OOIR: Observatory of International Research

Papers

(The median citation count of Journal of Biomedical Semantics is 3. 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 2022-06-01 to 2026-06-01.)

Article	Citations
ClarID: a human-readable and compact identifier specification for biomedical metadata integration	42
Representing dental restoration materials in the oral health and disease ontology	36
PhenoDEF: a corpus for annotating sentences with information of phenotype definitions in biomedical literature	24
Comparing generative and extractive approaches to information extraction from abstracts describing randomized clinical trials	24
Semantic classification of Indonesian consumer health questions	23
Mapping between clinical and preclinical terminologies: eTRANSAFE’s Rosetta stone approach	20
Explanatory argumentation in natural language for correct and incorrect medical diagnoses	19
Gene expression knowledge graph for patient representation and diabetes prediction	14
Features of a FAIR vocabulary	13
The CLEAR Principle: organizing data and metadata into semantically meaningful types of FAIR Digital Objects to increase their human explorability and cognitive interoperability	12
Enriching the FIDEO ontology with food-drug interactions from online knowledge sources	12
From narrative evidence to computable knowledge: a decision-relevant corpus for medicinal herb–disease relationships	11
New and revised gene ontology biological process terms describe multiorganism interactions critical for understanding microbial pathogenesis and sequences of concern	10
BioBLP: a modular framework for learning on multimodal biomedical knowledge graphs	9
MedLexSp – a medical lexicon for Spanish medical natural language processing	8
Multi-task transfer learning for the prediction of entity modifiers in clinical text: application to opioid use disorder case detection	8
Semantics in action: a guide for representing clinical data elements with SNOMED CT	6
Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis	6
Assessing resolvability, parsability, and consistency of RDF resources: a use case in rare diseases	6
An extensible and unifying approach to retrospective clinical data modeling: the BrainTeaser Ontology	6
MeSH2Matrix: combining MeSH keywords and machine learning for biomedical relation classification based on PubMed	5
Automatic transparency evaluation for open knowledge extraction systems	5
Semantically enabling clinical decision support recommendations	5
Analysis and implementation of the DynDiff tool when comparing versions of ontology	5
Standardizing free-text data exemplified by two fields from the Immune Epitope Database	5

Concretizing plan specifications as realizables within the OBO foundry	5
Development and validation of the early warning system scores ontology	5
Classifying literature mentions of biological pathogens as experimentally studied using natural language processing	4
Data management plans as linked open data: exploiting ARGOS FAIR and machine actionable outputs in the OpenAIRE research graph	4
Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research	4
Improving the classification of cardinality phenotypes using collections	4
Semantic units: organizing knowledge graphs into semantically meaningful units of representation	4
Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs	4
Elucidating the semantics-topology trade-off for knowledge inference-based pharmacological discovery	3
Unveiling differential adverse event profiles in vaccines via LLM text embeddings and ontology semantic analysis	3
Enriched knowledge representation in biological fields: a case study of literature-based discovery in Alzheimer’s disease	3
BabelFSH—a toolkit for an effective HL7 FHIR-based terminology provision	3
An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows	3
Constructing a knowledge graph for open government data: the case of Nova Scotia disease datasets	3
FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards	3
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology	3
Performance assessment of ontology matching systems for FAIR data	3
Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features	3
BASIL DB: bioactive semantic integration and linking database	3
Ontology development and use for cholangiocarcinoma risk factors and predictions: a term enrichment data analysis and machine learning classification	3