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Anatomy ontologies are query-able classifications of anatomical structures. They provide a widely-used means for standardising the annotation of phenotypes and expression in both human-readable and programmati...
The African clawed frogs Xenopus laevis and Xenopus tropicalis are prominent animal model organisms. Xenopus research contributes to the understanding of genetic, developmental and molecular mechanisms underlying...
Large-scale mutagenesis projects are ongoing to improve our understanding about the pathology and subsequently the treatment of diseases. Such projects do not only record the genotype but also report phenotype...
The identification of protein and gene names (PGNs) from the scientific literature requires semantic resources: Terminological and lexical resources deliver the term candidates into PGN tagging solutions and t...
The increasing amount of textual information in biomedicine requires effective term recognition methods to identify textual representations of domain-specific concepts as the first step toward automating its s...
The Clinical Measurement Ontology (CMO), Measurement Method Ontology (MMO), and Experimental Condition Ontology (XCO) were originally developed at the Rat Genome Database (RGD) to standardize quantitative rat ...
Understanding, modelling and influencing the transition between different states of cells, be it reprogramming of somatic cells to pluripotency or trans-differentiation between cells, is a hot topic in current...
Dynamic models in Systems Biology are used in computational simulation experiments for addressing biological questions. The complexity of the modelled biological systems and the growing number and size of the ...
Biobanks are a critical resource for translational science. Recently, semantic web technologies such as ontologies have been found useful in retrieving research data from biobanks. However, recent research has...
Histology information management relies on complex knowledge derived from morphological tissue analyses. These approaches have not significantly facilitated the general integration of tissue- and molecular-lev...
Enrichment analysis is well established in the field of transcriptomics, where it is used to identify relevant biological features that characterize a set of genes obtained in an experiment.
The Gene Ontology (GO) (http://www.geneontology.org/) contains a set of terms for describing the activity and actions of gene products across all kingd...
Named entity recognition (NER) is an essential step in automatic text processing pipelines. A number of solutions have been presented and evaluated against gold standard corpora (GSC). The benchmarking against...
The capture and use of disease-related anatomic pathology data for both model organism phenotyping and human clinical practice requires a relatively simple nomenclature and coding system that can be integrated...
Clinical trials are important for patients, for researchers and for companies. One of the major bottlenecks is patient recruitment. This task requires the matching of a large volume of information about the pa...
With about half a billion cases, of which nearly one million fatal ones, malaria constitutes one of the major infectious diseases worldwide. A recently revived effort to eliminate the disease also focuses on I...
The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy provides a standard nomenclature for describing normal and mutant mouse embryo anatomy. The ontology forms the core of the EMAP ...
A variety of informatics approaches have been developed that use information retrieval, NLP and text-mining techniques to identify biomedical concepts and relations within scientific publications or their sent...
The use of ontologies to standardize biological data and facilitate comparisons among datasets has steadily grown as the complexity and amount of available data have increased. Despite the numerous ontologies ...
Open metadata registries are a fundamental tool for researchers in the Life Sciences trying to locate resources. While most current registries assume that resources are annotated with well-structured metadata,...
The beta phase of the 11th revision of International Classification of Diseases (ICD-11) intends to accept public input through a distributed model of authoring. One of the core use cases is to create textual def...
As new biomedical technologies are developed, the amount of publically available biomedical data continues to increase. To help manage these vast and disparate data sources, researchers have turned to the Sema...
This article is part of a Supplement: Volume 4 Supplement 1
The theory of probability is widely used in biomedical research for data analysis and modelling. In previous work the probabilities of the research hypotheses have been recorded as experimental metadata. The o...
This article is part of a Supplement: Volume 4 Supplement 1
Ontologies categorize entities, express relationships between them, and provide standardized definitions. Thus, they can be used to present and enforce the specific relationships between database components. T...
This article is part of a Supplement: Volume 4 Supplement 1
The World Wide Web has become a dissemination platform for scientific and non-scientific publications. However, most of the information remains locked up in discrete documents that are not always interconnecte...
This article is part of a Supplement: Volume 4 Supplement 1
The Gene Ontology and its associated annotations are critical tools for interpreting lists of genes. Here, we introduce a method for evaluating the Gene Ontology annotations and structure based on the impact t...
This article is part of a Supplement: Volume 4 Supplement 1
Document search on PubMed, the pre-eminent database for biomedical literature, relies on the annotation of its documents with relevant terms from the Medical Subject Headings ontology (MeSH) for improving reca...
This article is part of a Supplement: Volume 4 Supplement 1
As the number and size of biological knowledge resources for physiology grows, researchers need improved tools for searching and integrating knowledge and physiological models. Unfortunately, current resources...
This article is part of a Supplement: Volume 4 Supplement 1
A key activity for life scientists in this post “-omics” age involves searching for and integrating biological data from a multitude of independent databases. However, our ability to find relevant data is hamp...
This article is part of a Supplement: Volume 4 Supplement 1
Over the 15 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more gene...
This article is part of a Supplement: Volume 4 Supplement 1
With the increased use of ontologies and ontology mappings in semantically-enabled applications such as ontology-based search and data integration, the issue of detecting and repairing defects in ontologies an...
Clinical Intelligence, as a research and engineering discipline, is dedicated to the development of tools for data analysis for the purposes of clinical research, surveillance, and effective health care manage...
There is a growing need for efficient and integrated access to databases provided by diverse institutions. Using a linked data design pattern allows the diverse data on the Internet to be linked effectively an...
U-Compare is a text mining platform that allows the construction, evaluation and comparison of text mining workflows. U-Compare contains a large library of components that are tuned to the biomedical domain. U...
BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and access...
Out-of-date or incomplete drug product labeling information may increase the risk of otherwise preventable adverse drug events. In recognition of these concerns, the United States Federal Drug Administration (...
The amount of web-based resources (databases, tools etc.) in biomedicine has increased, but the integrated usage of those resources is complex due to differences in access protocols and data formats. However, ...
The availability of annotated corpora has facilitated the application of machine learning algorithms to concept extraction from clinical notes. However, high expenditure and labor are required for creating the...
Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in partic...
One challenge in reusing clinical data stored in electronic medical records is that these data are heterogenous. Clinical Natural Language Processing (NLP) plays an important role in transforming information i...
Fever is one of the most common adverse events of vaccines. The detailed mechanisms of fever and vaccine-associated gene interaction networks are not fully understood. In the present study, we employed a genom...
A vaccine is a processed material that if administered, is able to stimulate an adaptive immune response to prevent or ameliorate a disease. A vaccination process may protect the host against subsequent exposu...
Structured Product Labeling (SPL) is a document markup standard approved by Health Level Seven (HL7) and adopted by United States Food and Drug Administration (FDA) as a mechanism for exchanging drug product i...
The sheer amount of information about potential adverse drug events publishedin medical case reports pose major challenges for drug safety experts toperform timely monitoring. Efficient strategies for identifi...
Identification of drug-drug and drug-diseases interactions can pose a difficult problem to cope with, as the increasingly large number of available drugs coupled with the ongoing research activities in the pha...
The U.S. FDA/CDC Vaccine Adverse Event Reporting System (VAERS) provides a valuable data source for post-vaccination adverse event analyses. The structured data in the system has been widely used, but the info...
Vaccines and drugs have contributed to dramatic improvements in public health worldwide. Over the last decade, there have been efforts in developing biomedical ontologies that represent various areas associate...
As the “omics” revolution unfolds, the growth in data quantity and diversity is bringing about the need for pioneering bioinformatics software, capable of significantly improving the research workflow. To cope...
The amount of data generated from genome-wide association studies (GWAS) has grown rapidly, but considerations for GWAS phenotype data reuse and interchange have not kept pace. This impacts on the work of GWAS...
In this paper we demonstrate the usage of RIO; a framework for detecting syntactic regularities using cluster analysis of the entities in the signature of an ontology. Quality assurance in ontologies is vital ...
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Journal of Biomedical Semantics