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Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation
2017
Nucleic Acids Research
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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
2013
Nucleic Acids Research
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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
2009
Genome Research
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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
2016
Database: The Journal of Biological Databases and Curation
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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
2010
Database: The Journal of Biological Databases and Curation
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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
2009
Nucleic Acids Research
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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
2015
Nucleic Acids Research
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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
2012
Database: The Journal of Biological Databases and Curation
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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
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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
2009
Nucleic Acids Research
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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
2015
Mammalian Genome
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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
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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
2007
Nucleic Acids Research
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A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
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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
2018
Nucleic Acids Research
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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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