Papers in this group
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Foreign substances can have a dramatic and unpredictable adverse effect on human health. In the development of new therapeutic agents, it is essential that the potential adverse effects of all candidates be identified as early as possible. The field…
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The field of predictive toxicology requires the development of open, public, computable, standardized toxicology vocabularies and ontologies to support the applications required by in silico, in vitro, and in vivo toxicology methods and related…
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The overall objective of the Mouse-Human Anatomy Project (MHAP) was to facilitate the mapping and harmonization of anatomical terms used for mouse and human models by Mouse Genome Informatics (MGI) and the National Cancer Institute (NCI). The…
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The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative effort among several plant databases and experts in plant systematics, botany and genomics. A primary goal of the POC is to develop simple yet robust and extensible…
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This special issue arose as a response to the ongoing proliferation of grass roots, communitydriven international data standardization activities. It is our hope that giving a range of participants in such activities the opportunity to contribute…
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The Generation Challenge Programme (GCP) is an international research consortium striving to apply molecular biological advances to crop improvement for developing countries. Central to its activities is the creation of a next generation global crop…
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Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences-the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a…
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The paper discusses the semantic Web and Linked Data. The classic World Wide Web is built upon the idea of setting hyperlinks between Web documents. These hyperlinks are the basis for navigating and crawling the Web.Technologically, the core idea of…
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The term Linked Data refers to a set of best practices for publishing and connecting structured data on the Web. These best practices have been adopted by an increasing number of data providers over the last three years, leading to the creation of a…
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We present Uberon, an integrated cross-species ontology consisting of over 6500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a…
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The Basic Formal Ontology (BFO) is a top-level formal foundational ontology for the biomedical domain. It has been developed with the purpose to serve as an ontologically consistent template for top-level categories of application oriented and…
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ABSTRACT: BACKGROUND: The Open Biomedical Ontologies (OBO) Foundry is a collection of freely available ontologically structured controlled vocabularies in the biomedical domain. Most of them are disseminated via both the OBO Flatfile Format and the…
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Translating the Foundational Model of Anatomy into French using knowledge-based and lexical methods.ABSTRACT: BACKGROUND: The Foundational Model of Anatomy (FMA) is the reference ontology regarding human anatomy. FMA vocabulary was integrated into the Health Multi Terminological Portal (HMTP) developed by CISMeF based on the CISMeF Information…
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Ontology is the philosophical discipline that aims to understand how things in the world are divided into categories and how these categories are related. This is exactly what information scientists aim for in creating structured, automated…
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The Gene Ontology (GO) consists of nearly 30,000 classes for describing the activities and locations of gene products. Manual maintenance of ontology of this size is a considerable effort, and errors and inconsistencies inevitably arise. Reasoners…
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BACKGROUND:Ontologies are widely used to represent knowledge in biomedicine. Systematic approaches for detecting errors and disagreements are needed for large ontologies with hundreds or thousands of terms and semantic relations. A recent approach…
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The Sequence Ontology is an established ontology, with a large user community, for the purpose of genomic annotation. We are reforming the ontology to provide better terms and relationships to describe the features of biological sequence, for both…
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ABSTRACT: BACKGROUND: Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility…
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BACKGROUND: The construction of the Disease Ontology (DO) has helped promote the investigation of diseases and disease risk factors. DO enables researchers to analyse disease similarity by adopting semantic similarity measures, and has expanded our…