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Chapter
Named Entity Recognition
This chapter provides an overview of named entity recognition (NER) from biomedical text, which is an algorithmic approach to identifying the span of text that represents medical concepts and their class. Read...
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Chapter
Medical Concept Normalization
Medical concept normalization, which maps clinical entities to concepts in standard terminology, is essential for supporting downstream computational applications in clinical settings. This chapter starts with...
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Chapter
Relation Extraction
This chapter introduces methods for extracting the relations between entities mentioned in electronic health records, scientific literature, reports, and similar biomedical text. The contents of this chapter w...
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Article
Open AccessSerial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models
The PubMed archive contains more than 34 million articles; consequently, it is becoming increasingly difficult for a biomedical researcher to keep up-to-date with different knowledge domains. Computationally e...
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Article
Open AccessA haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes
The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modificatio...
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Protocol
A Simple Computational Approach to Identify Potential Drugs for Multiple Sclerosis and Cognitive Disorders from Expert Curated Resources
Multiple sclerosis, a disease of central nervous system leads to potential disability. In the USA, one million cases are diagnosed with multiple sclerosis in 2019. Multiple sclerosis is identified as one of th...
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Book
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Protocol
A Text Mining Protocol for Extracting Drug–Drug Interaction and Adverse Drug Reactions Specific to Patient Population, Pharmacokinetics, Pharmacodynamics, and Disease
Drug-drug interactions (DDIs) and adverse drug reactions (ADR) are experienced by many patients, especially by elderly population due to their multiple comorbidities and polypharmacy. Databases such as PubMed ...
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Protocol
Biomedical Literature Mining and Its Components
The published biomedical articles are the best source of knowledge to understand the importance of biomedical entities such as disease, drugs, and their role in different patient population groups. The number ...
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Protocol
A Text Mining Protocol for Predicting Drug–Drug Interaction and Adverse Drug Reactions from PubMed Articles
Drug–drug interactions (DDIs) and adverse drug reactions (ADRs) occur during the pharmacotherapy of multiple comorbidities and in susceptible individuals. DDIs and ADRs limit the therapeutic outcomes in pharma...
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Protocol
Extracting Significant Comorbid Diseases from MeSH Index of PubMed
Text mining is an important research area to be explored in terms of understanding disease associations and have an insight in disease comorbidities. The reason for comorbid occurrence in any patient may be ge...
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Chapter
Basics of Fungal Siderophores: Classification, Iron Transport and Storage, Chemistry and Biosynthesis, Application, and More
Iron is needed in micro-quantities for cellular homeostasis. In humans, iron is bound to transferrin and ferritin, the essential proteins for cellular functions. The human body maintains an optimal iron conten...
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Chapter
A Summary on Up-To-Date Research on Fungal Siderophores on Disease, Treatment and Pathogenicity Based on Text Mining, Bioinformatics and Experts’ Opinion
Knowledge of fungal siderophores related to humans is important in the diagnosis and treatment of life-threatening infections like aspergillosis, candidiasis, histoplasmosis, etc., caused by fungi. Current res...
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Protocol
Automated Extraction and Visualization of Protein–Protein Interaction Networks and Beyond: A Text-Mining Protocol
Proteins perform their functions by interacting with other proteins. Protein–protein interaction (PPI) is critical for understanding the functions of individual proteins, the mechanisms of biological processes...
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Article
Open AccessGenetic signature to provide robust risk assessment of psoriatic arthritis development in psoriasis patients
Psoriatic arthritis (PsA) is a complex chronic musculoskeletal condition that occurs in ~30% of psoriasis patients. Currently, no systematic strategy is available that utilizes the differences in genetic archi...
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Article
Open AccessMachine learning workflow to enhance predictions of Adverse Drug Reactions (ADRs) through drug-gene interactions: application to drugs for cutaneous diseases
Adverse drug reactions (ADRs) pose critical public health issues, affecting over 6% of hospitalized patients. While knowledge of potential drug-drug interactions (DDI) is necessary to prevent ADR, the rapid pa...
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Article
Atypical Presentation of Gastrointestinal Stromal Tumours—A Case Report
Gastrointestinal stromal tumors (GISTs) are benign mesenchymal tumors of the gastrointestinal tract (GIT). Their clinical presentations are variable. We report a case of a 31-year-old man who presented with pa...
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Reference Work Entry In depth
Template Filling, Text Mining
