Entrezpy: a Python library to dynamically interact with the NCBI Entrez databases

Abstract

Abstract Summary Entrezpy is a Python library that automates the querying and downloading of data from the Entrez databases at National Center for Biotechnology Information by interacting with E-Utilities. Entrezpy implements complex queries by automatically creating E-Utility parameters from the results obtained that can then be used directly in subsequent queries. Entrezpy also allows the user to cache and retrieve results locally, implements interactions with all Entrez databases as part of an analysis pipeline and adjusts parameters within an ongoing query or using prior results. Entrezpy’s modular design enables it to easily extend and adjust existing E-Utility functions. Availability and implementation Entrezpy is implemented in Python 3 (≥3.6) and depends only on the Python Standard Library. It is available via PyPi (https://pypi.org/project/entrezpy/) and at https://gitlab.com/ncbipy/entrezpy.git. Entrezpy is licensed under the LGPLv3 and also at http://entrezpy.readthedocs.io/.