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 2021-06-01 to 2025-06-01.)

Article	Citations
PhenoDEF: a corpus for annotating sentences with information of phenotype definitions in biomedical literature	42
Extending electronic medical records vector models with knowledge graphs to improve hospitalization prediction	39
Comparing generative and extractive approaches to information extraction from abstracts describing randomized clinical trials	25
Explanatory argumentation in natural language for correct and incorrect medical diagnoses	18
Gene expression knowledge graph for patient representation and diabetes prediction	17
Improving reusability along the data life cycle: a regulatory circuits case study	17
New and revised gene ontology biological process terms describe multiorganism interactions critical for understanding microbial pathogenesis and sequences of concern	17
An annotated dataset for extracting gene-melanoma relations from scientific literature	17
Syntax-based transfer learning for the task of biomedical relation extraction	12
Enriching the FIDEO ontology with food-drug interactions from online knowledge sources	12
Features of a FAIR vocabulary	11
BioBLP: a modular framework for learning on multimodal biomedical knowledge graphs	11
Multi-task transfer learning for the prediction of entity modifiers in clinical text: application to opioid use disorder case detection	10
Assessing resolvability, parsability, and consistency of RDF resources: a use case in rare diseases	9
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data	9
MedLexSp – a medical lexicon for Spanish medical natural language processing	9
Semantics in action: a guide for representing clinical data elements with SNOMED CT	8
An extensible and unifying approach to retrospective clinical data modeling: the BrainTeaser Ontology	8
Residual refinement for interactive skin lesion segmentation	8
Semantically enabling clinical decision support recommendations	7
Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis	7
Automatic transparency evaluation for open knowledge extraction systems	6
Defining health data elements under the HL7 development framework for metadata management	6
Development and validation of the early warning system scores ontology	6
Ontology-based identification and prioritization of candidate drugs for epilepsy from literature	6

MeSH2Matrix: combining MeSH keywords and machine learning for biomedical relation classification based on PubMed	5
Concretizing plan specifications as realizables within the OBO foundry	5
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	5
Standardizing free-text data exemplified by two fields from the Immune Epitope Database	5
Classifying literature mentions of biological pathogens as experimentally studied using natural language processing	5
Semantic units: organizing knowledge graphs into semantically meaningful units of representation	4
Data management plans as linked open data: exploiting ARGOS FAIR and machine actionable outputs in the OpenAIRE research graph	4
Analysis and implementation of the DynDiff tool when comparing versions of ontology	4
Linking common human diseases to their phenotypes; development of a resource for human phenomics	4
Constructing a knowledge graph for open government data: the case of Nova Scotia disease datasets	3
Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs	3
Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research	3
Performance assessment of ontology matching systems for FAIR data	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
An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows	3
Elucidating the semantics-topology trade-off for knowledge inference-based pharmacological discovery	2
BioVerbNet: a large semantic-syntactic classification of verbs in biomedicine	2
Multiple sampling schemes and deep learning improve active learning performance in drug-drug interaction information retrieval analysis from the literature	2
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology	2
Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features	2
FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards	2
Digital evolution: Novo Nordisk’s shift to ontology-based data management	2
Prefrontal fNIRS-based clinical data analysis of brain functions in individuals abusing different types of drugs	2
CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature	2
Toward a systematic conflict resolution framework for ontologies	2
Enriched knowledge representation in biological fields: a case study of literature-based discovery in Alzheimer’s disease	2