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Knowledge Bases

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AgeAnno: a knowledgebase of single-cell annotation of aging in human.

Nucleic acids research
Aging is a complex process that accompanied by molecular and cellular alterations. The identification of tissue-/cell type-specific biomarkers of aging and elucidation of the detailed biological mechanisms of aging-related genes at the single-cell le...

Dual-process system based on mixed semantic fusion for Chinese medical knowledge-based question answering.

Mathematical biosciences and engineering : MBE
Chinese medical knowledge-based question answering (cMed-KBQA) is a vital component of the intelligence question-answering assignment. Its purpose is to enable the model to comprehend questions and then deduce the proper answer from the knowledge bas...

mOWL: Python library for machine learning with biomedical ontologies.

Bioinformatics (Oxford, England)
MOTIVATION: Ontologies contain formal and structured information about a domain and are widely used in bioinformatics for annotation and integration of data. Several methods use ontologies to provide background knowledge in machine learning tasks, wh...

Annotation of biologically relevant ligands in UniProtKB using ChEBI.

Bioinformatics (Oxford, England)
MOTIVATION: To provide high quality, computationally tractable annotation of binding sites for biologically relevant (cognate) ligands in UniProtKB using the chemical ontology ChEBI (Chemical Entities of Biological Interest), to better support effort...

GlycoEnzOnto: a GlycoEnzyme pathway and molecular function ontology.

Bioinformatics (Oxford, England)
MOTIVATION: The 'glycoEnzymes' include a set of proteins having related enzymatic, metabolic, transport, structural and cofactor functions. Currently, there is no established ontology to describe glycoEnzyme properties and to relate them to glycan bi...

Development of a Knowledge Base for Chronic Wound Management Using the Decision Model & Notation.

Studies in health technology and informatics
Chronic wounds have significant impacts on patient health-related quality of life (HRQoL) and the healthcare expenditures. Various complex decision-making scenarios arise from wound management. Clinical decision-making systems (CDSS) can assist in re...

Exploration of the Decision Model and Notation (DMN) Standard for Representation of Knowledge Bases Encoded in the Arden Syntax.

Studies in health technology and informatics
CONTEXT: Arden Syntax encodes knowledge as Medical Logic Modules (MLMs). Current work involves improvement of its representation of business processes.

REDIRECT: Mapping Drug Prescriptions and Evidence from Biomedical Literature.

Studies in health technology and informatics
To enhance their practice, healthcare professionals need to cross-link various usage recommendations provided by heterogeneous vocabularies that must be retrieved and integrated conjointly. This is the aim of the Knowledge Warehouse / K-Ware platform...

Attention-based Knowledge Graph Representation Learning for Predicting Drug-drug Interactions.

Briefings in bioinformatics
Drug-drug interactions (DDIs) are known as the main cause of life-threatening adverse events, and their identification is a key task in drug development. Existing computational algorithms mainly solve this problem by using advanced representation lea...

Knowledge-based BERT: a method to extract molecular features like computational chemists.

Briefings in bioinformatics
Molecular property prediction models based on machine learning algorithms have become important tools to triage unpromising lead molecules in the early stages of drug discovery. Compared with the mainstream descriptor- and graph-based methods for mol...