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The Findable, Accessible, Interoperable and Reusable(FAIR) Principles explicitly require the use of FAIR vocabularies, but what precisely constitutes a FAIR vocabulary remains unclear. Being able to define FAI...
Drug-drug interaction (DDI) information retrieval (IR) is an important natural language process (NLP) task from the PubMed literature. For the first time, active learning (AL) is studied in DDI IR analysis. DD...
The majority of available datasets in open government data are statistical. They are widely published by various governments to be used by the public and data consumers. However, most open government data port...
Evaluating the impact of environmental exposures on organism health is a key goal of modern biomedicine and is critically important in an age of greater pollution and chemicals in our environment. Environmenta...
Medical lexicons enable the natural language processing (NLP) of health texts. Lexicons gather terms and concepts from thesauri and ontologies, and linguistic data for part-of-speech (PoS) tagging, lemmatizati...
Information pertaining to mechanisms, management and treatment of disease-causing pathogens including viruses and bacteria is readily available from research publications indexed in MEDLINE. However, identifyi...
Intense research has been done in the area of biomedical natural language processing. Since the breakthrough of transfer learning-based methods, BERT models are used in a variety of biomedical and clinical app...
The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and saf...
Vaccine information in European electronic health record (EHR) databases is represented using various clinical and database-specific coding systems and drug vocabularies. The lack of harmonization constitutes ...
Health data analytics is an area that is facing rapid change due to the acceleration of digitization of the health sector, and the changing landscape of health data and clinical terminology standards. Our rese...
The Vaccine Ontology (VO) is a biomedical ontology that standardizes vaccine annotation. Errors in VO will affect a multitude of applications that it is being used in. Quality assurance of VO is imperative to ...
The concept of Data Management Plan (DMP) has emerged as a fundamental tool to help researchers through the systematical management of data. The Research Data Alliance DMP Common Standard (DCS) working group d...
The original article was published in Journal of Biomedical Semantics 2022 13:17
Ontology matching should contribute to the interoperability aspect of FAIR data (Findable, Accessible, Interoperable, and Reusable). Multiple data sources can use different ontologies for annotating their data...
In times of exponential data growth in the life sciences, machine-supported approaches are becoming increasingly important and with them the need for FAIR (Findable, Accessible, Interoperable, Reusable) and eS...
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
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 ...
Most previous relation extraction (RE) studies have focused on intra sentence relations and have ignored relations that span sentences, i.e. inter sentence relations. Such relations connect entities at the doc...
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...
The high volume of research focusing on extracting patient information from electronic health records (EHRs) has led to an increase in the demand for annotated corpora, which are a precious resource for both t...
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...
In life sciences, there has been a long-standing effort of standardization and integration of reference datasets and databases. Despite these efforts, many studies data are provided using specific and non-stan...
Health data from different specialties or domains generallly have diverse formats and meanings, which can cause semantic communication barriers when these data are exchanged among heterogeneous systems. As suc...
The European Platform on Rare Disease Registration (EU RD Platform) aims to address the fragmentation of European rare disease (RD) patient data, scattered among hundreds of independent and non-coordinating re...
Transfer learning is a common practice in image classification with deep learning where the available data is often limited for training a complex model with millions of parameters. However, transferring langu...
Population-based cancer registries are a critical reference source for the surveillance and control of cancer. Cancer registries work extensively with the internationally recognised TNM classification system u...
Artificial intelligence methods applied to electronic medical records (EMRs) hold the potential to help physicians save time by sharpening their analysis and decisions, thereby improving the health of patients...
Text mining can be applied to automate knowledge extraction from unstructured data included in medical reports and generate quality indicators applicable for medical documentation. The primary objective of thi...
Electronic Laboratory Notebooks (ELNs) are used to document experiments and investigations in the wet-lab. Protocols in ELNs contain a detailed description of the conducted steps including the necessary inform...
Drug repurposing can improve the return of investment as it finds new uses for existing drugs. Literature-based analyses exploit factual knowledge on drugs and diseases, e.g. from databases, and combine it wit...
Melanoma is one of the least common but the deadliest of skin cancers. This cancer begins when the genes of a cell suffer damage or fail, and identifying the genes involved in melanoma is crucial for understan...
The advancement of science and technologies play an immense role in the way scientific experiments are being conducted. Understanding how experiments are performed and how results are derived has become signif...
Image segmentation is a difficult and classic problem. It has a wide range of applications, one of which is skin lesion segmentation. Numerous researchers have made great efforts to tackle the problem, yet the...
The activation degree of the orbitofrontal cortex (OFC) functional area in drug abusers is directly related to the craving for drugs and the tolerance to punishment. Currently, among the clinical research on d...
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...
Medical experts in the domain of Diabetes Mellitus (DM) acquire specific knowledge from diabetic patients through monitoring and interaction. This allows them to know the disease and information about other co...
With COVID-19 still in its pandemic stage, extensive research has generated increasing amounts of data and knowledge. As many studies are published within a short span of time, we often lose an integrative and...
In recent years a large volume of clinical genomics data has become available due to rapid advances in sequencing technologies. Efficient exploitation of this genomics data requires linkage to patient phenotyp...
Transfer learning aims at enhancing machine learning performance on a problem by reusing labeled data originally designed for a related, but distinct problem. In particular, domain adaptation consists for a sp...
The ontology authoring step in ontology development involves having to make choices about what subject domain knowledge to include. This may concern sorting out ontological differences and making choices betwe...
The revolution in molecular biology has shown how protein function and structure are based on specific sequences of amino acids. Thus, an important feature in many papers is the mention of the significance of ...
Effective response to public health emergencies, such as we are now experiencing with COVID-19, requires data sharing across multiple disciplines and data systems. Ontologies offer a powerful data sharing tool...
Recent advances in representation learning have enabled large strides in natural language understanding; However, verbal reasoning remains a challenge for state-of-the-art systems. External sources of structur...
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 ...
Named Entity Recognition is a common task in Natural Language Processing applications, whose purpose is to recognize named entities in textual documents. Several systems exist to solve this task in the biomedi...
Iranian traditional medicine, also known as Persian Medicine, is a holistic school of medicine with a long prolific history. It describes numerous concepts and the relationships between them. However, no unifi...
A wide array of existing instruments are commonly used to assess childhood behavior and development for the evaluation of social, emotional and behavioral disorders such as Autism Spectrum Disorder (ASD), atte...
Biomedical ontologies contain a wealth of metadata that constitutes a fundamental infrastructural resource for text mining. For several reasons, redundancies exist in the ontology ecosystem, which lead to the ...
Medical texts such as radiology reports or electronic health records are a powerful source of data for researchers. Anonymization methods must be developed to de-identify documents containing personal informat...
The amount of available data, which can facilitate answering scientific research questions, is growing. However, the different formats of published data are expanding as well, creating a serious challenge when...
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Journal of Biomedical Semantics