Details:

Alternative Title:
BMC Bioinformatics
Personal Author:
Yu, Wei ; Yesupriya, Ajay ; Wulf, Anja ; Qu, Junfeng ; Khoury, Muin J ; ... More +
Yu, Wei ; Yesupriya, Ajay ; Wulf, Anja ; Qu, Junfeng ; Khoury, Muin J ; Gwinn, Marta Less -
Description:
Background

Identifying relevant research in an ever-growing body of published literature is becoming increasingly difficult. Establishing domain-specific knowledge bases may be a more effective and efficient way to manage and query information within specific biomedical fields. Adopting controlled vocabulary is a critical step toward data integration and interoperability in any information system. We present an open source infrastructure that provides a powerful capacity for managing and mining data within a domain-specific knowledge base. As a practical application of our infrastructure, we presented two applications – Literature Finder and Investigator Browser – as well as a tool set for automating the data curating process for the human genome published literature database. The design of this infrastructure makes the system potentially extensible to other data sources.

Results

Information retrieval and usability tests demonstrated that the system had high rates of recall and precision, 90% and 93% respectively. The system was easy to learn, easy to use, reasonably speedy and effective.

Conclusion

The open source system infrastructure presented in this paper provides a novel approach to managing and querying information and knowledge from domain-specific PubMed data. Using the controlled vocabulary UMLS enhanced data integration and interoperability and the extensibility of the system. In addition, by using MVC-based design and Java as a platform-independent programming language, this system provides a potential infrastructure for any domain-specific knowledge base in the biomedical field.


Subjects:
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Algorithms Artificial Intelligence Chromosome Mapping Cooperative Behavior Database Management Systems Genetic Predisposition To Disease Health Knowledge, Attitudes, Practice Humans Information Dissemination Information Storage And Retrieval Internet Methodology Article Natural Language Processing PubMed Software
Source:
BMC Bioinformatics. 2007; 8:436.
Document Type:
Journal Article
Collection(s):
CDC Public Access
Main Document Checksum:
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urn:sha256:1b5bb0ba8900603f4367f1c2e4fb8ca8ae3c2a8b55523dc38f426e5f0d7282e6
Download URL:
https://stacks.cdc.gov/view/cdc/3358/cdc_3358_DS1.pdf
File Type:

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