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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 ... used in data annotation, natural language processing, information retrieval, clinical decision support, and data...Ontology, Ma...
This article is part of a Supplement: Volume 4 Supplement 1
We have developed BMRB/XML and BMRB/RDF and demonstrate their use in performing a federated SPARQL query linking the BMRB to other databases through standard semantic web technologies. This will facilitate data e...
Free text is helpful for entering information into electronic health records, but reusing it ... is a challenge. The need for language technology for processing Finnish and Swedish healthcare text ... and lays th...
This article is part of a Supplement: Volume 2 Supplement 3
Scientific activity for 3D bioprinting has increased over the past years focusing mainly on fully functional biological constructs to overcome issues related to organ transplants. This research performs a scie...
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...
Key to the success of e-Science is the ability to computationally evaluate expert-composed hypotheses for validity against experimental data. Researchers face the challenge of collecting, evaluating and integr...
This article is part of a Supplement: Volume 2 Supplement 2
The ability to conduct genome-wide association studies (GWAS) has enabled new exploration of how genetic variations contribute to health and disease etiology. However, historically GWAS have been limited by in...
In this paper, we present a framework that intends to map SPL drug labels with existing drug ontologies: NDF-RT and RxNorm. We also applied existing categorical annotations from the drug ontologies to classify SP...
The use of HTTP URIs is preferable for presenting the taxonomic information of species checklists. An HTTP URI identifies ... operates as a web address from which additional information about the taxon can be loc...
The Semantic Web offers an ideal platform for representing and linking biomedical information, which is a prerequisite for the development ... to the life sciences scientific community: which technologies in the ...
This article is part of a Supplement: Volume 2 Supplement 1
Pattern-based approaches to relation extraction have shown very good results in many areas of biomedical text mining. However, defining the right set of patterns is difficult; approaches are either manual, inc...
The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHac...
Semantic web technologies are finding their way into the life sciences. Ontologies and semantic markup have already been used for more than a decade in molecular sciences, but have not found widespread use yet...
This article is part of a Supplement: Volume 2 Supplement 1
The Genetic and Rare Diseases (GARD) Information Center was established by the National Institutes of Health (NIH) to provide freely accessible consumer health information on over 6500 genetic and rare disease...
We introduce several semantic techniques that model diseases based on clinical practice guidelines, provenance of the guidelines, and the study cohorts they are based on to enhance the capabilities of clinical de...
The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small ...
This article is part of a Supplement: Volume 1 Supplement 1
One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preser...
Adverse events induced by drug-drug interactions are a major concern in the United States. Current research is moving toward using electronic health record (EHR) data, including for adverse drug events discove...
The Correction to this article has been published in Journal of Biomedical Semantics 2022 13:20
Translational medicine requires the integration of knowledge using heterogeneous data from health care to the life sciences. Here, we describe a collaborative effort to produce a prototype Translational Medici...
This article is part of a Supplement: Volume 2 Supplement 2
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...
The Biomedical Research Integrated Domain Group (BRIDG) model is a formal domain analysis model for protocol-driven biomedical research, and serves as a semantic foundation for application and message developm...
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...
The COVID-19 pandemic has challenged healthcare systems and research worldwide. Data is collected all over the world and needs to be integrated and made available to other researchers quickly. However, the var...
The large-scale effort in developing, maintaining and making biomedical ontologies available motivates the application of similarity measures to compare ontology concepts or, by extension, the entities describ...
The size, velocity, and heterogeneity of Big Data outclasses conventional data management tools and requires data and metadata to be fully machine-actionable (i.e., eScience-compliant) and thus findable, acces...
The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past dec...
Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems ...
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 ... -readable. The connectivity...
This article is part of a Supplement: Volume 4 Supplement 1
Bacterial identification and characterization at subspecies level is commonly known as Microbial Typing. Currently, these methodologies are fundamental tools in Clinical Microbiology and bacterial population gene...
Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a..., which can, for example, serve as “switches” that toggle between different functions of a glycoprotein or glycol...
The limited availability of clinical texts for Natural Language Processing purposes is hindering the progress of the field. This article investigates the use of synthetic data for the annotation and automated ...
The evidence-based medicine paradigm requires the ability to aggregate and compare outcomes of interventions across different trials. This can be facilitated and partially automatized by information extraction...
Establishing robust links among gene expression, pathways and phenotypes is critical for understanding diseases and developing treatments. In recent years there have been many efforts to develop the computatio...
A key challenge for improving the quality of health care is to be able to use a common framework to work with patient information acquired in any of the health and life science disciplines. Patient information...
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...
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...
Wikis contain increasing amounts of diverse, biological information useful for elucidating the connections between genes ... disease. The Gene Wiki+ shows how wiki technology can be used in concert with natural.....
This article is part of a Supplement: Volume 3 Supplement 1
We developed the Genetic Glyco-Diseases Ontology (GGDonto) and a RDF/SPARQL-based user interface using Semantic Web technologies. In particular, we represented the GGDonto ... the hierarchy of the ontology, view ...
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 (...
With the advent of inexpensive assay technologies, there has been an unprecedented growth in genomics data as well as the number of databases in which it is stored. In these databases, sample annotation using ...
This article is part of a Supplement: Volume 5 Supplement 1
Chronic renal disease is a global health problem. The identification of suitable biomarkers could facilitate early detection and diagnosis and allow better understanding of the underlying pathology. One of the...
This article is part of a Supplement: Volume 2 Supplement 2
Information technology has the potential to increase the pace ... helping researchers in formulating, publishing and finding information. There are numerous projects that employ ontologies and Semantic Web technologies
This article is part of a Supplement: Volume 1 Supplement 1
The HL7 Clinical Document Architecture (CDA) constrains the HL7 Reference Information model (RIM) to specify the format of HL7-compliant clinical documents, dubbed CDA documents. The use of clinical terminologies...
Using knowledge representation for biomedical projects is now commonplace. In previous work, we represented the knowledge found in a college-level biology textbook in a fashion useful for answering questions. ...
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 pharma...
A common safety vocabulary can facilitate integration of information from disparate systems and processes to permit ... . A team of clinical, safety, and information technology experts is necessary to integrate t...
The lack of established standards to describe and annotate biological assays and screening outcomes in the domain of drug and chemical probe discovery is a severe limitation to utilize public and proprietary d...
This article is part of a Supplement: Volume 5 Supplement 1
Evidence-based medicine propagates that medical/clinical decisions are made by taking into account high-quality evidence, most notably in the form of randomized clinical trials. Evidence-based decision-making ...
Personalized drug prescription can be benefited from the use of intelligent information management and sharing. International standard classifications and ... developed in order to provide unique and unambiguous
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Journal of Biomedical Semantics