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Journal of Biomedical Semantics
Scopus
ISSN 2041-1480 · BMC · 316 articles in the index
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Journal Article
Ontology development and use for cholangiocarcinoma risk factors and predictions: a term enrichment data analysis and machine learning classification
Abstract Background Cholangiocarcinoma (CCA) is a critical public health problem in Thailand. The prevalence is much higher than other areas in the world. Data about CCA are stored in different data sources and standards in both research data sets and electronic health records (EHR). Objective This…
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Journal Article
A practical and nuanced framework for entity linking evaluation
Abstract Background Entity linking maps textual mentions with entities in vocabularies. While accuracy is the primary metric for entity linking evaluation, it fails to capture the complexity of model behaviour. Results We propose an entity linking evaluation framework that clarifies the target…
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Journal Article
Annotating and indexing scientific articles with rare diseases
Abstract Background Around 30 million people in Europe are affected by a rare (or orphan) disease, defined as a condition occurring in fewer than 1 in 2,000 individuals. The primary challenge is to automatically and efficiently identify scientific articles and guidelines that address a particular…
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Journal Article
An application-based ontological knowledge base of medications to support health literacy and adherence for the consumer population: an aging population use case
Abstract Background The geriatric population is a vulnerable population that has higher rate of chronic disease and represents the largest portion of healthcare delivered. This population is vulnerable to medication non-adherence. Patient medication non-adherence is a problem that can lead to…
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Journal Article
Immune biomarkers, profiles, and responses: a vaccine ontology perspective
Abstract Background Vaccines have the ability to induce a range of immune responses under different conditions, for example stimulating the production of neutralizing antibodies to block pathogen entry or activating cytotoxic T cells to eliminate infected cells. Many such immune responses have not…
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Journal Article
BERTopic-driven term extraction from biomedical texts toward ontology population: evaluating vaccine ontology with Plotkin’s vaccines corpus
Abstract Background Ontologies are essential for structuring biomedical knowledge, supporting semantic integration, reasoning, and data interoperability. In vaccinology, ontology population is particularly critical, as vaccines span diverse domains. A well-defined Vaccine Ontology enables…
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Journal Article
A pragmatist approach to bridging tables and ontologies through LinkML and punning
Abstract Background Ontologies support data integration and knowledge discovery across multiple life science disciplines through the application of formal semantics that define hierarchical and cross-hierarchical relationships which enable automated reasoning capabilities. At the same time, tabular…
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Journal Article
Knowledge graph embedding and alignment of incomplete electronic health records for critical care applications
Abstract Background Data-driven AI models in clinical care increasingly rely on integrating data from heterogeneous sources to improve predictive performance. Traditional Electronic Health Record (EHR) systems however pose significant challenges for data integration due to the use of diverse…
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Journal Article
FAIR in practice: minimum metadata schema for bioinformatics analytics by machines
Abstract Background One pillar of FAIR principles adoption is Reusability by machines to enable for example more efficient data analytics in fields such as Bioinformatics. However, it is not clear to what extent current metadata exposed by datasets and tools in common repositories enable this. In…
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Journal Article
Utilizing BERTopic modeling for concept discovery in the domain of gerotranscendence and solitude
Abstract Background Ontology development is a complex, iterative process that traditionally requires extensive collaboration between ontology developers and subject matter experts. While effective, this manual approach is time-consuming, labor-intensive, and prone to cognitive bias. To streamline…
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Journal Article
Prenatal monitoring in primary health care: a design science research-based approach to FHIR interoperability
Abstract Background This research addresses the development and validation of an information model for pregnancy monitoring that, through the Fast Healthcare Interoperability Resources (FHIR) specification, seeks to promote interoperability for the quality of prenatal care by multidisciplinary…
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Journal Article
Benchmarking MeSH-augmented embeddings for biomedical document similarity
Abstract Background The extensive volume of biomedical scientific literature requires efficient methods for retrieving relevant documents based on semantic technologies and biomedical concepts. While embedding-based methods have shown improvements over traditional keyword-based methods, the…
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Journal Article
Terminology binding with SNOMED CT to bridge differences in information structures: a feasibility study
Abstract Background Safe and accurate sharing of healthcare information is essential for good health and well-being. Information must be exchanged among multiple parties, making the transformation between different information structures unavoidable. It has been suggested that such a transformation…
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Journal Article
Introducing the TOP framework: a novel phenotyping solution for collaborative phenotype algorithm development and application
Abstract Background Phenotyping, the comprehensive assessment of observable characteristics, is essential for advancing medical understanding and personalised healthcare. However, traditional phenotyping methods are often manual, time-intensive, and limited in scope. To address these challenges…
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Journal Article
From narrative evidence to computable knowledge: a decision-relevant corpus for medicinal herb–disease relationships
Abstract Background Traditional medicine (TM) employs medicinal herbs (MHs) to manage diverse health conditions, yet much of this evidence remains embedded in narrative biomedical text, limiting its use in computational analysis and decision making. As integrative medicine increasingly demands…
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Journal Article
Advancing the bioassay ontology through integrated PK/PD and safety pharmacology representation
Abstract The latest release of the BioAssay Ontology (BAO), version 2.8.16, introduces major updates that expand its ability to describe and categorize assays related to pharmacokinetics, pharmacodynamics, and safety pharmacology. These refinements, driven by collaboration with the Semantic…
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Journal Article
Representing dental restoration materials in the oral health and disease ontology
Abstract Background Semantic clarity and standardization in representing dental restoration materials are essential for ensuring interoperability across research and clinical settings. However, existing ontologies, including those in the Open Biological and Biomedical Ontology (OBO) Foundry…
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Journal Article
ECLed– a tool supporting the effective use of the SNOMED CT Expression Constraint Language
Abstract Background The Expression Constraint Language (ECL) is a powerful query language for SNOMED CT, enabling precise semantic queries across clinical concepts. However, its complex syntax and reliance on the SNOMED CT Concept Model make it difficult for non-experts to use, limiting its broader…
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Journal Article
ClarID: a human-readable and compact identifier specification for biomedical metadata integration
Abstract Background In biomedical research, subjects and biospecimens are commonly tracked using simple IDs or UUIDs, which guarantee uniqueness but convey no embedded semantic information. Contextual metadata (such as tissue type, diagnosis, or assay) is often stored separately, making…
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Journal Article
Representing dental caries and dysbiosis within the oral microbiome in the Oral Health and Disease Ontology
Abstract Background Dental caries is an oral health condition in which cariogenic bacteria demineralize and decay teeth. It arises due to interaction between the host, environment, and oral microbiome. Current terminologies and ontologies, however, do not accurately represent the important role…