Difference between revisions of "Template:Article of the week"

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(Updated article of the week text.)
(Updated article of the week text.)
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<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Tab1 Kyobe BiopresBiobank2017 15-2.png|240px]]</div>
<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Fig1 Zheng JMIRMedInfo2017 5-2.png|240px]]</div>
'''"[[Journal:Selecting a laboratory information management system for biorepositories in low- and middle-income countries: The H3Africa experience and lessons learned|Selecting a laboratory information management system for biorepositories in low- and middle-income countries: The H3Africa experience and lessons learned]]"'''
'''"[[Journal:Effective information extraction framework for heterogeneous clinical reports using online machine learning and controlled vocabularies|Effective information extraction framework for heterogeneous clinical reports using online machine learning and controlled vocabularies]]"'''


Biorepositories in Africa need significant infrastructural support to meet International Society for Biological and Environmental Repositories (ISBER) Best Practices to support population-based genomics research. ISBER recommends a biorepository information management system which can manage workflows from biospecimen receipt to distribution. The H3Africa Initiative set out to develop regional African biorepositories where Uganda, Nigeria, and South Africa were successfully awarded grants to develop the state-of-the-art biorepositories. The biorepositories carried out an elaborate process to evaluate and choose a [[laboratory information management system]] (LIMS) with the aim of integrating the three geographically distinct sites. In this article, we review the processes, African experience, and lessons learned, and we make recommendations for choosing a biorepository LIMS in the African context. ('''[[Selecting a laboratory information management system for biorepositories in low- and middle-income countries: The H3Africa experience and lessons learned|Full article...]]''')<br />
Extracting structured data from narrated medical reports is challenged by the complexity of heterogeneous structures and vocabularies and often requires significant manual effort. Traditional machine-based approaches lack the capability to take user feedback for improving the extraction algorithm in real time.
 
Our goal was to provide a generic [[information]] extraction framework that can support diverse clinical reports and enables a dynamic interaction between a human and a machine that produces highly accurate results.
 
A clinical information extraction system IDEAL-X has been built on top of online machine learning. It processes one document at a time, and user interactions are recorded as feedback to update the learning model in real time. The updated model is used to predict values for extraction in subsequent documents. Once prediction accuracy reaches a user-acceptable threshold, the remaining documents may be batch processed. A customizable controlled vocabulary may be used to support extraction. ('''[[Journal:Effective information extraction framework for heterogeneous clinical reports using online machine learning and controlled vocabularies|Full article...]]''')<br />
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''Recently featured'':  
''Recently featured'':  
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: ▪ [[Journal:Baobab Laboratory Information Management System: Development of an open-source laboratory information management system for biobanking|Baobab Laboratory Information Management System: Development of an open-source laboratory information management system for biobanking]]
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Revision as of 16:00, 18 July 2017

Fig1 Zheng JMIRMedInfo2017 5-2.png

"Effective information extraction framework for heterogeneous clinical reports using online machine learning and controlled vocabularies"

Extracting structured data from narrated medical reports is challenged by the complexity of heterogeneous structures and vocabularies and often requires significant manual effort. Traditional machine-based approaches lack the capability to take user feedback for improving the extraction algorithm in real time.

Our goal was to provide a generic information extraction framework that can support diverse clinical reports and enables a dynamic interaction between a human and a machine that produces highly accurate results.

A clinical information extraction system IDEAL-X has been built on top of online machine learning. It processes one document at a time, and user interactions are recorded as feedback to update the learning model in real time. The updated model is used to predict values for extraction in subsequent documents. Once prediction accuracy reaches a user-acceptable threshold, the remaining documents may be batch processed. A customizable controlled vocabulary may be used to support extraction. (Full article...)

Recently featured:

Selecting a laboratory information management system for biorepositories in low- and middle-income countries: The H3Africa experience and lessons learned
Baobab Laboratory Information Management System: Development of an open-source laboratory information management system for biobanking
The FAIR Guiding Principles for scientific data management and stewardship