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Tracking and coordinating an international curation effort for the CCDS Project

R. A. Harte, C. M. Farrell, J. E. Loveland, M.-M. Suner, L. Wilming, B. Aken, D. Barrell, A. Frankish, C. Wallin, S. Searle, M. Diekhans, J. Harrow (+1 others)
2012 Database: The Journal of Biological Databases and Curation  
Here, we present the current status of the CCDS database and details on our procedures to track and coordinate our efforts.  ...  The CCDS project consists of analysis of automated whole-genome annotation builds to identify identical CDS annotations, quality assurance testing and manual curation support.  ...  Acknowledgements We wish to thank the programmers, database and curation staff at Ensembl, NCBI, WTSI and UCSC for their contribution to the CCDS analysis, maintenance and continuing curation efforts.  ... 
doi:10.1093/database/bas008 pmid:22434842 pmcid:PMC3308164 fatcat:3rppcgpcovf7deqvave3x3lafe

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  
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  ...  Importantly, the project coordinates on manually reviewing inconsistent protein annotations between sites, as well as annotations for which new evidence suggests a revision is needed, to progressively  ...  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

Curation at the NCBI: Genomes, Genes, & Sequence Standards

Kim Pruitt, David Webb, Michael Murphy, Janet Weber, Terence Murphy, Wendy Wu, Bhanu Rajput, Garth Brown, Catherine Farrell, Jennifer Hart, Melissa Landrum, Lillian Riddick (+2 others)
2009 Nature Precedings  
These projects are supported by several collaborations to provide:1) support to the international consortium maintaining the assemblies for human and mouse (GRC); 2) sequence standards for chromosomes,  ...  Abstract: Genes Extensive communication and coordination occurs between NCBI's RefSeq curation staff, the HUGO Gene Nomenclature Committee (HGNC), the Sanger Institute's Havana curation group, and other  ...  Exception The development of common curation guidelines used by NCBI's RefSeq curators, the Sanger Instutute's Havana curators, and the UCSC CCDS curation staff has improved efficiency and reduced the  ... 
doi:10.1038/npre.2009.3287.1 fatcat:aobuk2zzcbfedkx72soqlopprq

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  ...  Acknowledgments We would like to recognize Francoise Thibaud-Nissen for providing the overview graphic depicting NCBI's eukaryotic genome annotation pipeline and statistics from the annotation releases  ... 
doi:10.1007/s00335-015-9585-8 pmid:26215545 pmcid:PMC4602073 fatcat:h7gzfdaghzeith7en6ejocoksi

NCBI Reference Sequences: current status, policy and new initiatives

K. D. Pruitt, T. Tatusova, W. Klimke, D. R. Maglott
2009 Nucleic Acids Research  
We report here on the recent growth of the database, recent changes to feature annotations and record types for eukaryotic (primarily vertebrate) species and policies regarding species inclusion and genome  ...  The database includes over 5300 organisms spanning prokaryotes, eukaryotes and viruses, with records for more than 5.5 3 10 6 proteins (RefSeq release 30).  ...  RELATED INITIATIVES CCDS Collaborators for the Consensus CDS (CCDS) project have made a significant focus on coordinating curation of the human proteome in the past 2 years.  ... 
doi:10.1093/nar/gkn721 pmid:18927115 pmcid:PMC2686572 fatcat:77xptvs54fghxb3dur3ykwycgq

A unified gene catalog for the laboratory mouse reference genome

Y. Zhu, J. E. Richardson, P. Hale, R. M. Baldarelli, D. J. Reed, J. M. Recla, R. Sinclair, T. B. K. Reddy, C. J. Bult
2015 Mammalian Genome  
We report here a semi-automated process by which mouse genome feature predictions and curated annotations (i.e.  ...  The authors thank all of the curators at NCBI and HAVANA for their collaborative efforts to improve annotations for the reference mouse genome. The authors thank Dr.  ...  Joel Graber for his critical review of an early version of this manuscript.  ... 
doi:10.1007/s00335-015-9571-1 pmid:26084703 pmcid:PMC4534496 fatcat:rxxquwdntbcvvdyngyfxnel2le

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  
The authors also thank UniProtKB curators, scientific experts and CCDS users for their helpful inputs. FUNDING  ...  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  ...  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

The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium

M. Ringwald, V. Iyer, J. C. Mason, K. R. Stone, H. D. Tadepally, J. A. Kadin, C. J. Bult, J. T. Eppig, D. J. Oakley, S. Briois, E. Stupka, V. Maselli (+6 others)
2010 Nucleic Acids Research  
ACKNOWLEDGEMENTS We would like to thank all our colleagues from the different IKMC programs for making their data available to the IKMC web portal project and for very collegial and productive interactions  ...  Finally, we would like to thank UCSC and Ensembl for displaying IKMC allele tracks on their genome browsers, and all external resources that provide data to the IKMC web portal.  ...  (International-Data Coordination Center) project funded by the EC.  ... 
doi:10.1093/nar/gkq879 pmid:20929875 pmcid:PMC3013768 fatcat:qrhhuo6nxrhgdkfqrdqsoegxwe

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  
These requirements depend on whether the project is part of a comparative genome-sequencing project or a genome project for an organism for which there is no sequence data available from a closely related  ...  All annotated Arabidopsis genes are shown in the TAIR genome browser, GBrowse and the various evidence types used by curators for annotation can be selected for display in over 50 data tracks.  ... 
doi:10.1093/database/baq001 pmid:20428316 pmcid:PMC2860899 fatcat:ibdlwzv74veqrb6mzl7nkyr3km

RefSeq: an update on mammalian reference sequences

Kim D. Pruitt, Garth R. Brown, Susan M. Hiatt, Françoise Thibaud-Nissen, Alexander Astashyn, Olga Ermolaeva, Catherine M. Farrell, Jennifer Hart, Melissa J. Landrum, Kelly M. McGarvey, Michael R. Murphy, Nuala A. O'Leary (+17 others)
2013 Nucleic Acids Research  
We also describe a revised protein annotation policy for alternatively spliced transcripts with more divergent predicted proteins and we summarize the current status of the RefSeqGene project.  ...  archives and from computation, curation and collaboration (http://www.ncbi.nlm. nih.gov/refseq/).  ...  ACKNOWLEDGEMENTS 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  ... 
doi:10.1093/nar/gkt1114 pmid:24259432 pmcid:PMC3965018 fatcat:wid54lruqrdzndb4oghwltdrqa

Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany

Sandra Orchard, Juan Pablo Albar, Eric W. Deutsch, Martin Eisenacher, Juan A. Vizcaíno, Henning Hermjakob
2011 Proteomics  
ME and CS are funded from P.U.R.E. (Protein Unit for Research in Europe), a project of Nordrhein-Westfalen, a federal state of Germany.  ...  EWD is also funded by NIH/NIGMS grant number R01 GM087221, NIH/NIGMS grant number PM50 GMO76547/Center for Systems Biology, and the Systems Biology initiative from the Grand Duchy of Luxembourg.  ...  This is a coordination action project in the 7th Framework Programme of the European Commission, which started on January 2011 and will last for 3 years.  ... 
doi:10.1002/pmic.201190117 pmid:22045680 pmcid:PMC4362542 fatcat:6hlzsx3tbrbydctwm4phfty66u

Database resources of the National Center for Biotechnology Information

E. W. Sayers, T. Barrett, D. A. Benson, E. Bolton, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, S. Federhen, M. Feolo, I. M. Fingerman (+30 others)
2010 Nucleic Acids Research  
for the data in GenBank and other biological data made available through the NCBI Web site.  ...  ABSTRACT In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources  ...  consortia and internal curation efforts.  ... 
doi:10.1093/nar/gkq1172 pmid:21097890 pmcid:PMC3013733 fatcat:evc3u4jqubchjoqyvc3ff5qple

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

Jasmine Y Young, John D Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M Berrisford, G Jawahar Swaminathan, Thomas J Oldfield, Aleksandras Gutmanas, Reiko Igarashi (+39 others)
2018 Database: The Journal of Biological Databases and Curation  
The V C The Author(s) worldwide PDB (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR principles: Findability, Accessibility, Interoperability and Reusability  ...  This article outlines the importance of biocuration for structural biology data deposited to the PDB and describes wwPDB biocuration processes and the role of expert Biocurators in sustaining a highquality  ...  Acknowledgements The authors thank all the members of the worldwide Protein Data Bank (wwPDB) for their support and feedback, Kim Henrick for his direction to the PDB in Europe (PDBe) biocuration team  ... 
doi:10.1093/database/bay002 pmid:29688351 pmcid:PMC5804564 fatcat:pymncvy65zghjgdhleavnz7oce

Ensembl 2007

T. J. P. Hubbard, B. L. Aken, K. Beal, B. Ballester, M. Caccamo, Y. Chen, L. Clarke, G. Coates, F. Cunningham, T. Cutts, T. Down, S. C. Dyer (+46 others)
2007 Nucleic Acids Research  
The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of chordate genome sequences.  ...  Some of the major features added during the year include the first complete gene sets for genomes with low-sequence coverage, the introduction of new strain variation data and the introduction of new orthology  ...  ACKNOWLEDGEMENTS The Ensembl project is principally funded by the Wellcome Trust with additional funding from EMBL, NIH-NIAID and BBSRC.  ... 
doi:10.1093/nar/gkl996 pmid:17148474 pmcid:PMC1761443 fatcat:7x6v5vzkhfbbhptb3ctp2oeqvu
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