title: An eUtils toolset and its use for creating a pipeline to link genomics and proteomics analyses to domain-specific biomedical literature.
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.
authors.affiliation: Department of Medicine, Program of Applied Translational Research, Yale University School of Medicine, New Haven, CT, USA. Prakash.Nadkarni@yale.edu.
authors.forename: Prakash M
authors.initials: PM
authors.lastname: Nadkarni
authors.forename: Chirag R
authors.initials: CR
authors.lastname: Parikh