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Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)
Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)
Ontologies are fundamental components of informatics infrastructure in domains such as biomedical, environmental, and food...
MeSH2Matrix: combining MeSH keywords and machine learning for biomedical relation classification based on PubMed
MeSH2Matrix: combining MeSH keywords and machine learning for biomedical relation classification based on PubMed
Biomedical relation classification has been significantly improved by the application of advanced machine learning techniq...
Annotation of epilepsy clinic letters for natural language processing
Annotation of epilepsy clinic letters for natural language processing
Natural language processing (NLP) is increasingly being used to extract structured information from unstructured text to a...
An extensible and unifying approach to retrospective clinical data modeling: the BrainTeaser Ontology
An extensible and unifying approach to retrospective clinical data modeling: the BrainTeaser Ontology
Automatic disease progression prediction models require large amounts of training data, which are seldom available, especi...
Concretizing plan specifications as realizables within the OBO foundry
Concretizing plan specifications as realizables within the OBO foundry
Within the Open Biological and Biomedical Ontology (OBO) Foundry, many ontologies represent the execution of a plan specif...
Mapping vaccine names in clinical trials to vaccine ontology using cascaded fine-tuned domain-specific language models
Mapping vaccine names in clinical trials to vaccine ontology using cascaded fine-tuned domain-specific language models
Vaccines have revolutionized public health by providing protection against infectious diseases. They stimulate the immune ...
Chemical entity normalization for successful translational development of Alzheimer’s disease and dementia therapeutics
Chemical entity normalization for successful translational development of Alzheimer’s disease and dementia therapeutics
Identifying chemical mentions within the Alzheimer’s and dementia literature can provide a powerful tool to further ...
Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis
Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis
The exploration of cancer vaccines has yielded a multitude of studies, resulting in a diverse collection of information. T...
Multi-task transfer learning for the prediction of entity modifiers in clinical text: application to opioid use disorder case detection
Multi-task transfer learning for the prediction of entity modifiers in clinical text: application to opioid use disorder case detection
The semantics of entities extracted from a clinical text can be dramatically altered by modifiers, including entity negati...
Optimized continuous homecare provisioning through distributed data-driven semantic services and cross-organizational workflows
Optimized continuous homecare provisioning through distributed data-driven semantic services and cross-organizational workflows
In healthcare, an increasing collaboration can be noticed between different caregivers, especially considering the shift t...
Explanatory argumentation in natural language for correct and incorrect medical diagnoses
Explanatory argumentation in natural language for correct and incorrect medical diagnoses
A huge amount of research is carried out nowadays in Artificial Intelligence to propose automated ways to analyse medical ...
Semantic units: organizing knowledge graphs into semantically meaningful units of representation
Semantic units: organizing knowledge graphs into semantically meaningful units of representation
In today’s landscape of data management, the importance of knowledge graphs and ontologies is escalating as critical...
Leveraging logical definitions and lexical features to detect missing IS-A relations in biomedical terminologies
Leveraging logical definitions and lexical features to detect missing IS-A relations in biomedical terminologies
Biomedical terminologies play a vital role in managing biomedical data. Missing IS-A relations in a biomedical terminology...
Elucidating the semantics-topology trade-off for knowledge inference-based pharmacological discovery
Elucidating the semantics-topology trade-off for knowledge inference-based pharmacological discovery
Leveraging AI for synthesizing the deluge of biomedical knowledge has great potential for pharmacological discovery with a...
Ontological representation, modeling, and analysis of parasite vaccines
Ontological representation, modeling, and analysis of parasite vaccines
Pathogenic parasites are responsible for multiple diseases, such as malaria and Chagas disease, in humans and livestock. T...
Comparing generative and extractive approaches to information extraction from abstracts describing randomized clinical trials
Comparing generative and extractive approaches to information extraction from abstracts describing randomized clinical trials
Systematic reviews of Randomized Controlled Trials (RCTs) are an important part of the evidence-based medicine paradigm. H...
RecSOI: recommending research directions using statements of ignorance
RecSOI: recommending research directions using statements of ignorance
The more science advances, the more questions are asked. This compounding growth can make it difficult to keep up with cur...
Enriching the FIDEO ontology with food-drug interactions from online knowledge sources
Enriching the FIDEO ontology with food-drug interactions from online knowledge sources
The increasing number of articles on adverse interactions that may occur when specific foods are consumed with certain dru...
The use of foundational ontologies in biomedical research
The use of foundational ontologies in biomedical research
The FAIR principles recommend the use of controlled vocabularies, such as ontologies, to define data and metadata concepts...
BioBLP: a modular framework for learning on multimodal biomedical knowledge graphs
BioBLP: a modular framework for learning on multimodal biomedical knowledge graphs
Knowledge graphs (KGs) are an important tool for representing complex relationships between entities in the biomedical dom...
Assessing resolvability, parsability, and consistency of RDF resources: a use case in rare diseases
Assessing resolvability, parsability, and consistency of RDF resources: a use case in rare diseases
Healthcare data and the knowledge gleaned from it play a key role in improving the health of current and future patients. ...
Impact of COVID-19 research: a study on predicting influential scholarly documents using machine learning and a domain-independent knowledge graph
Impact of COVID-19 research: a study on predicting influential scholarly documents using machine learning and a domain-independent knowledge graph
Multiple studies have investigated bibliometric features and uncategorized scholarly documents for the influential scholar...
Data management plans as linked open data: exploiting ARGOS FAIR and machine actionable outputs in the OpenAIRE research graph
Data management plans as linked open data: exploiting ARGOS FAIR and machine actionable outputs in the OpenAIRE research graph
Open Science Graphs (OSGs) are scientific knowledge graphs representing different entities of the research lifecycle (e.g....
Context-based refinement of mappings in evolving life science ontologies
Context-based refinement of mappings in evolving life science ontologies
Biomedical computational systems benefit from ontologies and their associated mappings. Indeed, aligned ontologies in life...
Analysis and implementation of the DynDiff tool when comparing versions of ontology
Analysis and implementation of the DynDiff tool when comparing versions of ontology
Ontologies play a key role in the management of medical knowledge because they have the properties to support a wide range...
Development and validation of the early warning system scores ontology
Development and validation of the early warning system scores ontology
Clinical early warning scoring systems, have improved patient outcomes in a range of specializations and global contexts. ...
Automatic transparency evaluation for open knowledge extraction systems
Automatic transparency evaluation for open knowledge extraction systems
This paper proposes Cyrus, a new transparency evaluation framework, for Open Knowledge Extraction (OKE) systems. Cyrus is ...
Automatic classification of experimental models in biomedical literature to support searching for alternative methods to animal experiments
Automatic classification of experimental models in biomedical literature to support searching for alternative methods to animal experiments
Current animal protection laws require replacement of animal experiments with alternative methods, whenever such methods a...
Multi-domain knowledge graph embeddings for gene-disease association prediction
Multi-domain knowledge graph embeddings for gene-disease association prediction
Predicting gene-disease associations typically requires exploring diverse sources of information as well as sophisticated ...
An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows
An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows
With the capacity to produce and record data electronically, Scientific research and the data associated with it have grow...
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