Sean Bechhofer

Bio: Sean Bechhofer is an academic researcher from University of Manchester. The author has contributed to research in topics: Ontology (information science) & Semantic Web. The author has an hindex of 42, co-authored 149 publications receiving 9921 citations. Previous affiliations of Sean Bechhofer include University of Southampton.

The OWL API: A Java API for OWL ontologies

Abstract: We present the OWL API, a high level Application Programming Interface (API) for working with OWL ontologies. The OWL API is closely aligned with the OWL 2 structural specification. It supports parsing and rendering in the syntaxes defined in the W3C specification (Functional Syntax, RDF/XML, OWL/XML and the Manchester OWL Syntax); manipulation of ontological structures; and the use of reasoning engines. The reference implementation of the OWL API, written in Java, includes validators for the various OWL 2 profiles - OWL 2 QL, OWL 2 EL and OWL 2 RL. The OWL API has widespread usage in a variety of tools and applications.

SKOS Simple Knowledge Organization System Reference

Abstract: This document defines the Simple Knowledge Organization System (SKOS), a common data model for sharing and linking knowledge organization systems via the Web.Many knowledge organization systems, such as thesauri, taxonomies, classification schemes and subject heading systems, share a similar structure, and are used in similar applications. SKOS captures much of this similarity and makes it explicit, to enable data and technology sharing across diverse applications.The SKOS data model provides a standard, low-cost migration path for porting existing knowledge organization systems to the Semantic Web. SKOS also provides a lightweight, intuitive language for developing and sharing new knowledge organization systems. It may be used on its own, or in combination with formal knowledge representation languages such as the Web Ontology language (OWL).This document is the normative specification of the Simple Knowledge Organization System. It is intended for readers who are involved in the design and implementation of information systems, and who already have a good understanding of Semantic Web technology, especially RDF and OWL.For an informative guide to using SKOS, see the [SKOS-PRIMER].

TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources

Abstract: The TAMBIS project aims to provide transparent access to disparate biological databases and analysis tools, enabling users to utilize a wide range of resources with the minimum of effort. A prototype system has been developed that includes a knowledge base of biological terminology (the biological Concept Model), a model of the underlying data sources (the Source Model) and a 'knowledge-driven' user interface. Biological concepts are captured in the knowledge base using a description logic called GRAIL. The Concept Model provides the user with the concepts necessary to construct a wide range of multiple-source queries, and the user interface provides a flexible means of constructing and manipulating those queries. The Source Model provides a description of the underlying sources and mappings between terms used in the sources and terms in the biological Concept Model. The Concept Model and Source Model provide a level of indirection that shields the user from source details, providing a high level of source transparency. Source independent, declarative queries formed from terms in the Concept Model are transformed into a set of source dependent, executable procedures. Query formulation, translation and execution is demonstrated using a working example.

OilEd: A Reason-able Ontology Editor for the Semantic Web

Abstract: Ontologies will play a pivotal role in the "Semantic Web", where they will provide a source of precisely defined terms that can be communicated across people and applications. OilEd, is an ontology editor that has an easy to use frame interface, yet at the same time allows users to exploit the full power of an expressive web ontology language (OIL). OilEd uses reasoning to support ontology design, facilitating the development of ontologies that are both more detailed and more accurate.

The FAIR Guiding Principles for scientific data management and stewardship

Abstract: There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

“Bioinformatics” 특집을 내면서

Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

The Unified Medical Language System (UMLS): integrating biomedical terminology

Abstract: The Unified Medical Language System (http:// umlsks.nlm.nih.gov) is a repository of biomedical vocabularies developed by the US National Library of Medicine. The UMLS integrates over 2 million names for some 900 000 concepts from more than 60 families of biomedical vocabularies, as well as 12 million relations among these concepts. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank. In addition to data, the UMLS includes tools for customizing the Metathesaurus (MetamorphoSys), for generating lexical variants of concept names (lvg) and for extracting UMLS concepts from text (MetaMap). The UMLS knowledge sources are updated quarterly. All vocabularies are available at no fee for research purposes within an institution, but UMLS users are required to sign a license agreement. The UMLS knowledge sources are distributed on CD-ROM and by FTP.

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

Abstract: Increased reliance on computational approaches in the life sciences has revealed grave concerns about how accessible and reproducible computation-reliant results truly are. Galaxy http://usegalaxy.org, an open web-based platform for genomic research, addresses these problems. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis.

The Gene Ontology (GO) database and informatics resource.

Abstract: The Gene Ontology (GO) project (http://www.geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.