OOIR: Observatory of International Research

Papers

(The median citation count of Journal of Biomedical Semantics is 2. 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 2021-10-01 to 2025-10-01.)

Article	Citations
Extending electronic medical records vector models with knowledge graphs to improve hospitalization prediction	45
Comparing generative and extractive approaches to information extraction from abstracts describing randomized clinical trials	26
PhenoDEF: a corpus for annotating sentences with information of phenotype definitions in biomedical literature	21
Improving reusability along the data life cycle: a regulatory circuits case study	19
An annotated dataset for extracting gene-melanoma relations from scientific literature	18
Mapping between clinical and preclinical terminologies: eTRANSAFE’s Rosetta stone approach	18
Semantic classification of Indonesian consumer health questions	18
Gene expression knowledge graph for patient representation and diabetes prediction	17
Explanatory argumentation in natural language for correct and incorrect medical diagnoses	17
Features of a FAIR vocabulary	14
New and revised gene ontology biological process terms describe multiorganism interactions critical for understanding microbial pathogenesis and sequences of concern	14
BioBLP: a modular framework for learning on multimodal biomedical knowledge graphs	13
Multi-task transfer learning for the prediction of entity modifiers in clinical text: application to opioid use disorder case detection	11
Enriching the FIDEO ontology with food-drug interactions from online knowledge sources	11
MedLexSp – a medical lexicon for Spanish medical natural language processing	11
Semantics in action: a guide for representing clinical data elements with SNOMED CT	8
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data	8
Residual refinement for interactive skin lesion segmentation	8
Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis	8
Assessing resolvability, parsability, and consistency of RDF resources: a use case in rare diseases	8
Semantically enabling clinical decision support recommendations	6
An extensible and unifying approach to retrospective clinical data modeling: the BrainTeaser Ontology	6
Defining health data elements under the HL7 development framework for metadata management	5
Automatic transparency evaluation for open knowledge extraction systems	5
Development and validation of the early warning system scores ontology	5

Standardizing free-text data exemplified by two fields from the Immune Epitope Database	5
Analysis and implementation of the DynDiff tool when comparing versions of ontology	4
Concretizing plan specifications as realizables within the OBO foundry	4
FAIR data representation in times of eScience: a comparison of instance-based and class-based semantic representations of empirical data using phenotype descriptions as example	4
Ontology-based identification and prioritization of candidate drugs for epilepsy from literature	4
Classifying literature mentions of biological pathogens as experimentally studied using natural language processing	4
MeSH2Matrix: combining MeSH keywords and machine learning for biomedical relation classification based on PubMed	3
An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows	3
Unveiling differential adverse event profiles in vaccines via LLM text embeddings and ontology semantic analysis	3
Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features	3
Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research	3
Improving the classification of cardinality phenotypes using collections	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
Data management plans as linked open data: exploiting ARGOS FAIR and machine actionable outputs in the OpenAIRE research graph	3
Semantic units: organizing knowledge graphs into semantically meaningful units of representation	3
Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs	3
Elucidating the semantics-topology trade-off for knowledge inference-based pharmacological discovery	3
Performance assessment of ontology matching systems for FAIR data	3
Enriched knowledge representation in biological fields: a case study of literature-based discovery in Alzheimer’s disease	2
Multiple sampling schemes and deep learning improve active learning performance in drug-drug interaction information retrieval analysis from the literature	2
Sentences, entities, and keyphrases extraction from consumer health forums using multi-task learning	2
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology	2
FAIR Data Cube, a FAIR data infrastructure for integrated multi-omics data analysis	2
Three-layered semantic framework for public health intelligence	2
BASIL DB: bioactive semantic integration and linking database	2
Prefrontal fNIRS-based clinical data analysis of brain functions in individuals abusing different types of drugs	2
Digital evolution: Novo Nordisk’s shift to ontology-based data management	2