Collecting and managing taxonomic data with NCBI-taxonomist

Jan P Buchmann; Edward C Holmes

doi:10.1093/bioinformatics/btaa1027

Collecting and managing taxonomic data with NCBI-taxonomist

Bioinformatics. 2021 Apr 1;36(22-23):5548-5550. doi: 10.1093/bioinformatics/btaa1027.

Authors

Jan P Buchmann¹, Edward C Holmes¹

Affiliation

¹ Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia.

Abstract

Summary: We present NCBI-taxonomist-a command-line tool written in Python that collects and manages taxonomic data from the National Center for Biotechnology Information (NCBI). NCBI-taxonomist does not depend on a pre-downloaded taxonomic database but can store data locally. NCBI-taxonomist has six commands to map, collect, extract, resolve, import and group taxonomic data that can be linked together to create powerful analytical pipelines. Because many lifescience databases use the same taxonomic information, the data managed by NCBI-taxonomist is not limited to NCBI and can be used to find data linked to taxonomic information present in other scientific databases.

Availability and implementation: NCBI-taxonomist is implemented in Python 3 (≥3.8) and available at https://gitlab.com/janpb/ncbi-taxonomist and via PyPi (https://pypi.org/project/ncbi-taxonomist/), as a Docker container (https://gitlab.com/janpb/ncbi-taxonomist/container_registry/) and Singularity (v3.5.3) image (https://cloud.sylabs.io/library/jpb/ncbi-taxonomist). NCBI-taxonomist is licensed under the GPLv3.

Grants and funding

FL170100022/Australian Laureate Fellowship