Literature DB >> 16901214

Evidence standards in experimental and inferential INSDC Third Party Annotation data.

Guy Cochrane1, Kirsty Bates, Rolf Apweiler, Yoshio Tateno, Jun Mashima, Takehide Kosuge, Ilene Karsch Mizrachi, Susan Schafer, Michael Fetchko.   

Abstract

The Third Party Annotation (TPA) project collects and presents high-quality annotation of nucleotide sequence. Annotation is submitted by researchers who have not themselves generated novel nucleotide sequence. In its first few years, the resource has proven to be popular with submitters from a range of biological research areas. Central to the project is the requirement for high-quality data, resulting from experimental and inferred analysis discussed in peer-reviewed publications. The data are divided into two tiers: those with experimental evidence and those with inferential evidence. Standards for TPA are detailed and illustrated with the aid of case studies.

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Year:  2006        PMID: 16901214     DOI: 10.1089/omi.2006.10.105

Source DB:  PubMed          Journal:  OMICS        ISSN: 1536-2310


  17 in total

Review 1.  New metrics for comparative genomics.

Authors:  Michael Y Galperin; Eugene Kolker
Journal:  Curr Opin Biotechnol       Date:  2006-09-15       Impact factor: 9.740

2.  Fungal genome resources at NCBI.

Authors:  B Robbertse; T Tatusova
Journal:  Mycology       Date:  2011-09

3.  The minimum information about a genome sequence (MIGS) specification.

Authors:  Dawn Field; George Garrity; Tanya Gray; Norman Morrison; Jeremy Selengut; Peter Sterk; Tatiana Tatusova; Nicholas Thomson; Michael J Allen; Samuel V Angiuoli; Michael Ashburner; Nelson Axelrod; Sandra Baldauf; Stuart Ballard; Jeffrey Boore; Guy Cochrane; James Cole; Peter Dawyndt; Paul De Vos; Claude DePamphilis; Robert Edwards; Nadeem Faruque; Robert Feldman; Jack Gilbert; Paul Gilna; Frank Oliver Glöckner; Philip Goldstein; Robert Guralnick; Dan Haft; David Hancock; Henning Hermjakob; Christiane Hertz-Fowler; Phil Hugenholtz; Ian Joint; Leonid Kagan; Matthew Kane; Jessie Kennedy; George Kowalchuk; Renzo Kottmann; Eugene Kolker; Saul Kravitz; Nikos Kyrpides; Jim Leebens-Mack; Suzanna E Lewis; Kelvin Li; Allyson L Lister; Phillip Lord; Natalia Maltsev; Victor Markowitz; Jennifer Martiny; Barbara Methe; Ilene Mizrachi; Richard Moxon; Karen Nelson; Julian Parkhill; Lita Proctor; Owen White; Susanna-Assunta Sansone; Andrew Spiers; Robert Stevens; Paul Swift; Chris Taylor; Yoshio Tateno; Adrian Tett; Sarah Turner; David Ussery; Bob Vaughan; Naomi Ward; Trish Whetzel; Ingio San Gil; Gareth Wilson; Anil Wipat
Journal:  Nat Biotechnol       Date:  2008-05       Impact factor: 54.908

4.  DDBJ progress report.

Authors:  Eli Kaminuma; Takehide Kosuge; Yuichi Kodama; Hideo Aono; Jun Mashima; Takashi Gojobori; Hideaki Sugawara; Osamu Ogasawara; Toshihisa Takagi; Kousaku Okubo; Yasukazu Nakamura
Journal:  Nucleic Acids Res       Date:  2010-11-09       Impact factor: 16.971

5.  The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments.

Authors:  Yuichi Kodama; Jun Mashima; Eli Kaminuma; Takashi Gojobori; Osamu Ogasawara; Toshihisa Takagi; Kousaku Okubo; Yasukazu Nakamura
Journal:  Nucleic Acids Res       Date:  2011-11-22       Impact factor: 16.971

6.  EMBL Nucleotide Sequence Database in 2006.

Authors:  Tamara Kulikova; Ruth Akhtar; Philippe Aldebert; Nicola Althorpe; Mikael Andersson; Alastair Baldwin; Kirsty Bates; Sumit Bhattacharyya; Lawrence Bower; Paul Browne; Matias Castro; Guy Cochrane; Karyn Duggan; Ruth Eberhardt; Nadeem Faruque; Gemma Hoad; Carola Kanz; Charles Lee; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Dariusz Lorenc; Hamish McWilliam; Gaurab Mukherjee; Francesco Nardone; Maria Pilar Garcia Pastor; Sheila Plaister; Siamak Sobhany; Peter Stoehr; Robert Vaughan; Dan Wu; Weimin Zhu; Rolf Apweiler
Journal:  Nucleic Acids Res       Date:  2006-12-05       Impact factor: 16.971

7.  The Vertebrate Genome Annotation browser 10 years on.

Authors:  Jennifer L Harrow; Charles A Steward; Adam Frankish; James G Gilbert; Jose M Gonzalez; Jane E Loveland; Jonathan Mudge; Dan Sheppard; Mark Thomas; Stephen Trevanion; Laurens G Wilming
Journal:  Nucleic Acids Res       Date:  2013-12-06       Impact factor: 16.971

8.  DDBJ launches a new archive database with analytical tools for next-generation sequence data.

Authors:  Eli Kaminuma; Jun Mashima; Yuichi Kodama; Takashi Gojobori; Osamu Ogasawara; Kousaku Okubo; Toshihisa Takagi; Yasukazu Nakamura
Journal:  Nucleic Acids Res       Date:  2009-10-22       Impact factor: 16.971

9.  DDBJ new system and service refactoring.

Authors:  Osamu Ogasawara; Jun Mashima; Yuichi Kodama; Eli Kaminuma; Yasukazu Nakamura; Kousaku Okubo; Toshihisa Takagi
Journal:  Nucleic Acids Res       Date:  2012-11-24       Impact factor: 16.971

10.  Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database.

Authors:  Guy Cochrane; Ruth Akhtar; Philippe Aldebert; Nicola Althorpe; Alastair Baldwin; Kirsty Bates; Sumit Bhattacharyya; James Bonfield; Lawrence Bower; Paul Browne; Matias Castro; Tony Cox; Fehmi Demiralp; Ruth Eberhardt; Nadeem Faruque; Gemma Hoad; Mikyung Jang; Tamara Kulikova; Alberto Labarga; Rasko Leinonen; Steven Leonard; Quan Lin; Rodrigo Lopez; Dariusz Lorenc; Hamish McWilliam; Gaurab Mukherjee; Francesco Nardone; Sheila Plaister; Stephen Robinson; Siamak Sobhany; Robert Vaughan; Dan Wu; Weimin Zhu; Rolf Apweiler; Tim Hubbard; Ewan Birney
Journal:  Nucleic Acids Res       Date:  2007-11-26       Impact factor: 16.971

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