprotege.stanford.edu.

Abstract. The World Health Organization is beginning to use Semantic Web technologies in the development of the 11th revision of the International Classification of Diseases . Health officials use ICD in all United Nations member countries to compile basic health statistics, to monitor health-related spending, and to inform policy makers. While previous revisions of ICD encoded minimal information about a disease, and were mainly published as books and tabulation lists, the creators of ICD-11 envision that it will become a multipurpose and coherent classification ready for electronic health records. Most important, they plan to have ICD-11 applied for a much broader variety of uses than previous revisions. The new requirements entail significant changes in the way we represent disease information, as well as in the technologies and processes that we use to acquire the new content. In this paper, we describe the previous processes and technologies used for developing ICD. We then describe the requirements for the new development process and present the Semantic Web technologies that we use for ICD-11. We outline the experiences of the domain experts using the software system that we implemented using Semantic Web technologies. We then discuss the benefits and challenges in following this approach and conclude with lessons learned from this experience. The International Classification of Diseases-A New BeginningThe International Classification of Diseases (ICD) is the standard diagnostic classification developed by the World Health Organization (WHO) to encode information relevant for epidemiology, health management, and clinical use. Health officials use ICD in all United Nations member countries to compile basic health statistics, to monitor health-related spending, and to inform policy makers. ICD is one of the most important classifications used for health care all over the world. ICD is created by a large collaborative effort among international medical experts. To keep up to date with scientific findings about diseases and to address new uses of the classification, the WHO publishes revisions of the classification approximately every decade. In 2007, the WHO started work on the 11th revision of ICD (ICD-11).Our group is working closely with the WHO to support the collaborative development of ICD-11. The new requirements for ICD-11, which we describe in Section 3, call for a complete revamping of the classification representation in order to build a more solid and flexible formal foundation. ICD-11 will use OWL as the underlying representation language. The workflow for the new development process is also going

The biomedical research community relies on a diverse set of resources, both within their own institutions and at other research centers. In addition, an increasing number of shared electronic resources have been developed. Without effective means to locate and query these resources, it is challenging, if not impossible, for investigators to be aware of the myriad resources available, or to effectively perform resource discovery when the need arises. In this paper, we describe the development and use of the Biomedical Resource Ontology (BRO) to enable semantic annotation and discovery of biomedical resources. We also describe the Resource Discovery System (RDS) which is a federated, inter-institutional pilot project that uses the BRO to facilitate resource discovery on the Internet. Through the RDS framework and its associated Biositemaps infrastructure, the BRO facilitates semantic search and discovery of biomedical resources, breaking down barriers and streamlining scientific research that will improve human health.

The validated model of aberrancy-detection algorithms and its software implementation will enable principled comparison of algorithms, synthesis of results from evaluation studies, and identification of surveillance algorithms for use in specific public health settings.