George M Garrity
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View article: Identifying genomic data use with the Data Citation Explorer
Identifying genomic data use with the Data Citation Explorer Open
View article: Identifying genomic data use with the Data Citation Explorer
Identifying genomic data use with the Data Citation Explorer Open
Increases in sequencing capacity, combined with rapid accumulation of publications and associated data resources, have increased the complexity of maintaining associations between literature and genomic data. As the volume of literature an…
View article: Establishing semantic equivalence between concepts
Establishing semantic equivalence between concepts Open
A method for establishing semantic equivalence between a plurality of concepts including: providing an Orthogonal Semantic Equivalence Map in which first, second, and third extensional concept models are related; selecting or de-selecting …
View article: Methods for data classification
Methods for data classification Open
The present invention provides methods for classifying data and uncovering and correcting annotation errors. In particular, the present invention provides a self-organizing, self-correcting algorithm for use in classifying data. Additional…
View article: Classification of nucleotide sequences by latent semantic analysis
Classification of nucleotide sequences by latent semantic analysis Open
DNA sequences are analyzed using latent semantic analysis. A set of nucleotide sequences is received in which the set has a first number of sequences. A set of basis vectors is determined, in which the set has a second number of basis vect…
View article: Semiotic indexing of digital resources
Semiotic indexing of digital resources Open
A method of classifying a plurality of documents. The method includes steps of providing a first set of classification terms and a second set of classification terms, the second set of classification terms being different from the first se…
View article: Systems and methods for automatically identifying and linking names in digital resources
Systems and methods for automatically identifying and linking names in digital resources Open
The present invention provides systems and methods for automatically identifying name-like-strings in digital resources, matching these name-like-string against a set of names held in an expertly curated database, and for those name-like-s…
View article: Lists of names of prokaryotic Candidatus taxa
Lists of names of prokaryotic Candidatus taxa Open
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. …
View article: On neotypes and nomina nova: commentary on “Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa”, by C.B. Fitzgerald et al. (BMC Genomics (2018) 19:931)
On neotypes and nomina nova: commentary on “Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa”, by C.B. Fitzgerald et al. (BMC Genomics (2018) 19:931) Open
View article: A Genus Definition for <i>Bacteria</i> and <i>Archaea</i> Based on a Standard Genome Relatedness Index
A Genus Definition for <i>Bacteria</i> and <i>Archaea</i> Based on a Standard Genome Relatedness Index Open
In recent decades, the taxonomy of Bacteria and Archaea , and therefore genus designation, has been largely based on the use of a single ribosomal gene, the 16S rRNA gene, as a taxonomic marker. We propose an approach to delineate genera t…
View article: Genomic Encyclopedia of Bacteria and Archaea (GEBA) VI: learning from type strains
Genomic Encyclopedia of Bacteria and Archaea (GEBA) VI: learning from type strains Open
Type strains of species are one of the most valuable resources in microbiology. During the last decade, the Genomic Encyclopedia of Bacteria and Archaea (GEBA) projects at the US Department of Energy Joint Genome Institute (JGI) and their …
View article: Valid publication of the names Caecibacterium and Caecibacterium sporoformans
Valid publication of the names Caecibacterium and Caecibacterium sporoformans Open
Descriptions of the genus Caecibacterium and its proposed type species Caecibacterium sporoformans were published in the IJSEM by Onrust et al. ( Int J Syst Evol Microbiol 2017;67:4589–4594). The type strain was deposited as LMG 27730 and …
View article: A genus definition for <i>Bacteria</i> and <i>Archaea</i> based on genome relatedness and taxonomic affiliation
A genus definition for <i>Bacteria</i> and <i>Archaea</i> based on genome relatedness and taxonomic affiliation Open
Genus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose an approach to demarcate genera that rel…
View article: Proposal to emend Rules 50a and 50b of the International Code of Nomenclature of Prokaryotes
Proposal to emend Rules 50a and 50b of the International Code of Nomenclature of Prokaryotes Open
Rules 50a and 50b of the International Code of Nomenclature of Prokaryotes respectively regulate the elevation of a subspecies to the rank of a species and the lowering of a species to the rank of subspecies. The Code does not indicate tha…
View article: Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea Open
View article: Erratum: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
Erratum: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life Open
In the version of this article initially published, the wrong Creative Commons Attribution license (cc-by-nc rather than cc-by) was inserted. The error has been corrected in the HTML and PDF versions of the article.
View article: Erratum: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Erratum: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea Open
View article: Proposal of the suffix –ota to denote phyla. Addendum to ‘Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes’
Proposal of the suffix –ota to denote phyla. Addendum to ‘Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes’ Open
As an addendum to the earlier proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes (Oren et al., Int J Syst Evol Microbiol 2015;65:4284-4287) we propose the suffix -ota to denote phyla, replacing …
View article: Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 67, part 8, of the IJSEM
Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 67, part 8, of the IJSEM Open
Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our princi…
View article: List of new names and new combinations previously effectively, but not validly, published
List of new names and new combinations previously effectively, but not validly, published Open
Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our princi…
View article: Uncultivated microbes—in need of their own nomenclature?
Uncultivated microbes—in need of their own nomenclature? Open
View article: Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 67, part 7, of the IJSEM
Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 67, part 7, of the IJSEM Open
Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our princi…
View article: Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 67, part 6, of the IJSEM
Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 67, part 6, of the IJSEM Open
Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our princi…
View article: List of new names and new combinations previously effectively, but not validly, published
List of new names and new combinations previously effectively, but not validly, published Open
Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our princi…
View article: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea Open
View article: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life Open
View article: ‘Localimania’ revisited: guidelines for the formation of specific epithets for names of prokaryotes based on names of institutions or their acronyms. A proposal for emendation of Appendix 9 to the International Code of Nomenclature of Prokaryotes
‘Localimania’ revisited: guidelines for the formation of specific epithets for names of prokaryotes based on names of institutions or their acronyms. A proposal for emendation of Appendix 9 to the International Code of Nomenclature of Prokaryotes Open
We here present a survey of the increasing use of the -ensis (-ense) ending for the formation of specific epithets that do not refer to geographical locations but to names of research institutes or their acronyms. To our opinion the use of…
View article: A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?
A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet? Open
Taxonomy is often criticized for being too conservative and too slow and having limited relevance because it has not taken into consideration the latest methods and findings. Yet the cumulative work product of its practitioners underpins c…
View article: Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015)
Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015) Open
View article: Notification that new names of prokaryotes, new combinations and new taxonomic opinions have appeared in volume 65, part 11, of the IJSEM
Notification that new names of prokaryotes, new combinations and new taxonomic opinions have appeared in volume 65, part 11, of the IJSEM Open
This listing of names of prokaryotes published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission…