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

Article	Citations
Comparing generative and extractive approaches to information extraction from abstracts describing randomized clinical trials	51
Extending electronic medical records vector models with knowledge graphs to improve hospitalization prediction	29
PhenoDEF: a corpus for annotating sentences with information of phenotype definitions in biomedical literature	29
Improving reusability along the data life cycle: a regulatory circuits case study	27
Semantic classification of Indonesian consumer health questions	21
Gene expression knowledge graph for patient representation and diabetes prediction	21
Mapping between clinical and preclinical terminologies: eTRANSAFE’s Rosetta stone approach	21
An annotated dataset for extracting gene-melanoma relations from scientific literature	19
Enriching the FIDEO ontology with food-drug interactions from online knowledge sources	18
Explanatory argumentation in natural language for correct and incorrect medical diagnoses	18
BioBLP: a modular framework for learning on multimodal biomedical knowledge graphs	17
The CLEAR Principle: organizing data and metadata into semantically meaningful types of FAIR Digital Objects to increase their human explorability and cognitive interoperability	14
New and revised gene ontology biological process terms describe multiorganism interactions critical for understanding microbial pathogenesis and sequences of concern	11
Features of a FAIR vocabulary	11
MedLexSp – a medical lexicon for Spanish medical natural language processing	11
Multi-task transfer learning for the prediction of entity modifiers in clinical text: application to opioid use disorder case detection	10
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data	9
Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis	8
An extensible and unifying approach to retrospective clinical data modeling: the BrainTeaser Ontology	8
Semantics in action: a guide for representing clinical data elements with SNOMED CT	7
Assessing resolvability, parsability, and consistency of RDF resources: a use case in rare diseases	7
Semantically enabling clinical decision support recommendations	6
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
Defining health data elements under the HL7 development framework for metadata management	5

Concretizing plan specifications as realizables within the OBO foundry	5
Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research	4
Analysis and implementation of the DynDiff tool when comparing versions of ontology	4
MeSH2Matrix: combining MeSH keywords and machine learning for biomedical relation classification based on PubMed	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
Automatic transparency evaluation for open knowledge extraction systems	4
Elucidating the semantics-topology trade-off for knowledge inference-based pharmacological discovery	3
Semantic units: organizing knowledge graphs into semantically meaningful units of representation	3
Improving the classification of cardinality phenotypes using collections	3
Unveiling differential adverse event profiles in vaccines via LLM text embeddings and ontology semantic analysis	3
Constructing a knowledge graph for open government data: the case of Nova Scotia disease datasets	3
An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows	3
Performance assessment of ontology matching systems for FAIR data	3
FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards	3
Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features	3
Data management plans as linked open data: exploiting ARGOS FAIR and machine actionable outputs in the OpenAIRE research graph	3
Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs	3
BASIL DB: bioactive semantic integration and linking database	3