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Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation

Shashikant Pujar, Nuala A O'Leary, Catherine M Farrell, Jane E Loveland, Jonathan M Mudge, Craig Wallin, Carlos G Girón, Mark Diekhans, If Barnes, Ruth Bennett, Andrew E Berry, Eric Cox (+25 others)
2017 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors wish to thank all programmers and other staff at NCBI, EMBL-EBI, UCSC, HGNC and MGI, who contributed to CCDS analyses and maintenance of the CCDS database and its internal  ...  The authors also thank UniProtKB curators, scientific experts and CCDS users for their helpful inputs. FUNDING  ...  Guidelines Coordinated curation of human and mouse coding region annotation by experts in the CCDS collaboration is crucial for maintaining the high quality of the CCDS dataset.  ... 
doi:10.1093/nar/gkx1031 pmid:29126148 pmcid:PMC5753299 fatcat:xlfpwnmezjejtbg7dyatdwspvi

Current status and new features of the Consensus Coding Sequence database

Catherine M. Farrell, Nuala A. O'Leary, Rachel A. Harte, Jane E. Loveland, Laurens G. Wilming, Craig Wallin, Mark Diekhans, Daniel Barrell, Stephen M. J. Searle, Bronwen Aken, Susan M. Hiatt, Adam Frankish (+31 others)
2013 Nucleic Acids Research  
The Consensus Coding Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) is a collaborative effort to maintain a dataset of proteincoding regions that are identically annotated on the human and  ...  We also present a summary of recent and future curation targets.  ...  ACKNOWLEDGEMENTS The authors wish to thank the programmers, database and curation staff at Ensembl, NCBI, HAVANA and UCSC for their contributions to the CCDS analysis, maintenance and continuing curation  ... 
doi:10.1093/nar/gkt1059 pmid:24217909 pmcid:PMC3965069 fatcat:go2bm4timjdhzc6ecp42w77k7m

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

K. D. Pruitt, J. Harrow, R. A. Harte, C. Wallin, M. Diekhans, D. R. Maglott, S. Searle, C. M. Farrell, J. E. Loveland, B. J. Ruef, E. Hart, M.-M. Suner (+37 others)
2009 Genome Research  
converge on a complete protein-coding set for the human and mouse reference genomes, while maintaining a high standard of reliability and biological accuracy.  ...  The collaborative consensus coding sequence (CCDS) project tracks identical protein annotations on the reference mouse and human genomes with a stable identifier (CCDS ID), and ensures that they are consistently  ...  Acknowledgments We thank the programmer, database, and curation staff at Ensembl, NCBI, WTSI, and UCSC for their contribution to the CCDS analysis, maintenance, and continuing curation efforts.  ... 
doi:10.1101/gr.080531.108 pmid:19498102 pmcid:PMC2704439 fatcat:tqvb4qxbbjfcbdpjhieg6zokae

The UniProtKB guide to the human proteome

Lionel Breuza, Sylvain Poux, Anne Estreicher, Maria Livia Famiglietti, Michele Magrane, Michael Tognolli, Alan Bridge, Delphine Baratin, Nicole Redaschi
2016 Database: The Journal of Biological Databases and Curation  
We will show how manual expert curation of UniProtKB/Swiss-Prot is complemented by expert-driven automatic annotation to build a comprehensive, high-quality and traceable resource.  ...  For this purpose, they need high-quality resources providing comprehensive gene and protein sets for their organisms of interest.  ...  Acknowledgements The human proteome has been prepared by Ioannis Xenarios, Lydie Bougueleret, Amos Bairoch, Lucila Aimo, Andrea Auchincloss, Kristian Axelsen, Ghislaine Argoud-Puy, Parit Bansal, Pierre-Alain  ... 
doi:10.1093/database/bav120 pmid:26896845 pmcid:PMC4761109 fatcat:zkylcolt6bdvlppb2pq4kyuzp4

Meeting report: a workshop on Best Practices in Genome Annotation

R. Madupu, L. M. Brinkac, J. Harrow, L. G. Wilming, U. Bohme, P. Lamesch, L. I. Hannick
2010 Database: The Journal of Biological Databases and Curation  
Conflict of interest. None declared.  ...  As part of the CCDS (consensus coding sequence) project (30, 31) , the Havana team collaborates with other annotation groups focusing on producing a reference gene set consistent among human and mouse  ...  , protein-coding regions, regulatory features, simple sequence repeats and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) (17) regions.  ... 
doi:10.1093/database/baq001 pmid:20428316 pmcid:PMC2860899 fatcat:ibdlwzv74veqrb6mzl7nkyr3km

NCBI Reference Sequences: current status, policy and new initiatives

K. D. Pruitt, T. Tatusova, W. Klimke, D. R. Maglott
2009 Nucleic Acids Research  
NCBI's Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins.  ...  Feature annotation is applied by a combination of curation, collaboration, propagation from other sources and computation.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkn721 pmid:18927115 pmcid:PMC2686572 fatcat:77xptvs54fghxb3dur3ykwycgq

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

Nuala A. O'Leary, Mathew W. Wright, J. Rodney Brister, Stacy Ciufo, Diana Haddad, Rich McVeigh, Bhanu Rajput, Barbara Robbertse, Brian Smith-White, Danso Ako-Adjei, Alexander Astashyn, Azat Badretdin (+43 others)
2015 Nucleic Acids Research  
a standard set of stable, non-redundant reference sequences.  ...  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:/  ...  and accuracy of the represented sequence, structural annotation, and functional annotation.  ... 
doi:10.1093/nar/gkv1189 pmid:26553804 pmcid:PMC4702849 fatcat:2bm7d5coyvfotaj23hnj3mce6m

Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference

P. Gaudet, C. Arighi, F. Bastian, A. Bateman, J. A. Blake, M. J. Cherry, P. D'Eustachio, R. Finn, M. Giglio, L. Hirschman, R. Kania, W. Klimke (+16 others)
2012 Database: The Journal of Biological Databases and Curation  
This research was supported in part by the Intramural Research Program of the National Library of Medicine, NIH.  ...  The publication fees of this article has been paid by the 2012 International Biocuration Conference committee and the International Society for Biocuration.  ...  Kim Pruitt described the Consensus Coding Sequence (CCDS) project, is a collaboration between multiple centers with a goal of producing a set of high-quality protein coding region annotations for the human  ... 
doi:10.1093/database/bas036 pmid:23110974 pmcid:PMC3483532 fatcat:v56fpejv3jftbo62gjdhjyswja

Database resources of the National Center for Biotechnology Information

2013 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other  ...  California, Santa Cruz (UCSC) to identify a set of human and mouse protein coding regions that are consistently annotated and of high quality.  ...  Reference sequences. The NCBI RefSeq database (27) is a nonredundant set of curated and computationally derived sequences for transcripts, proteins and genomic regions.  ... 
doi:10.1093/nar/gkt1146 pmid:24259429 pmcid:PMC3965057 fatcat:otokyran6rhjvhb2wtyt2z6hvu

Database resources of the National Center for Biotechnology Information

Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Lewis Y. Geer (+28 others)
2009 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other  ...  California, Santa Cruz (UCSC) to identify a set of human and mouse protein coding regions that are consistently annotated and of high quality.  ...  Reference sequences. The NCBI RefSeq database (27) is a nonredundant set of curated and computationally derived sequences for transcripts, proteins and genomic regions.  ... 
doi:10.1093/nar/gkp967 pmid:19910364 pmcid:PMC2808881 fatcat:duzfi6ea4rdvvb5wbhr7z2mbpq

Mouse genome annotation by the RefSeq project

Kelly M. McGarvey, Tamara Goldfarb, Eric Cox, Catherine M. Farrell, Tripti Gupta, Vinita S. Joardar, Vamsi K. Kodali, Michael R. Murphy, Nuala A. O'Leary, Shashikant Pujar, Bhanu Rajput, Sanjida H. Rangwala (+5 others)
2015 Mammalian Genome  
Complete and accurate annotation of the mouse genome is critical to the advancement of research conducted on this important model organism.  ...  We thank our collaborators, especially the HUGO Gene Nomenclature Committee, the Mouse Genome Database, Rat Genome Database, UniProt and CCDS curators at the University of California Santa Cruz and the  ...  We sincerely value your input to help improve the RefSeq database content. Compliance with ethical standards Conflict of Interest The authors declare that they have no conflict of interest.  ... 
doi:10.1007/s00335-015-9585-8 pmid:26215545 pmcid:PMC4602073 fatcat:h7gzfdaghzeith7en6ejocoksi

Database Resources of the National Center for Biotechnology Information

2016 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other  ...  DNA AND RNA Reference sequences The NCBI Reference Sequence (RefSeq) database (9) is a non-redundant set of curated and computationally derived sequences for transcripts, proteins and genomic regions  ...  As part of standard submission procedures, NCBI produces conceptual translations for any sequence in GenBank (1) that contains a coding sequence and places these protein sequences in the Entrez Protein  ... 
doi:10.1093/nar/gkw1071 pmid:27899561 pmcid:PMC5210554 fatcat:itaqk5uwv5bv7gm7f55zunbcwq

Database resources of the National Center for Biotechnology Information

D. L. Wheeler, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, R. Edgar, S. Federhen, L. Y. Geer, Y. Kapustin (+18 others)
2007 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other  ...  DNA AND RNA Reference sequences The NCBI Reference Sequence (RefSeq) database (9) is a non-redundant set of curated and computationally derived sequences for transcripts, proteins and genomic regions  ...  As part of standard submission procedures, NCBI produces conceptual translations for any sequence in GenBank (1) that contains a coding sequence and places these protein sequences in the Entrez Protein  ... 
doi:10.1093/nar/gkl1031 pmid:17170002 pmcid:PMC1781113 fatcat:pj7gnwwlpnbmza7c4ae7yatega

The Universal Protein Resource (UniProt)

2007 Nucleic Acids Research  
The primary mission of UniProt is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive  ...  cross-references and querying interfaces freely accessible to the scientific community.  ...  UniProt recently joined the Consensus CDS (CCDS) project (13), a collaborative effort to identify a core set of consistently annotated and high quality human and mouse protein-coding regions.  ... 
doi:10.1093/nar/gkm895 pmid:18045787 pmcid:PMC2238893 fatcat:pbq7vsuwtfafzco3f5dcfipvba

GENCODE reference annotation for the human and mouse genomes

Adam Frankish, Mark Diekhans, Anne-Maud Ferreira, Rory Johnson, Irwin Jungreis, Jane Loveland, Jonathan M Mudge, Cristina Sisu, James Wright, Joel Armstrong, If Barnes, Andrew Berry (+43 others)
2018 Nucleic Acids Research  
The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics  ...  Specifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines.  ...  ACKNOWLEDGEMENTS We thank Tim Hubbard and Jennifer Harrow for their leadership in the GENCODE project from 2003-2016 as well as all groups and group members involved in the GENCODE project since its inception  ... 
doi:10.1093/nar/gky955 pmid:30357393 pmcid:PMC6323946 fatcat:vg5kuecy5rc7xewce5u3xczdba
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