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New software opens doors for biologists working with publicly available data.

Research software from McMaster provides new avenues for geneticists to access and interpret datasets from the National Centre for Biotechnology Information (NCBI).

Feb 26, 2020

NCBImeta: efficient and comprehensive metadata retrieval from NCBI databases

Authors: Katherine Eaton

Journal of Open Source Software, February 2020. DOI: https://doi.org/10.21105/joss.01990

Abstract

NCBImeta is a command-line application that downloads and organizes biological metadata from the National Centre for Biotechnology Information (NCBI). While the NCBI web portal provides an interface for searching and filtering molecular data, the output offers limited options for record retrieval and comparison on a much larger and broader scale. NCBImeta tackles this problem by creating a reformatted local database of NCBI metadata based on user search queries and customizable fields. The output of NCBImeta, optionally a SQLite database or text file(s), can then be used by computational biologists for applications such as record filtering, project discovery, sample interpretation, and meta-analyses of published work.

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