AIMC Topic: Knowledge Bases
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Multiple features for clinical relation extraction: A machine learning approach.
Journal of biomedical informatics
Feb 3, 2020
Relation extraction aims to discover relational facts about entity mentions from plain texts. In this work, we focus on clinical relation extraction; namely, given a medical record with mentions of drugs and their attributes, we identify relations be...
Untargeted Metabolomics for Metabolic Diagnostic Screening with Automated Data Interpretation Using a Knowledge-Based Algorithm.
International journal of molecular sciences
Feb 1, 2020
Untargeted metabolomics may become a standard approach to address diagnostic requests, but, at present, data interpretation is very labor-intensive. To facilitate its implementation in metabolic diagnostic screening, we developed a method for automat...
Scientific and Regulatory Considerations for an Ontogeny Knowledge Base for Pediatric Clinical Pharmacology.
Clinical pharmacology and therapeutics
Jan 26, 2020
Understanding all aspects of developmental biology, or pediatric ontogeny, that affect drug therapy from the fetus to the adolescent child is the holy grail of pediatric scientists and clinical pharmacologists. The scientific community is now close t...
Knowledge-Based Tradeoff Hyperplanes for Head and Neck Treatment Planning.
International journal of radiation oncology, biology, physics
Jan 24, 2020
PURPOSE: To develop a tradeoff hyperplane model to facilitate tradeoff decision-making before inverse planning.
Evolving knowledge graph similarity for supervised learning in complex biomedical domains.
BMC bioinformatics
Jan 3, 2020
BACKGROUND: In recent years, biomedical ontologies have become important for describing existing biological knowledge in the form of knowledge graphs. Data mining approaches that work with knowledge graphs have been proposed, but they are based on ve...
JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants.
BMC genomics
Dec 24, 2019
BACKGROUND: Jatropha curcas is an oil-bearing plant, and has seeds with high oil content (~ 40%). Several advantages, such as easy genetic transformation and short generation duration, have led to the emergence of J. curcas as a model for woody energ...
Knowledge Base Commons (KBCommons) v1.1: a universal framework for multi-omics data integration and biological discoveries.
BMC genomics
Dec 20, 2019
BACKGROUND: Knowledge Base Commons (KBCommons) v1.1 is a universal and all-inclusive web-based framework providing generic functionalities for storing, sharing, analyzing, exploring, integrating and visualizing multiple organisms' genomics and integr...
A hybrid automated treatment planning solution for esophageal cancer.
Radiation oncology (London, England)
Dec 19, 2019
OBJECTIVE: This study aims to investigate a hybrid automated treatment planning (HAP) solution that combines knowledge-based planning (KBP) and script-based planning for esophageal cancer.
UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase).
Journal of proteomics
Dec 14, 2019
UniprotR is a software package designed to easily retrieve, cluster and visualize protein data from UniProt knowledgebase (UniProtKB) using R language. The package is implemented mainly to process, parse and illustrate proteomics data in a handy and ...
ROBOKOP KG and KGB: Integrated Knowledge Graphs from Federated Sources.
Journal of chemical information and modeling
Dec 12, 2019
A proliferation of data sources has led to the notional existence of an implicit Knowledge Graph (KG) that contains vast amounts of biological knowledge contributed by distributed Application Programming Interfaces (APIs). However, challenges arise w...
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