4 years ago

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

Michael Murphy, Tamara Goldfarb, Bronwen L Aken, Bhanu Rajput, Mike P Kay, Catherine M Farrell, Kim D Pruitt, Terence Murphy, Lillian D Riddick, Monica McAndrews, If Barnes, Vinita Joardar, Toby Hunt, Fergal J Martin, Nuala A O'Leary, Adam Frankish, Jose M Gonzalez, Mark Diekhans, Craig Wallin, Elspeth A Bruford, Claire Davidson, John Jackson, Ruth Bennett, Carol J Bult, Shashikant Pujar, Marie-Marthe Suner, Andrew E Berry, Ruth L Seal, Jonathan M Mudge, Kelly M McGarvey, Eric Cox, Jane E Loveland, Sanjida H Rangwala, Vamsi K Kodali, Carlos G Girón, Sophia Zhu, David Webb
The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community.

Publisher URL: http://doi.org/10.1093/nar/gkx1031

DOI: 10.1093/nar/gkx1031

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