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Type material in the NCBI Taxonomy Database

Scott Federhen
2014 Nucleic Acids Research  
The NCBI Taxonomy Database (http: //www.ncbi.nlm.nih.gov/taxonomy) now includes annotation of type material that we use to flag sequences from type in GenBank and in Genomes.  ...  Type material is the taxonomic device that ties formal names to the physical specimens that serve as exemplars for the species.  ...  INTRODUCTION The NCBI Taxonomy Database (1) serves as the standard nomenclature and classification for the International Sequence Database (INSD) comprised of GenBank at the NCBI, ENA at the EBI/EMBL and  ... 
doi:10.1093/nar/gku1127 pmid:25398905 pmcid:PMC4383940 fatcat:mvhne3nzlvfk7lndskpvy7ckf4

NCBI Taxonomy: a comprehensive update on curation, resources and tools

Conrad L Schoch, Stacy Ciufo, Mikhail Domrachev, Carol L Hotton, Sivakumar Kannan, Rogneda Khovanskaya, Detlef Leipe, Richard Mcveigh, Kathleen O'Neill, Barbara Robbertse, Shobha Sharma, Vladimir Soussov (+4 others)
2020 Database: The Journal of Biological Databases and Curation  
The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications for every sequence in the nucleotide and protein sequence databases of the International Nucleotide  ...  Database URL: https://www.ncbi.nlm.nih.gov/taxonomy  ...  In addition to acknowledging the collaborative efforts of our colleagues at NCBI, INSDC and beyond, we remember the contributions of Scott Federhen, who initiated and guided many improvements to the NCBI  ... 
doi:10.1093/database/baaa062 pmid:32761142 fatcat:bnhdt2p6szf4rb2b2cerhg2bbq

Improving taxonomic accuracy for fungi in public sequence databases: applying 'one name one species' in well-defined genera with Trichoderma/Hypocrea as a test case

Barbara Robbertse, Pooja K Strope, Priscila Chaverri, Romina Gazis, Stacy Ciufo, Michael Domrachev, Conrad L Schoch
2017 Database: The Journal of Biological Databases and Curation  
In this case study the recent taxonomic information was applied to do a complete taxonomic audit for the genus Trichoderma in the NCBI Taxonomy database.  ...  This database is focused on sequences obtained from type material stored in public collections.  ...  Commission on the Taxonomy of Fungi (ICTF).  ... 
doi:10.1093/database/bax072 pmid:29220466 pmcid:PMC5641268 fatcat:t4oypzpx4nfatl3avfhn44u5ka

Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI

Stacy Ciufo, Sivakumar Kannan, Shobha Sharma, Azat Badretdin, Karen Clark, Seán Turner, Slava Brover, Conrad L. Schoch, Avi Kimchi, Michael DiCuccio
2018 International Journal of Systematic and Evolutionary Microbiology  
We present the methods used to make such comparisons, the current status of GenBank verifications, and recent developments in confirming species assignments in new genome submissions.  ...  This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, distribution and reproduction in any medium, provided the original author  ...  Acknowledgements We would like to acknowledge Scott Federhen, who laid the groundwork for this project and dedicate this paper in his memory.  ... 
doi:10.1099/ijsem.0.002809 pmid:29792589 fatcat:ccxyy6rf4vh37hahjqhlcj2cli

Genome-Based Virus Taxonomy with the ICTV Database Extension

Shinduck Kang, Young-Chang Kim
2018 Genomics & Informatics  
This virus taxonomy web system was specifically designed to extend the virus taxonomy up to strain and isolation, which was then connected with the NCBI database to facilitate searching for specific viral  ...  Presently, the 10th virus taxonomy has been published.  ...  Acknowledgments This work was supported by an intramural research grant of Chungbuk National University in 2015.  ... 
doi:10.5808/gi.2018.16.4.e22 pmid:30602083 pmcid:PMC6440660 fatcat:aro27yxa3nacddswh6xr5y5jwi

The NCBI BioCollections Database

Shobha Sharma, Stacy Ciufo, Elena Starchenko, Dakshesh Darji, Larry Chlumsky, Ilene Karsch-Mizrachi, Conrad L Schoch
2018 Database: The Journal of Biological Databases and Curation  
The National Center for Biotechnology Information BioCollections Database was established to allow the association of specimen vouchers and related sequence records to their home institutions.  ...  This process also allows cross-linking from the home institution for quick identification of all records originating from each collection. Database URL: https://www.ncbi.nlm.nih.gov/biocollections  ...  Acknowledgements The authors would like to acknowledge Scott Federhen and dedicate this paper in his memory.  ... 
doi:10.1093/database/bay006 pmid:29688360 pmcid:PMC5824777 fatcat:yepa4drzlba6rdaku6fk5eisvy

Using standard keywords in publications to facilitate updates of new fungal taxonomic names

Conrad L. Schoch, M. Catherine Aime, Wilhelm de Beer, Pedro W. Crous, Kevin D. Hyde, Lyubomir Penev, Keith A. Seifert, Marc Stadler, Ning Zhang, Andrew N. Miller
2017 IMA Fungus  
The combination of manual curation and the reliance on updates from submitters to the public sequence databases is currently inefficient and impedes the comprehensive and timely release of records with  ...  As a result, the potential for automated searches of publication aggregators are improved, as well as the accurate curation of taxonomic information.  ...  ACKNOWLEDGEMENTS We are grateful to Stacy Ciufo (NCBI) for her help in preparing the figure and table.  ... 
doi:10.1007/bf03449466 fatcat:sfpucaty2fesjcrpvbxpcsefai

RESCRIPt: Reproducible sequence taxonomy reference database management

Michael S. Robeson, Devon R. O'Rourke, Benjamin D. Kaehler, Michal Ziemski, Matthew R. Dillon, Jeffrey T. Foster, Nicholas A. Bokulich, Mihaela Pertea
2021 PLoS Computational Biology  
RESCRIPt provides tools to democratize the process of reference database acquisition and management, enabling researchers to reproducibly and transparently create reference materials for diverse research  ...  To highlight the breadth and capabilities of RESCRIPt, we provide several examples for working with popular databases for microbiome profiling (SILVA, Greengenes, NCBI-RefSeq, GTDB), eDNA and diet metabarcoding  ...  Acknowledgments We would like to thank the QIIME 2 developers and users for providing feedback on RESCRIPt.  ... 
doi:10.1371/journal.pcbi.1009581 pmid:34748542 pmcid:PMC8601625 fatcat:y7r5ny5zqzhddaylx2psitwrpu

OGG: a Biological Ontology for Representing Genes and Genomes in Specific Organisms

Yongqun He, Yue Liu, Bin Zhao
2014 International Conference on Biomedical Ontology  
To integrate with other ontologies, OGG is aligned with the Basic Formal Ontology (BFO). OGGspecific term IDs and annotations are designed by mapping to NCBI Taxonomy IDs and NCBI Entrez Gene IDs.  ...  In this report, we present the development of the Ontology of Genes and Genomes (OGG), a biological ontology in the domain of genes and genomes.  ...  This ASFV isolate is not classified in the NCBI Taxonomy database and thus does not have an NCBI Taxonomy ID (or an NCBITaxon ontology term ID).  ... 
dblp:conf/icbo/HeLZ14 fatcat:fdlmhfgl3bdn7eupxichz5pzvy

In memoriam –Scott Federhen (October 21, 1952 - May 5, 2016)

Conrad L. Schoch, Ilene Karsch-Mizrachi, James M. Ostell
2016 Standards in Genomic Sciences  
The authors declare that they have no competing interests.  ...  Recently, Scott was instrumental in greatly expanding the annotation of type material in the NCBI taxonomic database. This allowed for improved taxonomic accuracy.  ...  The INSDC continues to follow the NCBI Taxonomy Database classification.  ... 
doi:10.1186/s40793-016-0160-z fatcat:guhwdsqsunhxnhnfay7ibwpfiu

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

C. L. Schoch, B. Robbertse, V. Robert, D. Vu, G. Cardinali, L. Irinyi, W. Meyer, R. H. Nilsson, K. Hughes, A. N. Miller, P. M. Kirk, K. Abarenkov (+89 others)
2014 Database: The Journal of Biological Databases and Curation  
Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible  ...  The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures.  ...  Finally, any type material data were uploaded as permanent name types in the NCBI Taxonomy database.  ... 
doi:10.1093/database/bau061 pmid:24980130 pmcid:PMC4075928 fatcat:oqjotp6vvzbrtdddii6nc67zy4

RESCRIPt: Reproducible sequence taxonomy reference database management for the masses [article]

Michael S Robeson, Devon R O'Rourke, Benjamin D Kaehler, Michal Ziemski, Matthew R Dillon, Jeffrey T Foster, Nicholas A Bokulich
2020 bioRxiv   pre-print
Results: To highlight the breadth and capabilities of RESCRIPt, we provide several examples for working with popular databases for microbiome profiling (SILVA, Greengenes, NCBI-RefSeq, GTDB), eDNA, and  ...  Conclusions: RESCRIPt provides tools to democratize the process of reference database acquisition and management, enabling researchers to reproducibly and transparently create reference materials for diverse  ...  The use of genomes sequenced from type material provides these two databases with a 767 .  ... 
doi:10.1101/2020.10.05.326504 fatcat:7wg6yno7dbfhtgfosxnitt6jum

Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank

Allison Piovesan, Maria Caracausi, Marco Ricci, Pierluigi Strippoli, Lorenza Vitale, Maria Chiara Pelleri
2015 DNA Research  
We have developed GeneBase, a full parser of the National Center for Biotechnology Information (NCBI) Gene database, which generates a fully structured local database with an intuitive user-friendly graphic  ...  The structuring of the data, the creation of additional calculation fields and the integration with nucleotide sequences allow users to make many types of comparisons and calculations that are useful for  ...  Acknowledgements We specially thank the Fondazione Umano Progresso, Milano, Italy, for supporting the research on trisomy 21 conducted at the DIMES Department.  ... 
doi:10.1093/dnares/dsv028 pmid:26581719 pmcid:PMC4675715 fatcat:ho5uaaypnjh4ba5idne5ddiyjy

Taxallnomy: Closing gaps in the NCBI Taxonomy [article]

Tetsu Sakamoto, J. Miguel Ortega
2020 bioRxiv   pre-print
From taxallnomy, users can obtain the complete taxonomic lineage with 33 nodes of all taxa available in the NCBI Taxonomy database.  ...  The new hierarchical structure was named taxallnomy and it contains 33 hierarchical levels corresponding to the 33 taxonomic ranks currently used in the NCBI Taxonomy database.  ...  MATERIAL AND METHODS Dataset Dump files with taxonomic information provided by NCBI Taxonomy FTP server (ftp.ncbi.nih.gov/pub/taxonomy/) were used for the construction of the taxallnomy database.  ... 
doi:10.1101/2020.05.28.119461 fatcat:g5v4hkhysnhszbuephnavokmhu

Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy [article]

Donovan H. Parks, Maria Chuvochina, Pierre-Alain Chaumeil, Christian Rinke, Aaron J. Mussig, Philip Hugenholtz
2019 bioRxiv   pre-print
AbstractWe recently introduced the Genome Taxonomy Database (GTDB), a phylogenetically consistent, genome-based taxonomy providing rank normalized classifications for nearly 150,000 genomes from domain  ...  In contrast to previous ANI studies, we selected a single representative genome to serve as the nomenclatural type for circumscribing each species with type strains used where available.  ...  Acknowledgements We thank the members of the Microba Taxonomy Workshop for helpful discussions relating to establishing species clusters.  ... 
doi:10.1101/771964 fatcat:gbisngnexve3rlcxojdxi64tmq
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