An eUtils toolset and its use for creating a pipeline to link genomics and proteomics analyses to domain-specific biomedical literature

Prakash M. Nadkarni, Chirag R. Parikh

Research output: Contribution to journalArticle

Abstract

Background: Numerous biomedical software applications access databases maintained by the US National Center for Biotechnology Information (NCBI). To ease software automation, NCBI provides a powerful but complex Web-service-based programming interface, eUtils. This paper describes a toolset that simplifies eUtils use through a graphical front-end that can be used by non-programmers to construct data-extraction pipelines. The front-end relies on a code library that provides high-level wrappers around eUtils functions, and which is distributed as open-source, allowing customization and enhancement by individuals with programming skills.Methods: We initially created an application that queried eUtils to retrieve nephrology-specific biomedical literature citations for a user-definable set of genes. We later augmented the application code to create a general-purpose library that accesses eUtils capability as individual functions that could be combined into user-defined pipelines.Results: The toolset's use is illustrated with an application that serves as a front-end to the library and can be used by non-programmers to construct user-defined pipelines. The operation of the library is illustrated for the literature-surveillance application, which serves as a case-study. An overview of the library is also provided.Conclusions: The library simplifies use of the eUtils service by operating at a higher level, and also transparently addresses robustness issues that would need to be individually implemented otherwise, such as error recovery and prevention of overloading of the eUtils service.

Original languageEnglish (US)
Article number9
JournalJournal of Clinical Bioinformatics
Volume2
Issue number1
DOIs
StatePublished - Apr 16 2012

Keywords

  • Entrez Programming Utilities
  • Proteomics Analysis
  • Pubmed filters

ASJC Scopus subject areas

  • Health Informatics

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