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Literature DB >> 18769432

Big data: The future of biocuration.

Doug Howe¹, Maria Costanzo, Petra Fey, Takashi Gojobori, Linda Hannick, Winston Hide, David P Hill, Renate Kania, Mary Schaeffer, Susan St Pierre, Simon Twigger, Owen White, Seung Yon Rhee.

Abstract

Entities: Chemical Gene Species

Mesh：

Year: 2008 PMID： 18769432 PMCID： PMC2819144 DOI： 10.1038/455047a

Source DB: PubMed Journal: Nature ISSN： 0028-0836 Impact factor: 49.962

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17 in total

1. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Authors: A Brazma; P Hingamp; J Quackenbush; G Sherlock; P Spellman; C Stoeckert; J Aach; W Ansorge; C A Ball; H C Causton; T Gaasterland; P Glenisson; F C Holstege; I F Kim; V Markowitz; J C Matese; H Parkinson; A Robinson; U Sarkans; S Schulze-Kremer; J Stewart; R Taylor; J Vilo; M Vingron
Journal: Nat Genet Date: 2001-12 Impact factor: 38.330

2. Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).

Authors: Eric W Deutsch; Catherine A Ball; Jules J Berman; G Steven Bova; Alvis Brazma; Roger E Bumgarner; David Campbell; Helen C Causton; Jeffrey H Christiansen; Fabrice Daian; Delphine Dauga; Duncan R Davidson; Gregory Gimenez; Young Ah Goo; Sean Grimmond; Thorsten Henrich; Bernhard G Herrmann; Michael H Johnson; Martin Korb; Jason C Mills; Asa J Oudes; Helen E Parkinson; Laura E Pascal; Nicolas Pollet; John Quackenbush; Mirana Ramialison; Martin Ringwald; David Salgado; Susanna-Assunta Sansone; Gavin Sherlock; Christian J Stoeckert; Jason Swedlow; Ronald C Taylor; Laura Walashek; Anthony Warford; David G Wilkinson; Yi Zhou; Leonard I Zon; Alvin Y Liu; Lawrence D True
Journal: Nat Biotechnol Date: 2008-03 Impact factor: 54.908

Review 3. The minimum information about a proteomics experiment (MIAPE).

Authors: Chris F Taylor; Norman W Paton; Kathryn S Lilley; Pierre-Alain Binz; Randall K Julian; Andrew R Jones; Weimin Zhu; Rolf Apweiler; Ruedi Aebersold; Eric W Deutsch; Michael J Dunn; Albert J R Heck; Alexander Leitner; Marcus Macht; Matthias Mann; Lennart Martens; Thomas A Neubert; Scott D Patterson; Peipei Ping; Sean L Seymour; Puneet Souda; Akira Tsugita; Joel Vandekerckhove; Thomas M Vondriska; Julian P Whitelegge; Marc R Wilkins; Ioannnis Xenarios; John R Yates; Henning Hermjakob
Journal: Nat Biotechnol Date: 2007-08 Impact factor: 54.908

4. A proposed framework for the description of plant metabolomics experiments and their results.

Authors: Helen Jenkins; Nigel Hardy; Manfred Beckmann; John Draper; Aileen R Smith; Janet Taylor; Oliver Fiehn; Royston Goodacre; Raoul J Bino; Robert Hall; Joachim Kopka; Geoffrey A Lane; B Markus Lange; Jang R Liu; Pedro Mendes; Basil J Nikolau; Stephen G Oliver; Norman W Paton; Sue Rhee; Ute Roessner-Tunali; Kazuki Saito; Jørn Smedsgaard; Lloyd W Sumner; Trevor Wang; Sean Walsh; Eve Syrkin Wurtele; Douglas B Kell
Journal: Nat Biotechnol Date: 2004-12 Impact factor: 54.908

5. 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

6. Will a biological database be different from a biological journal?

Authors: Philip Bourne
Journal: PLoS Comput Biol Date: 2005-08 Impact factor: 4.475

Review 7. A biocurator perspective: annotation at the Research Collaboratory for Structural Bioinformatics Protein Data Bank.

Authors: Kyle Burkhardt; Bohdan Schneider; Jeramia Ory
Journal: PLoS Comput Biol Date: 2006-10-27 Impact factor: 4.475

Big data: The future of biocuration.

1. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

2. Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).

Review 3. The minimum information about a proteomics experiment (MIAPE).

4. A proposed framework for the description of plant metabolomics experiments and their results.

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

6. Will a biological database be different from a biological journal?

Review 7. A biocurator perspective: annotation at the Research Collaboratory for Structural Bioinformatics Protein Data Bank.

Review 8. The biocurator: connecting and enhancing scientific data.

9. GenBank.

10. A gene wiki for community annotation of gene function.

1. Transcriptional regulatory networks in Arabidopsis thaliana during single and combined stresses.

Review 2. Genotype-phenotype databases: challenges and solutions for the post-genomic era.

3. A knowledge-driven conditional approach to extract pharmacogenomics specific drug-gene relationships from free text.

4. Accreditation and attribution in data sharing.

5. Building an efficient curation workflow for the Arabidopsis literature corpus.

6. Metadata and annotations for multi-scale electrophysiological data.

Review 7. The mammalian phenotype ontology: enabling robust annotation and comparative analysis.

8. Inside FlyBase: biocuration as a career.

9. SpBase: the sea urchin genome database and web site.

10. The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.