Journal of Biomedical Semantics

Papers
(The median citation count of Journal of Biomedical Semantics is 1. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-02-01 to 2025-02-01.)
ArticleCitations
Automatic transparency evaluation for open knowledge extraction systems33
Defining health data elements under the HL7 development framework for metadata management26
We are not ready yet: limitations of state-of-the-art disease named entity recognizers16
Why and how to engage expert stakeholders in ontology development: insights from social and behavioural sciences15
An ontology network for Diabetes Mellitus in Mexico15
Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)14
End-to-End provenance representation for the understandability and reproducibility of scientific experiments using a semantic approach12
Elucidating the semantics-topology trade-off for knowledge inference-based pharmacological discovery11
Ontology-based identification and prioritization of candidate drugs for epilepsy from literature10
Comparing generative and extractive approaches to information extraction from abstracts describing randomized clinical trials9
Synthetic data for annotation and extraction of family history information from clinical text9
SemClinBr - a multi-institutional and multi-specialty semantically annotated corpus for Portuguese clinical NLP tasks8
Concretizing plan specifications as realizables within the OBO foundry8
Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features7
Improved characterisation of clinical text through ontology-based vocabulary expansion7
An annotated dataset for extracting gene-melanoma relations from scientific literature6
PhenoDEF: a corpus for annotating sentences with information of phenotype definitions in biomedical literature6
IrGO: Iranian traditional medicine General Ontology and knowledge base6
Extending electronic medical records vector models with knowledge graphs to improve hospitalization prediction6
Project Rosetta: a childhood social, emotional, and behavioral developmental feature mapping5
Improving reusability along the data life cycle: a regulatory circuits case study5
CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature4
FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards4
Analysis and implementation of the DynDiff tool when comparing versions of ontology4
Explanatory argumentation in natural language for correct and incorrect medical diagnoses4
The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond4
Leveraging logical definitions and lexical features to detect missing IS-A relations in biomedical terminologies4
RecSOI: recommending research directions using statements of ignorance4
Chemical entity normalization for successful translational development of Alzheimer’s disease and dementia therapeutics4
Annotation of epilepsy clinic letters for natural language processing4
ResidueFinder: extracting individual residue mentions from protein literature4
Automatic classification of experimental models in biomedical literature to support searching for alternative methods to animal experiments3
BioBLP: a modular framework for learning on multimodal biomedical knowledge graphs3
Impact of COVID-19 research: a study on predicting influential scholarly documents using machine learning and a domain-independent knowledge graph3
FAIR data representation in times of eScience: a comparison of instance-based and class-based semantic representations of empirical data using phenotype descriptions as example3
Enriching the FIDEO ontology with food-drug interactions from online knowledge sources2
Prefrontal fNIRS-based clinical data analysis of brain functions in individuals abusing different types of drugs2
Syntax-based transfer learning for the task of biomedical relation extraction2
Features of a FAIR vocabulary2
Applying the FAIR principles to data in a hospital: challenges and opportunities in a pandemic2
Transfer language space with similar domain adaptation: a case study with hepatocellular carcinoma2
Classifying literature mentions of biological pathogens as experimentally studied using natural language processing2
MeSH2Matrix: combining MeSH keywords and machine learning for biomedical relation classification based on PubMed2
Pathling: analytics on FHIR1
Improving the classification of cardinality phenotypes using collections1
Multi-task transfer learning for the prediction of entity modifiers in clinical text: application to opioid use disorder case detection1
Correction to: Semantic units: organizing knowledge graphs into semantically meaningful units of representation1
Text mining-based measurement of precision of polysomnographic reports as basis for intervention1
Alignment of vaccine codes using an ontology of vaccine descriptions1
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data1
BioVerbNet: a large semantic-syntactic classification of verbs in biomedicine1
An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows1
Data management plans as linked open data: exploiting ARGOS FAIR and machine actionable outputs in the OpenAIRE research graph1
SIENA: Semi-automatic semantic enhancement of datasets using concept recognition1
An annotated corpus of clinical trial publications supporting schema-based relational information extraction1
Optimized continuous homecare provisioning through distributed data-driven semantic services and cross-organizational workflows1
Assessing resolvability, parsability, and consistency of RDF resources: a use case in rare diseases1
Semantic units: organizing knowledge graphs into semantically meaningful units of representation1
Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research1
Linking common human diseases to their phenotypes; development of a resource for human phenomics1
MedLexSp – a medical lexicon for Spanish medical natural language processing1
Ontological representation, modeling, and analysis of parasite vaccines1
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