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 2022-08-01 to 2026-08-01.)

Article	Citations
Representing dental restoration materials in the oral health and disease ontology	50
Comparing generative and extractive approaches to information extraction from abstracts describing randomized clinical trials	41
ClarID: a human-readable and compact identifier specification for biomedical metadata integration	27
Mapping between clinical and preclinical terminologies: eTRANSAFE’s Rosetta stone approach	25
Gene expression knowledge graph for patient representation and diabetes prediction	24
Semantic classification of Indonesian consumer health questions	22
Explanatory argumentation in natural language for correct and incorrect medical diagnoses	21
BioBLP: a modular framework for learning on multimodal biomedical knowledge graphs	15
From narrative evidence to computable knowledge: a decision-relevant corpus for medicinal herb–disease relationships	15
New and revised gene ontology biological process terms describe multiorganism interactions critical for understanding microbial pathogenesis and sequences of concern	14
Features of a FAIR vocabulary	12
Enriching the FIDEO ontology with food-drug interactions from online knowledge sources	12
Multi-task transfer learning for the prediction of entity modifiers in clinical text: application to opioid use disorder case detection	9
Semantically enabling clinical decision support recommendations	9
MedLexSp – a medical lexicon for Spanish medical natural language processing	9
An extensible and unifying approach to retrospective clinical data modeling: the BrainTeaser Ontology	9
The CLEAR Principle: organizing data and metadata into semantically meaningful types of FAIR Digital Objects to increase their human explorability and cognitive interoperability	9
Assessing resolvability, parsability, and consistency of RDF resources: a use case in rare diseases	8
Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis	7
Semantics in action: a guide for representing clinical data elements with SNOMED CT	7
Development and validation of the early warning system scores ontology	7
Standardizing free-text data exemplified by two fields from the Immune Epitope Database	7
Automatic transparency evaluation for open knowledge extraction systems	6
Analysis and implementation of the DynDiff tool when comparing versions of ontology	6
Concretizing plan specifications as realizables within the OBO foundry	6

Towards reliable Spanish clinical text de-identification through comparative evaluation of language model approaches	6
Classifying literature mentions of biological pathogens as experimentally studied using natural language processing	5
Data management plans as linked open data: exploiting ARGOS FAIR and machine actionable outputs in the OpenAIRE research graph	5
MeSH2Matrix: combining MeSH keywords and machine learning for biomedical relation classification based on PubMed	5
Semantic units: organizing knowledge graphs into semantically meaningful units of representation	5
An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows	4
Constructing a knowledge graph for open government data: the case of Nova Scotia disease datasets	4
Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs	4
Unveiling differential adverse event profiles in vaccines via LLM text embeddings and ontology semantic analysis	4
Improving the classification of cardinality phenotypes using collections	4
Enriched knowledge representation in biological fields: a case study of literature-based discovery in Alzheimer’s disease	3
BASIL DB: bioactive semantic integration and linking database	3
Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features	3
BabelFSH—a toolkit for an effective HL7 FHIR-based terminology provision	3
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology	3
Elucidating the semantics-topology trade-off for knowledge inference-based pharmacological discovery	3
Representing dental caries and dysbiosis within the oral microbiome in the Oral Health and Disease Ontology	3
ACCELERATE-BASSO: early experiences and emerging best practices for ontology development in behavioral and social science research	3
FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards	3
Ontology development and use for cholangiocarcinoma risk factors and predictions: a term enrichment data analysis and machine learning classification	3