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 2022-05-01 to 2026-05-01.)

Article	Citations
PhenoDEF: a corpus for annotating sentences with information of phenotype definitions in biomedical literature	39
Representing dental restoration materials in the oral health and disease ontology	35
ClarID: a human-readable and compact identifier specification for biomedical metadata integration	25
Semantic classification of Indonesian consumer health questions	24
Comparing generative and extractive approaches to information extraction from abstracts describing randomized clinical trials	24
Mapping between clinical and preclinical terminologies: eTRANSAFE’s Rosetta stone approach	23
Gene expression knowledge graph for patient representation and diabetes prediction	20
Explanatory argumentation in natural language for correct and incorrect medical diagnoses	18
BioBLP: a modular framework for learning on multimodal biomedical knowledge graphs	13
Features of a FAIR vocabulary	12
The CLEAR Principle: organizing data and metadata into semantically meaningful types of FAIR Digital Objects to increase their human explorability and cognitive interoperability	12
New and revised gene ontology biological process terms describe multiorganism interactions critical for understanding microbial pathogenesis and sequences of concern	12
Multi-task transfer learning for the prediction of entity modifiers in clinical text: application to opioid use disorder case detection	10
Enriching the FIDEO ontology with food-drug interactions from online knowledge sources	10
Semantics in action: a guide for representing clinical data elements with SNOMED CT	8
Assessing resolvability, parsability, and consistency of RDF resources: a use case in rare diseases	8
MedLexSp – a medical lexicon for Spanish medical natural language processing	8
Semantically enabling clinical decision support recommendations	7
Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis	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
Classifying literature mentions of biological pathogens as experimentally studied using natural language processing	5
Standardizing free-text data exemplified by two fields from the Immune Epitope Database	5
Development and validation of the early warning system scores ontology	5

Analysis and implementation of the DynDiff tool when comparing versions of ontology	5
Concretizing plan specifications as realizables within the OBO foundry	5
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
Data management plans as linked open data: exploiting ARGOS FAIR and machine actionable outputs in the OpenAIRE research graph	4
Performance assessment of ontology matching systems for FAIR data	4
Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs	4
Semantic units: organizing knowledge graphs into semantically meaningful units of representation	4
An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows	4
Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research	4
Elucidating the semantics-topology trade-off for knowledge inference-based pharmacological discovery	3
Enriched knowledge representation in biological fields: a case study of literature-based discovery in Alzheimer’s disease	3
Representing dental caries and dysbiosis within the oral microbiome in the Oral Health and Disease Ontology	3
Ontology development and use for cholangiocarcinoma risk factors and predictions: a term enrichment data analysis and machine learning classification	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
BabelFSH—a toolkit for an effective HL7 FHIR-based terminology provision	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