Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation
Abstract 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...
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| Veröffentlicht in: | Nucleic acids research 2018-01, Vol.46 (D1), p.D221-D228 |
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| creator | Pujar, Shashikant O'Leary, Nuala A Farrell, Catherine M Loveland, Jane E Mudge, Jonathan M Wallin, Craig Girón, Carlos G Diekhans, Mark Barnes, If Bennett, Ruth Berry, Andrew E Cox, Eric Davidson, Claire Goldfarb, Tamara Gonzalez, Jose M Hunt, Toby Jackson, John Joardar, Vinita Kay, Mike P Kodali, Vamsi K Martin, Fergal J McAndrews, Monica McGarvey, Kelly M Murphy, Michael Rajput, Bhanu Rangwala, Sanjida H Riddick, Lillian D Seal, Ruth L Suner, Marie-Marthe Webb, David Zhu, Sophia Aken, Bronwen L Bruford, Elspeth A Bult, Carol J Frankish, Adam Murphy, Terence Pruitt, Kim D |
| description | Abstract
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. |
| doi_str_mv | 10.1093/nar/gkx1031 |
| format | Article |
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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.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkx1031</identifier><identifier>PMID: 29126148</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Animals ; Consensus Sequence ; Data Curation - methods ; Data Curation - standards ; Database Issue ; Databases, Genetic - standards ; Guidelines as Topic ; Humans ; Mice ; Molecular Sequence Annotation ; National Library of Medicine (U.S.) ; Open Reading Frames ; United States ; User-Computer Interface</subject><ispartof>Nucleic acids research, 2018-01, Vol.46 (D1), p.D221-D228</ispartof><rights>Published by Oxford University Press on behalf of Nucleic Acids Research 2017. 2018</rights><rights>Published by Oxford University Press on behalf of Nucleic Acids Research 2017.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c454t-1a296d3b3ccd3d665569236450d4d19d2ab0203eaaa51618b2d01e23f8b898533</citedby><cites>FETCH-LOGICAL-c454t-1a296d3b3ccd3d665569236450d4d19d2ab0203eaaa51618b2d01e23f8b898533</cites><orcidid>0000-0002-8380-5247 ; 0000-0002-1672-050X ; 0000-0002-0380-7171 ; 0000-0002-7669-2934 ; 0000-0002-0935-7271</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753299/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753299/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,1598,27901,27902,53766,53768</link.rule.ids><linktorsrc>$$Uhttps://dx.doi.org/10.1093/nar/gkx1031$$EView_record_in_Oxford_University_Press$$FView_record_in_$$GOxford_University_Press</linktorsrc><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29126148$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Pujar, Shashikant</creatorcontrib><creatorcontrib>O'Leary, Nuala A</creatorcontrib><creatorcontrib>Farrell, Catherine M</creatorcontrib><creatorcontrib>Loveland, Jane E</creatorcontrib><creatorcontrib>Mudge, Jonathan M</creatorcontrib><creatorcontrib>Wallin, Craig</creatorcontrib><creatorcontrib>Girón, Carlos G</creatorcontrib><creatorcontrib>Diekhans, Mark</creatorcontrib><creatorcontrib>Barnes, If</creatorcontrib><creatorcontrib>Bennett, Ruth</creatorcontrib><creatorcontrib>Berry, Andrew E</creatorcontrib><creatorcontrib>Cox, Eric</creatorcontrib><creatorcontrib>Davidson, Claire</creatorcontrib><creatorcontrib>Goldfarb, Tamara</creatorcontrib><creatorcontrib>Gonzalez, Jose M</creatorcontrib><creatorcontrib>Hunt, Toby</creatorcontrib><creatorcontrib>Jackson, John</creatorcontrib><creatorcontrib>Joardar, Vinita</creatorcontrib><creatorcontrib>Kay, Mike P</creatorcontrib><creatorcontrib>Kodali, Vamsi K</creatorcontrib><creatorcontrib>Martin, Fergal J</creatorcontrib><creatorcontrib>McAndrews, Monica</creatorcontrib><creatorcontrib>McGarvey, Kelly M</creatorcontrib><creatorcontrib>Murphy, Michael</creatorcontrib><creatorcontrib>Rajput, Bhanu</creatorcontrib><creatorcontrib>Rangwala, Sanjida H</creatorcontrib><creatorcontrib>Riddick, Lillian D</creatorcontrib><creatorcontrib>Seal, Ruth L</creatorcontrib><creatorcontrib>Suner, Marie-Marthe</creatorcontrib><creatorcontrib>Webb, David</creatorcontrib><creatorcontrib>Zhu, Sophia</creatorcontrib><creatorcontrib>Aken, Bronwen L</creatorcontrib><creatorcontrib>Bruford, Elspeth A</creatorcontrib><creatorcontrib>Bult, Carol J</creatorcontrib><creatorcontrib>Frankish, Adam</creatorcontrib><creatorcontrib>Murphy, Terence</creatorcontrib><creatorcontrib>Pruitt, Kim D</creatorcontrib><title>Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
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.</description><subject>Animals</subject><subject>Consensus Sequence</subject><subject>Data Curation - methods</subject><subject>Data Curation - standards</subject><subject>Database Issue</subject><subject>Databases, Genetic - standards</subject><subject>Guidelines as Topic</subject><subject>Humans</subject><subject>Mice</subject><subject>Molecular Sequence Annotation</subject><subject>National Library of Medicine (U.S.)</subject><subject>Open Reading Frames</subject><subject>United States</subject><subject>User-Computer Interface</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kT1vFDEQhi0EIsdBRY9coSC0xN9ZUyChhUCkSBRAbc2u5y4Lt_Zie1FCnR-O0V0iaKhG8jx-ZuyXkKecveLMypMA6WT7_Yozye-RFZdGNMoacZ-smGS64Uy1R-RRzt8Y44pr9ZAcCcuF4apdkZsuhowhL5kO0Y9hSzP-WDAMSI-77t3nF9RDgR4yvqZAc4HgIfnxF_oKFho39HKZINB6Tqe4ZKRzigXH0Bx0CbdjHUHzMs8xlXqvv6Z4NWMqdFgSlNp9TB5sYJfxyaGuydez91-6j83Fpw_n3duLZlBalYaDsMbLXg6Dl94YrY0V0ijNvPLcegE9E0wiAGhueNsLzzgKuWn71rZayjV5s_fOSz-hHzCUBDs3p3GCdO0ijO7fThgv3Tb-dPpUS2FtFRwfBCnWX8rFTWMecLeDgPXxjlsjxSm3tazJyz06pJhzws3dGM7cn9xczc0dcqv0s783u2Nvg6rA8z0Ql_m_pt-8PaQH</recordid><startdate>20180104</startdate><enddate>20180104</enddate><creator>Pujar, Shashikant</creator><creator>O'Leary, Nuala A</creator><creator>Farrell, Catherine M</creator><creator>Loveland, Jane E</creator><creator>Mudge, Jonathan M</creator><creator>Wallin, Craig</creator><creator>Girón, Carlos G</creator><creator>Diekhans, Mark</creator><creator>Barnes, If</creator><creator>Bennett, Ruth</creator><creator>Berry, Andrew E</creator><creator>Cox, Eric</creator><creator>Davidson, Claire</creator><creator>Goldfarb, Tamara</creator><creator>Gonzalez, Jose M</creator><creator>Hunt, Toby</creator><creator>Jackson, John</creator><creator>Joardar, Vinita</creator><creator>Kay, Mike P</creator><creator>Kodali, Vamsi K</creator><creator>Martin, Fergal J</creator><creator>McAndrews, Monica</creator><creator>McGarvey, Kelly M</creator><creator>Murphy, Michael</creator><creator>Rajput, Bhanu</creator><creator>Rangwala, Sanjida H</creator><creator>Riddick, Lillian D</creator><creator>Seal, Ruth L</creator><creator>Suner, Marie-Marthe</creator><creator>Webb, David</creator><creator>Zhu, Sophia</creator><creator>Aken, Bronwen L</creator><creator>Bruford, Elspeth A</creator><creator>Bult, Carol J</creator><creator>Frankish, Adam</creator><creator>Murphy, Terence</creator><creator>Pruitt, Kim D</creator><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-8380-5247</orcidid><orcidid>https://orcid.org/0000-0002-1672-050X</orcidid><orcidid>https://orcid.org/0000-0002-0380-7171</orcidid><orcidid>https://orcid.org/0000-0002-7669-2934</orcidid><orcidid>https://orcid.org/0000-0002-0935-7271</orcidid></search><sort><creationdate>20180104</creationdate><title>Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation</title><author>Pujar, Shashikant ; O'Leary, Nuala A ; Farrell, Catherine M ; Loveland, Jane E ; Mudge, Jonathan M ; Wallin, Craig ; Girón, Carlos G ; Diekhans, Mark ; Barnes, If ; Bennett, Ruth ; Berry, Andrew E ; Cox, Eric ; Davidson, Claire ; Goldfarb, Tamara ; Gonzalez, Jose M ; Hunt, Toby ; Jackson, John ; Joardar, Vinita ; Kay, Mike P ; Kodali, Vamsi K ; Martin, Fergal J ; McAndrews, Monica ; McGarvey, Kelly M ; Murphy, Michael ; Rajput, Bhanu ; Rangwala, Sanjida H ; Riddick, Lillian D ; Seal, Ruth L ; Suner, Marie-Marthe ; Webb, David ; Zhu, Sophia ; Aken, Bronwen L ; Bruford, Elspeth A ; Bult, Carol J ; Frankish, Adam ; Murphy, Terence ; Pruitt, Kim D</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c454t-1a296d3b3ccd3d665569236450d4d19d2ab0203eaaa51618b2d01e23f8b898533</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Animals</topic><topic>Consensus Sequence</topic><topic>Data Curation - 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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.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>29126148</pmid><doi>10.1093/nar/gkx1031</doi><orcidid>https://orcid.org/0000-0002-8380-5247</orcidid><orcidid>https://orcid.org/0000-0002-1672-050X</orcidid><orcidid>https://orcid.org/0000-0002-0380-7171</orcidid><orcidid>https://orcid.org/0000-0002-7669-2934</orcidid><orcidid>https://orcid.org/0000-0002-0935-7271</orcidid><oa>free_for_read</oa></addata></record> |
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| source | Oxford Journals Open Access Collection |
| subjects | Animals Consensus Sequence Data Curation - methods Data Curation - standards Database Issue Databases, Genetic - standards Guidelines as Topic Humans Mice Molecular Sequence Annotation National Library of Medicine (U.S.) Open Reading Frames United States User-Computer Interface |
| title | Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation |
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