Information Extraction in Biomedical Literature

Author(s):  
Min Song ◽  
Il-Yeol Song ◽  
Xiaohua Hu ◽  
Hyoil Han

Information extraction (IE) technology has been defined and developed through the US DARPA Message Understanding Conferences (MUCs). IE refers to the identification of instances of particular events and relationships from unstructured natural language text documents into a structured representation or relational table in databases. It has proved successful at extracting information from various domains, such as the Latin American terrorism, to identify patterns related to terrorist activities (MUC-4). Another domain, in the light of exploiting the wealth of natural language documents, is to extract the knowledge or information from these unstructured plain-text files into a structured or relational form. This form is suitable for sophisticated query processing, for integration with relational databases, and for data mining. Thus, IE is a crucial step for fully making text files more easily accessible.

2011 ◽  
pp. 314-321
Author(s):  
Min Song

Information extraction (IE) technology has been defined and developed through the US DARPA Message Understanding Conferences (MUCs). IE refers to the identification of instances of particular events and relationships from unstructured natural language text documents into a structured representation or relational table in databases. It has proved successful at extracting information from various domains, such as the Latin American terrorism, to identify patterns related to terrorist activities (MUC-4). Another domain, in the light of exploiting the wealth of natural language documents, is to extract the knowledge or information from these unstructured plain-text files into a structured or relational form. This form is suitable for sophisticated query processing, for integration with relational databases, and for data mining. Thus, IE is a crucial step for fully making text files more easily accessible.


2016 ◽  
Vol 78 (9-3) ◽  
Author(s):  
Rosmayati Mohemad ◽  
Abdul Razak Hamdan ◽  
Zulaiha Ali Othamn ◽  
Noor Maizura Mohamad Noor

The enormous amount of unstructured data presents the biggest challenge to decision makers in eliciting meaningful information to support business decision-making. This study explores the potential use of ontologies in extracting and populating the information from various combinations of unstructured and semi-structured data formats such as tabular, form-based and natural language-based text. The main objective of this study is to propose an architecture of information extraction for ontology population. Contractor selection is chosen as the domain of interest. Thus, this research focuses on the extraction of contractor profiles from tender documents in order to enrich ontological contractor profile by populating the relevant extracted information. The findings are significantly good in precision and recall, in which the performance measures have reached an accuracy of 100% precision and recall for extracting information in both tabular and form-based formats. However, the precision score of relevant information extracted in natural language text is average with a percentage of 42.86% due to the limitation of the linguistic approach for processing Malay texts. 


2020 ◽  
Vol 14 (01) ◽  
pp. 3-26
Author(s):  
Domenico Lembo ◽  
Federico Maria Scafoglieri

Information Extraction (IE) is the task of automatically organizing in a structured form data extracted from free text documents. In several contexts, it is often desirable that the extracted data are then organized according to an ontology, which provides a formal and conceptual representation of the domain of interest. Ontologies allow for a better data interpretation, as well as for their semantic integration with other information, as in Ontology-based Data Access (OBDA), a popular declarative framework for data management where an ontology is connected to a data layer through mappings. However, the data layer considered so far in OBDA has consisted essentially of relational databases, and how to declaratively couple an ontology with unstructured data sources is still unexplored. By leveraging the recent study on document spanners for rule-based IE by Fagin et al., in this paper, we propose a new framework that allows to map text documents to ontologies, in the spirit of OBDA. We investigate the problem of answering conjunctive queries in this framework. For ontologies specified in the Description Logics [Formula: see text] and [Formula: see text], we show that the problem is polynomial in the size of the underlying documents. We also provide algorithms to solve query answering by rewriting the input query on the basis of the ontology and its mapping toward the source documents. Through these techniques, we pursue a virtual approach, similar to that typically adopted in OBDA, which allows us to answer a query without having to first populate the entire ontology. Interestingly, for [Formula: see text], both the spanners used in the mapping and the one computed by the rewriting algorithm belong to the same class of expressiveness. This holds also for [Formula: see text], modulo some limitations on the form of the mapping. These results say that in these cases our framework can be easily implemented by decoupling ontology management and document access, which can be delegated to an external IE system able to process the extraction rules we use in the mapping.


2021 ◽  
Vol 11 (5) ◽  
pp. 663
Author(s):  
Elena D. Bazhanova ◽  
Alexander A. Kozlov ◽  
Anastasia V. Litovchenko

Epilepsy is a chronic neurological disorder characterized by recurring spontaneous seizures. Drug resistance appears in 30% of patients and it can lead to premature death, brain damage or a reduced quality of life. The purpose of the study was to analyze the drug resistance mechanisms, especially neuroinflammation, in the epileptogenesis. The information bases of biomedical literature Scopus, PubMed, Google Scholar and SciVerse were used. To obtain full-text documents, electronic resources of PubMed Central and Research Gate were used. The article examines the recent research of the mechanisms of drug resistance in epilepsy and discusses the hypotheses of drug resistance development (genetic, epigenetic, target hypothesis, etc.). Drug-resistant epilepsy is associated with neuroinflammatory, autoimmune and neurodegenerative processes. Neuroinflammation causes immune, pathophysiological, biochemical and psychological consequences. Focal or systemic unregulated inflammatory processes lead to the formation of aberrant neural connections and hyperexcitable neural networks. Inflammatory mediators affect the endothelium of cerebral vessels, destroy contacts between endothelial cells and induce abnormal angiogenesis (the formation of “leaky” vessels), thereby affecting the blood–brain barrier permeability. Thus, the analysis of pro-inflammatory and other components of epileptogenesis can contribute to the further development of the therapeutic treatment of drug-resistant epilepsy.


Author(s):  
Matheus C. Pavan ◽  
Vitor G. Santos ◽  
Alex G. J. Lan ◽  
Joao Martins ◽  
Wesley Ramos Santos ◽  
...  

2012 ◽  
Vol 30 (1) ◽  
pp. 1-34 ◽  
Author(s):  
Antonio Fariña ◽  
Nieves R. Brisaboa ◽  
Gonzalo Navarro ◽  
Francisco Claude ◽  
Ángeles S. Places ◽  
...  

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