title: Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records.
abstract: Microbial genome sequence submissions to the International Nucleotide Sequence Database Collaboration (INSDC) have been annotated with organism names that include the strain identifier. Each of these strain-level names has been assigned a unique 'taxid' in the NCBI Taxonomy Database. With the significant growth in genome sequencing, it is not possible to continue with the curation of strain-level taxids. In January 2014, NCBI will cease assigning strain-level taxids. Instead, submitters are encouraged provide strain information and rich metadata with their submission to the sequence database, BioProject and BioSample.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Federhen
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
authors.forename: Karen
authors.initials: K
authors.lastname: Clark
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
authors.forename: Tanya
authors.initials: T
authors.lastname: Barrett
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.
authors.forename: Helen
authors.initials: H
authors.lastname: Parkinson
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
authors.forename: James
authors.initials: J
authors.lastname: Ostell
authors.affiliation: DDBJ Center, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Japan.
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Kodama
authors.affiliation: DDBJ Center, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Mashima
authors.affiliation: DDBJ Center, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Japan.
authors.forename: Yasukazu
authors.initials: Y
authors.lastname: Nakamura
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.
authors.forename: Guy
authors.initials: G
authors.lastname: Cochrane
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
authors.forename: Ilene
authors.initials: I
authors.lastname: Karsch-Mizrachi