Analyzing trends in the scientific literature for insight


BD2KPubMed is a software tool that employs publicly available data to analyze scientific trends and research directions in a particular field of interest. The software collects metadata associated with individual articles from a custom query of the NCBI PubMed database, then ranks proteins by their occurrences in the referenced articles. The data are then summarized for visualization and trend analysis and quantify the impact of a particular protein to a research topic. Potential applications include gathering information to prioritize in-depth gene annotation and mass spectrometry assay development.


The beta version of BD2KPubMed is available for Windows, OS X and Linux. The client requires the Java Runtime Environment 8 to be installed on your system. Please note that this is an evaluation version of the software and is not to be modified, distributed or reproduced.

Download BD2KPubMed

To get started, extract the contents of the zip archieve to a folder and double click the bd2kpubmed_01.jar.

See the user manual for instructions on how to use BD2KPubMed.

Additional Information

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