Page 5 of 10
Trivalent Influenza Virus Vaccine (FLU3) is a traditional flu vaccine to protect people against three different flu viruses, including influenza A H1N1 virus, an influenza A H3N2 virus and one B virus.
Biomedical event extraction is one of the key tasks in biomedical text mining, supporting various applications such as database curation and hypothesis generation. Several systems, some of which have been appl...
In the United States, 795,000 people suffer strokes each year; 10–15 % of these strokes can be attributed to stenosis caused by plaque in the carotid artery, a major stroke phenotype risk factor. Studies compa...
As a special class of non-coding RNAs (ncRNAs), microRNAs (miRNAs) perform important roles in numerous biological and pathological processes. The realization of miRNA functions depends largely on how miRNAs re...
The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data ...
In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identificat...
The public health initiatives for obesity prevention are increasingly exploiting the advantages of smart technologies that can register various kinds of data related to physical, physiological, and behavioural...
Biobanking necessitates extensive integration of data to allow data analysis and specimen sharing. Ontologies have been demonstrated to be a promising approach in fostering better semantic integration of bioba...
MicroRNAs are increasingly being appreciated as critical players in human diseases, and questions concerning the role of microRNAs arise in many areas of biomedical research. There are several manually curated...
Biomedical text mining may target various kinds of valuable information embedded in the literature, but a critical obstacle to the extension of the mining targets is the cost of manual construction of labeled ...
The original article was published in Journal of Biomedical Semantics 2016 7:11
Although signing a vaccination (or immunization) informed consent form is not a federal requirement in the US and Canada, such a practice is required by many states and pharmacies. The content and structures o...
In previous work, we built the Drug Ontology (DrOn) to support comparative effectiveness research use cases. Here, we have updated our representation of ingredients to include both active ingredients (and thei...
To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts ...
MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium in...
The Simple Knowledge Organization System (SKOS) was introduced to the wider research community by a 2005 World Wide Web Consortium (W3C) working draft, and further developed and refined in a 2009 W3C recommend...
Authoring bio-ontologies is a task that has traditionally been undertaken by skilled experts trained in understanding complex languages such as the Web Ontology Language (OWL), in tools designed for such exper...
There have been relatively few attempts to represent vision or blindness ontologically. This is unsurprising as the related phenomena of sight and blindness are difficult to represent ontologically for a varie...
The Centre for Therapeutic Target Validation (CTTV - https://www.targetvalidation.org/) was established to generate therapeutic target evidence from ge...
Information about drug–drug interactions (DDIs) is crucial for computational applications such as pharmacovigilance and drug repurposing. However, existing sources of DDIs have the problems of low coverage, lo...
The Erratum to this article has been published in Journal of Biomedical Semantics 2016 7:21
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...
The “Vaccine and Drug Ontology Studies” (VDOS) international workshop series focuses on vaccine- and drug-related ontology modeling and applications. Drugs and vaccines have been critical to prevent and treat ...
It has been shown that exergames have multiple benefits for physical, mental and cognitive health. Only recently, however, researchers have started considering them as health monitoring tools, through collecti...
The Erratum to this article has been published in Journal of Biomedical Semantics 2016 7:31
Identifying partial mappings between two terminologies is of special importance when one terminology is finer-grained than the other, as is the case for the Human Phenotype Ontology (HPO), mainly used for rese...
Genotype-phenotype studies aim to identify causative relationships between genes and phenotypes. The International Mouse Phenotyping Consortium is a high throughput phenotyping program whose goal is to collect...
MHC molecules are a highly diverse family of proteins that play a key role in cellular immune recognition. Over time, different techniques and terminologies have been developed to identify the specific type(s)...
The specification of metadata in clinical and epidemiological study projects absorbs significant expense. The validity and quality of the collected data depend heavily on the precise and semantical correct rep...
The bio-ontologies and phenotypes special issue includes eight papers selected from the 11 papers presented at the Bio-Ontologies SIG (Special Interest Group) and the Phenotype Day at ISMB (Intelligent Systems...
Semantic web technologies have a tremendous potential for the integration of heterogeneous data sets. Therefore, an increasing number of widely used biological resources are becoming available in the RDF data ...
To promote research activities in a particular research area, it is important to efficiently identify current research trends, advances, and issues in that area. Although review papers in the research area can...
Biomedical ontologies are representations of classes of entities in the biomedical domain and how these classes are related in computer- and human-interpretable formats. Ontologies support data standardization...
Embryology is a complex morphologic discipline involving a set of entangled mechanisms, sometime difficult to understand and to visualize. Recent computer based techniques ranging from geometrical to physicall...
The increasing use of ontologies highlights the need for a library for working with ontologies that is efficient, accessible from various programming languages, and compatible with common computational platforms.
In the realm of knee pathology, magnetic resonance imaging (MRI) has the advantage of visualising all structures within the knee joint, which makes it a valuable tool for increasing diagnostic accuracy and pla...
Vaccines are one of the most important public health successes in last century. Besides effectiveness in reducing the morbidity and mortality from many infectious diseases, a successful vaccine program also re...
The Genome Variant Format (GVF) uses the Sequence Ontology (SO) to enable detailed annotation of sequence variation. The annotation includes SO terms for the type of sequence alteration, the genomic features t...
Large quantities of biomedical data are being produced at a rapid pace for a variety of organisms. With ontologies proliferating, data is increasingly being stored using the RDF data model and queried using RD...
The complexity and scale of the knowledge in the biomedical domain has motivated research work towards mining heterogeneous data from both structured and unstructured knowledge bases. Towards this direction, i...
In the clinical dentists and periodontal researchers’ community, there is an obvious demand for a systems model capable of linking the clinical presentation of periodontitis to underlying molecular knowledge. ...
There are numerous options available to achieve various tasks in bioinformatics, but until recently, there were no tools that could systematically identify mentions of databases and tools within the literature...
A large number of life science ontologies has been developed to support different application scenarios such as gene annotation or functional analysis. The continuous accumulation of new insights and knowledge...
Phenotypes form the basis for determining the existence of a disease against the given evidence. Much of this evidence though remains locked away in text – scientific articles, clinical trial reports and elect...
Discovering gene interactions and their characterizations from biological text collections is a crucial issue in bioinformatics. Indeed, text collections are large and it is very difficult for biologists to fu...
Mild traumatic brain injury (mTBI) has high prevalence in the military, among athletes, and in the general population worldwide (largely due to falls). Consequences can include a range of neuropsychological di...
There is limited consensus among drug information sources on what constitutes drug-drug interactions (DDIs). We investigate DDI information in two publicly available sources, NDF-RT and DrugBank.
To construct a comprehensive vaccine information ontology that can support personal health information applications using patient-consumer lexicon, and lead to outcomes that can improve patient education.
While the association between a drug and an adverse event (ADE) is generally detected at the level of individual drugs, ADEs are often discussed at the class level, i.e., at the level of pharmacologic classes ...
Lately, ontologies have become a fundamental building block in the process of formalising and storing complex biomedical information. The community-driven ontology curation process, however, ignores the possib...
Model repositories such as BioModels Database provide computational models of biological systems for the scientific community. These models contain rich semantic annotations that link model entities to concept...
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...
Speed
63 days to first decision for all manuscripts
272 days to first decision for reviewed manuscripts only
422 days from submission to acceptance
53 days from acceptance to publication
Citation Impact
2.160 - 2-year Impact Factor
1.967 - 5-year Impact Factor
1.548 - Source Normalized Impact per Paper (SNIP)
0.666 - SCImago Journal Rank (SJR)
Usage
217,157 downloads (2021)
24 Altmetric mentions
Journal of Biomedical Semantics