An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology

Details

• Alternative Title:
  BMC Bioinformatics
• Personal Author:
  Yu, Wei ; Yesupriya, Ajay ; Wulf, Anja ; Qu, Junfeng ; Khoury, Muin J ; Gwinn, Marta
• 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:
  • Methodology Article
  • Algorithms
  • Artificial Intelligence
  • Chromosome Mapping
  • Cooperative Behavior
  • Database Management Systems
  • Genetic Predisposition to Disease
  • Health Knowledge, Attitudes, Practice
  • Humans
  • Information Dissemination
  More +
• Source:
  BMC Bioinformatics. 2007; 8:436.
• Document Type:
  Journal Article
• Volume:
  8
• Download URL:
  https://stacks.cdc.gov/view/cdc/3358/cdc_3358_DS1.pdf
• File Type:
  [PDF - 813.97 KB]
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha-512:9dc4dbee4345b6575a78fde9cd45197bde831bccb6e0a68a512ef038340bb5aee058265edf7508bcefaad287897ef8c30aececc25e8f11f9cf66fd4053e0b309