OOIR: Observatory of International Research

Papers

(The median citation count of Journal of Biomedical Semantics is 1. 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 2021-04-01 to 2025-04-01.)

Article	Citations
Automatic transparency evaluation for open knowledge extraction systems	40
Concretizing plan specifications as realizables within the OBO foundry	36
We are not ready yet: limitations of state-of-the-art disease named entity recognizers	22
Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)	17
Elucidating the semantics-topology trade-off for knowledge inference-based pharmacological discovery	17
Standardizing free-text data exemplified by two fields from the Immune Epitope Database	17
Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features	15
Synthetic data for annotation and extraction of family history information from clinical text	13
Improved characterisation of clinical text through ontology-based vocabulary expansion	10
Ontology-based identification and prioritization of candidate drugs for epilepsy from literature	9
Defining health data elements under the HL7 development framework for metadata management	9
An ontology network for Diabetes Mellitus in Mexico	9
Extending electronic medical records vector models with knowledge graphs to improve hospitalization prediction	9
PhenoDEF: a corpus for annotating sentences with information of phenotype definitions in biomedical literature	8
End-to-End provenance representation for the understandability and reproducibility of scientific experiments using a semantic approach	8
SemClinBr - a multi-institutional and multi-specialty semantically annotated corpus for Portuguese clinical NLP tasks	8
Comparing generative and extractive approaches to information extraction from abstracts describing randomized clinical trials	8
Gene expression knowledge graph for patient representation and diabetes prediction	7
Explanatory argumentation in natural language for correct and incorrect medical diagnoses	6
The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond	6
Annotation of epilepsy clinic letters for natural language processing	6
An annotated dataset for extracting gene-melanoma relations from scientific literature	6
RecSOI: recommending research directions using statements of ignorance	6
Project Rosetta: a childhood social, emotional, and behavioral developmental feature mapping	6
IrGO: Iranian traditional medicine General Ontology and knowledge base	6

FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards	6
CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature	5
ResidueFinder: extracting individual residue mentions from protein literature	4
Leveraging logical definitions and lexical features to detect missing IS-A relations in biomedical terminologies	4
Impact of COVID-19 research: a study on predicting influential scholarly documents using machine learning and a domain-independent knowledge graph	4
Chemical entity normalization for successful translational development of Alzheimer’s disease and dementia therapeutics	4
Prefrontal fNIRS-based clinical data analysis of brain functions in individuals abusing different types of drugs	4
Improving reusability along the data life cycle: a regulatory circuits case study	4
Transfer language space with similar domain adaptation: a case study with hepatocellular carcinoma	3
Features of a FAIR vocabulary	3
Syntax-based transfer learning for the task of biomedical relation extraction	3
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	3
Applying the FAIR principles to data in a hospital: challenges and opportunities in a pandemic	2
Analysis and implementation of the DynDiff tool when comparing versions of ontology	2
Classifying literature mentions of biological pathogens as experimentally studied using natural language processing	2
Automatic classification of experimental models in biomedical literature to support searching for alternative methods to animal experiments	2
New and revised gene ontology biological process terms describe multiorganism interactions critical for understanding microbial pathogenesis and sequences of concern	2
Enriching the FIDEO ontology with food-drug interactions from online knowledge sources	2
MeSH2Matrix: combining MeSH keywords and machine learning for biomedical relation classification based on PubMed	2
BioBLP: a modular framework for learning on multimodal biomedical knowledge graphs	2
Linking common human diseases to their phenotypes; development of a resource for human phenomics	1
MedLexSp – a medical lexicon for Spanish medical natural language processing	1
Pathling: analytics on FHIR	1
An annotated corpus of clinical trial publications supporting schema-based relational information extraction	1
Multi-task transfer learning for the prediction of entity modifiers in clinical text: application to opioid use disorder case detection	1
Optimized continuous homecare provisioning through distributed data-driven semantic services and cross-organizational workflows	1
Ontological representation, modeling, and analysis of parasite vaccines	1
Enriched knowledge representation in biological fields: a case study of literature-based discovery in Alzheimer’s disease	1
Alignment of vaccine codes using an ontology of vaccine descriptions	1
BioVerbNet: a large semantic-syntactic classification of verbs in biomedicine	1
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data	1
Correction to: Semantic units: organizing knowledge graphs into semantically meaningful units of representation	1
Text mining-based measurement of precision of polysomnographic reports as basis for intervention	1
Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research	1