TY - JOUR
T1 - An eUtils toolset and its use for creating a pipeline to link genomics and proteomics analyses to domain-specific biomedical literature
AU - Nadkarni, Prakash M.
AU - Parikh, Chirag R.
N1 - Copyright:
Copyright 2012 Elsevier B.V., All rights reserved.
PY - 2012/4/16
Y1 - 2012/4/16
N2 - 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.
AB - 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.
KW - Entrez Programming Utilities
KW - Proteomics Analysis
KW - Pubmed filters
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U2 - 10.1186/2043-9113-2-9
DO - 10.1186/2043-9113-2-9
M3 - Article
C2 - 22507626
AN - SCOPUS:84866749391
SN - 2043-9113
VL - 2
JO - Journal of Clinical Bioinformatics
JF - Journal of Clinical Bioinformatics
IS - 1
M1 - 9
ER -