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Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject,
Scott Federhen1, Karen Clark1, Tanya Barrett1
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Standards in Genomic Sciences
|September 9, 2014
Summary
NCBI will stop assigning strain-level taxids for microbial genomes due to increased sequencing. Submitters should now provide detailed strain information and metadata directly to databases like BioProject and BioSample.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- Microbial genome sequences submitted to the International Nucleotide Sequence Database Collaboration (INSDC) are annotated with organism names including strain identifiers.
- Each strain-level name has been assigned a unique taxid in the NCBI Taxonomy Database.
- The rapid growth in genome sequencing has made the curation of strain-level taxids unsustainable.
Purpose of the Study:
- To announce a change in the NCBI's policy regarding the assignment of strain-level taxids.
- To inform researchers about the discontinuation of strain-level taxid curation by NCBI.
- To guide submitters on alternative methods for providing strain information.
Main Methods:
- NCBI will cease assigning strain-level taxids starting January 2014.
- Submitters will be encouraged to provide strain information and rich metadata.
- This information should accompany submissions to the sequence database, BioProject, and BioSample.
Main Results:
- Strain-level taxids will no longer be assigned by NCBI.
- Submitters must now rely on providing comprehensive metadata for strain identification.
- The responsibility for detailed strain information shifts to the data submitters.
Conclusions:
- The NCBI Taxonomy Database will discontinue assigning strain-level taxids for microbial genomes.
- Enhanced metadata and direct submission of strain information to BioProject and BioSample are the new standards.
- This change aims to streamline the annotation process in response to the expanding volume of genomic data.
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