Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the Internationa...

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Main Authors:	O'Leary, Nuala A., Wright, Mathew W., Brister, J. Rodney, Ciufo, Stacy, Haddad, Diana, McVeigh, Rich, Rajput, Bhanu, Robbertse, Barbara, Smith-White, Brian, Ako-Adjei, Danso, Astashyn, Alexander, Badretdin, Azat, Bao, Yiming, Blinkova, Olga, Brover, Vyacheslav, Chetvernin, Vyacheslav, Choi, Jinna, Cox, Eric, Ermolaeva, Olga, Farrell, Catherine M., Goldfarb, Tamara, Gupta, Tripti, Haft, Daniel, Hatcher, Eneida, Hlavina, Wratko, Joardar, Vinita S., Kodali, Vamsi K., Li, Wenjun, Maglott, Donna, Masterson, Patrick, McGarvey, Kelly M., Murphy, Michael R., O'Neill, Kathleen, Pujar, Shashikant, Rangwala, Sanjida H., Rausch, Daniel, Riddick, Lillian D., Schoch, Conrad, Shkeda, Andrei, Storz, Susan S., Sun, Hanzhen, Thibaud-Nissen, Francoise, Tolstoy, Igor, Tully, Raymond E., Vatsan, Anjana R., Wallin, Craig, Webb, David, Wu, Wendy, Landrum, Melissa J., Kimchi, Avi, Tatusova, Tatiana, DiCuccio, Michael, Kitts, Paul, Murphy, Terence D., Pruitt, Kim D.
Format:	Online
Language:	English
Published:	Oxford University Press 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702849/

id	pubmed-4702849
recordtype	oai_dc
spelling	pubmed-47028492016-01-07 Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation O'Leary, Nuala A. Wright, Mathew W. Brister, J. Rodney Ciufo, Stacy Haddad, Diana McVeigh, Rich Rajput, Bhanu Robbertse, Barbara Smith-White, Brian Ako-Adjei, Danso Astashyn, Alexander Badretdin, Azat Bao, Yiming Blinkova, Olga Brover, Vyacheslav Chetvernin, Vyacheslav Choi, Jinna Cox, Eric Ermolaeva, Olga Farrell, Catherine M. Goldfarb, Tamara Gupta, Tripti Haft, Daniel Hatcher, Eneida Hlavina, Wratko Joardar, Vinita S. Kodali, Vamsi K. Li, Wenjun Maglott, Donna Masterson, Patrick McGarvey, Kelly M. Murphy, Michael R. O'Neill, Kathleen Pujar, Shashikant Rangwala, Sanjida H. Rausch, Daniel Riddick, Lillian D. Schoch, Conrad Shkeda, Andrei Storz, Susan S. Sun, Hanzhen Thibaud-Nissen, Francoise Tolstoy, Igor Tully, Raymond E. Vatsan, Anjana R. Wallin, Craig Webb, David Wu, Wendy Landrum, Melissa J. Kimchi, Avi Tatusova, Tatiana DiCuccio, Michael Kitts, Paul Murphy, Terence D. Pruitt, Kim D. Database Issue The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55 000 organisms (>4800 viruses, >40 000 prokaryotes and >10 000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management. Oxford University Press 2016-01-04 2015-11-08 /pmc/articles/PMC4702849/ /pubmed/26553804 http://dx.doi.org/10.1093/nar/gkv1189 Text en Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	O'Leary, Nuala A. Wright, Mathew W. Brister, J. Rodney Ciufo, Stacy Haddad, Diana McVeigh, Rich Rajput, Bhanu Robbertse, Barbara Smith-White, Brian Ako-Adjei, Danso Astashyn, Alexander Badretdin, Azat Bao, Yiming Blinkova, Olga Brover, Vyacheslav Chetvernin, Vyacheslav Choi, Jinna Cox, Eric Ermolaeva, Olga Farrell, Catherine M. Goldfarb, Tamara Gupta, Tripti Haft, Daniel Hatcher, Eneida Hlavina, Wratko Joardar, Vinita S. Kodali, Vamsi K. Li, Wenjun Maglott, Donna Masterson, Patrick McGarvey, Kelly M. Murphy, Michael R. O'Neill, Kathleen Pujar, Shashikant Rangwala, Sanjida H. Rausch, Daniel Riddick, Lillian D. Schoch, Conrad Shkeda, Andrei Storz, Susan S. Sun, Hanzhen Thibaud-Nissen, Francoise Tolstoy, Igor Tully, Raymond E. Vatsan, Anjana R. Wallin, Craig Webb, David Wu, Wendy Landrum, Melissa J. Kimchi, Avi Tatusova, Tatiana DiCuccio, Michael Kitts, Paul Murphy, Terence D. Pruitt, Kim D.
spellingShingle	O'Leary, Nuala A. Wright, Mathew W. Brister, J. Rodney Ciufo, Stacy Haddad, Diana McVeigh, Rich Rajput, Bhanu Robbertse, Barbara Smith-White, Brian Ako-Adjei, Danso Astashyn, Alexander Badretdin, Azat Bao, Yiming Blinkova, Olga Brover, Vyacheslav Chetvernin, Vyacheslav Choi, Jinna Cox, Eric Ermolaeva, Olga Farrell, Catherine M. Goldfarb, Tamara Gupta, Tripti Haft, Daniel Hatcher, Eneida Hlavina, Wratko Joardar, Vinita S. Kodali, Vamsi K. Li, Wenjun Maglott, Donna Masterson, Patrick McGarvey, Kelly M. Murphy, Michael R. O'Neill, Kathleen Pujar, Shashikant Rangwala, Sanjida H. Rausch, Daniel Riddick, Lillian D. Schoch, Conrad Shkeda, Andrei Storz, Susan S. Sun, Hanzhen Thibaud-Nissen, Francoise Tolstoy, Igor Tully, Raymond E. Vatsan, Anjana R. Wallin, Craig Webb, David Wu, Wendy Landrum, Melissa J. Kimchi, Avi Tatusova, Tatiana DiCuccio, Michael Kitts, Paul Murphy, Terence D. Pruitt, Kim D. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
author_facet	O'Leary, Nuala A. Wright, Mathew W. Brister, J. Rodney Ciufo, Stacy Haddad, Diana McVeigh, Rich Rajput, Bhanu Robbertse, Barbara Smith-White, Brian Ako-Adjei, Danso Astashyn, Alexander Badretdin, Azat Bao, Yiming Blinkova, Olga Brover, Vyacheslav Chetvernin, Vyacheslav Choi, Jinna Cox, Eric Ermolaeva, Olga Farrell, Catherine M. Goldfarb, Tamara Gupta, Tripti Haft, Daniel Hatcher, Eneida Hlavina, Wratko Joardar, Vinita S. Kodali, Vamsi K. Li, Wenjun Maglott, Donna Masterson, Patrick McGarvey, Kelly M. Murphy, Michael R. O'Neill, Kathleen Pujar, Shashikant Rangwala, Sanjida H. Rausch, Daniel Riddick, Lillian D. Schoch, Conrad Shkeda, Andrei Storz, Susan S. Sun, Hanzhen Thibaud-Nissen, Francoise Tolstoy, Igor Tully, Raymond E. Vatsan, Anjana R. Wallin, Craig Webb, David Wu, Wendy Landrum, Melissa J. Kimchi, Avi Tatusova, Tatiana DiCuccio, Michael Kitts, Paul Murphy, Terence D. Pruitt, Kim D.
author_sort	O'Leary, Nuala A.
title	Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
title_short	Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
title_full	Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
title_fullStr	Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
title_full_unstemmed	Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
title_sort	reference sequence (refseq) database at ncbi: current status, taxonomic expansion, and functional annotation
description	The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55 000 organisms (>4800 viruses, >40 000 prokaryotes and >10 000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.
publisher	Oxford University Press
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702849/
_version_	1613520491439456256

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

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