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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...
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...
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...
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...
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...
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...
Improving the classification of cardinality phenotypes using collections
Improving the classification of cardinality phenotypes using collections
Phenotypes are observable characteristics of an organism and they can be highly variable. Information about phenotypes is ...
Semantically enabling clinical decision support recommendations
Semantically enabling clinical decision support recommendations
Clinical decision support systems have been widely deployed to guide healthcare decisions on patient diagnosis, treatment ...
FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards
FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards
The current rise of Open Science and Reproducibility in the Life Sciences requires the creation of rich, machine-actionabl...
Features of a FAIR vocabulary
Features of a FAIR vocabulary
The Findable, Accessible, Interoperable and Reusable(FAIR) Principles explicitly require the use of FAIR vocabularies, but...
Multiple sampling schemes and deep learning improve active learning performance in drug-drug interaction information retrieval analysis from the literature
Multiple sampling schemes and deep learning improve active learning performance in drug-drug interaction information retrieval analysis from the literature
Drug-drug interaction (DDI) information retrieval (IR) is an important natural language process (NLP) task from the PubMed...
Constructing a knowledge graph for open government data: the case of Nova Scotia disease datasets
Constructing a knowledge graph for open government data: the case of Nova Scotia disease datasets
The majority of available datasets in open government data are statistical. They are widely published by various governmen...
The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond
Evaluating the impact of environmental exposures on organism health is a key goal of modern biomedicine and is critically ...
MedLexSp – a medical lexicon for Spanish medical natural language processing
MedLexSp – a medical lexicon for Spanish medical natural language processing
Medical lexicons enable the natural language processing (NLP) of health texts. Lexicons gather terms and concepts from the...
Classifying literature mentions of biological pathogens as experimentally studied using natural language processing
Classifying literature mentions of biological pathogens as experimentally studied using natural language processing
Information pertaining to mechanisms, management and treatment of disease-causing pathogens including viruses and bacteria...
We are not ready yet: limitations of state-of-the-art disease named entity recognizers
We are not ready yet: limitations of state-of-the-art disease named entity recognizers
Intense research has been done in the area of biomedical natural language processing. Since the breakthrough of transfer l...
Alignment of vaccine codes using an ontology of vaccine descriptions
Alignment of vaccine codes using an ontology of vaccine descriptions
Vaccine information in European electronic health record (EHR) databases is represented using various clinical and databas...
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology
The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major glo...
Pathling: analytics on FHIR
Pathling: analytics on FHIR
Health data analytics is an area that is facing rapid change due to the acceleration of digitization of the health sector,...
Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs
Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs
The Vaccine Ontology (VO) is a biomedical ontology that standardizes vaccine annotation. Errors in VO will affect a multit...
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