Literature DB >> 21370078

Data standards for Omics data: the basis of data sharing and reuse.

Stephen A Chervitz1, Eric W Deutsch, Dawn Field, Helen Parkinson, John Quackenbush, Phillipe Rocca-Serra, Susanna-Assunta Sansone, Christian J Stoeckert, Chris F Taylor, Ronald Taylor, Catherine A Ball.   

Abstract

To facilitate sharing of Omics data, many groups of scientists have been working to establish the relevant data standards. The main components of data sharing standards are experiment description standards, data exchange standards, terminology standards, and experiment execution standards. Here we provide a survey of existing and emerging standards that are intended to assist the free and open exchange of large-format data.

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Year:  2011        PMID： 21370078      PMCID： PMC4152841          DOI： 10.1007/978-1-61779-027-0_2

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  69 in total

Review 1.  Microarray databases: standards and ontologies.

Authors:  Christian J Stoeckert; Helen C Causton; Catherine A Ball
Journal:  Nat Genet       Date:  2002-12       Impact factor: 38.330

2.  RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies.

Authors:  E Manduchi; G R Grant; H He; J Liu; M D Mailman; A D Pizarro; P L Whetzel; C J Stoeckert
Journal:  Bioinformatics       Date:  2004-01-22       Impact factor: 6.937

Review 3.  Standards for systems biology.

Authors:  Alvis Brazma; Maria Krestyaninova; Ugis Sarkans
Journal:  Nat Rev Genet       Date:  2006-08       Impact factor: 53.242

Review 4.  Data standards: a call to action.

Authors:  Cath Brooksbank; John Quackenbush
Journal:  OMICS       Date:  2006

Review 5.  Gene expression omnibus: microarray data storage, submission, retrieval, and analysis.

Authors:  Tanya Barrett; Ron Edgar
Journal:  Methods Enzymol       Date:  2006       Impact factor: 1.600

6.  A web-based interface for communication of data between the clinical and research environments without revealing identifying information.

Authors:  Peyton H Bland; Gary E Laderach; Charles R Meyer
Journal:  Acad Radiol       Date:  2007-06       Impact factor: 3.173

7.  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

8.  A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.

Authors:  Tim F Rayner; Philippe Rocca-Serra; Paul T Spellman; Helen C Causton; Anna Farne; Ele Holloway; Rafael A Irizarry; Junmin Liu; Donald S Maier; Michael Miller; Kjell Petersen; John Quackenbush; Gavin Sherlock; Christian J Stoeckert; Joseph White; Patricia L Whetzel; Farrell Wymore; Helen Parkinson; Ugis Sarkans; Catherine A Ball; Alvis Brazma
Journal:  BMC Bioinformatics       Date:  2006-11-06       Impact factor: 3.169

9.  Implementation of GenePattern within the Stanford Microarray Database.

Authors:  Jeremy Hubble; Janos Demeter; Heng Jin; Maria Mao; Michael Nitzberg; T B K Reddy; Farrell Wymore; Zachariah K Zachariah; Gavin Sherlock; Catherine A Ball
Journal:  Nucleic Acids Res       Date:  2008-10-25       Impact factor: 16.971

10.  Towards a data sharing culture: recommendations for leadership from academic health centers.

Authors:  Heather A Piwowar; Michael J Becich; Howard Bilofsky; Rebecca S Crowley
Journal:  PLoS Med       Date:  2008-09-02       Impact factor: 11.069
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  14 in total

Review 1.  Guidelines for the design, analysis and interpretation of 'omics' data: focus on human endometrium.

Authors:  Signe Altmäe; Francisco J Esteban; Anneli Stavreus-Evers; Carlos Simón; Linda Giudice; Bruce A Lessey; Jose A Horcajadas; Nick S Macklon; Thomas D'Hooghe; Cristina Campoy; Bart C Fauser; Lois A Salamonsen; Andres Salumets
Journal:  Hum Reprod Update       Date:  2013-09-29       Impact factor: 15.610

Review 2.  Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity.

Authors:  Josh Tycko; Vic E Myer; Patrick D Hsu
Journal:  Mol Cell       Date:  2016-08-04       Impact factor: 17.970

3.  The State of Data in Healthcare: Path Towards Standardization.

Authors:  Keith Feldman; Reid A Johnson; Nitesh V Chawla
Journal:  J Healthc Inform Res       Date:  2018-05-22

Review 4.  Techniques and Approaches to Genetic Analyses in Nephrological Disorders.

Authors:  Laurel K Willig
Journal:  J Pediatr Genet       Date:  2015-08-13

Review 5.  Studying Cellular Signal Transduction with OMIC Technologies.

Authors:  Benjamin D Landry; David C Clarke; Michael J Lee
Journal:  J Mol Biol       Date:  2015-08-03       Impact factor: 5.469

Review 6.  Making Sense of the Epigenome Using Data Integration Approaches.

Authors:  Emma Cazaly; Joseph Saad; Wenyu Wang; Caroline Heckman; Miina Ollikainen; Jing Tang
Journal:  Front Pharmacol       Date:  2019-02-19       Impact factor: 5.810

Review 7.  Data integration in biological research: an overview.

Authors:  Vasileios Lapatas; Michalis Stefanidakis; Rafael C Jimenez; Allegra Via; Maria Victoria Schneider
Journal:  J Biol Res (Thessalon)       Date:  2015-09-02       Impact factor: 1.889

8.  Community standards for open cell migration data.

Authors:  Alejandra N Gonzalez-Beltran; Paola Masuzzo; Christophe Ampe; Gert-Jan Bakker; Sébastien Besson; Robert H Eibl; Peter Friedl; Matthias Gunzer; Mark Kittisopikul; Sylvia E Le Dévédec; Simone Leo; Josh Moore; Yael Paran; Jaime Prilusky; Philippe Rocca-Serra; Philippe Roudot; Marc Schuster; Gwendolien Sergeant; Staffan Strömblad; Jason R Swedlow; Merijn van Erp; Marleen Van Troys; Assaf Zaritsky; Susanna-Assunta Sansone; Lennart Martens
Journal:  Gigascience       Date:  2020-05-01       Impact factor: 6.524

9.  Gene Tags Assessment by Comparative Genomics (GTACG): A User-Friendly Framework for Bacterial Comparative Genomics.

Authors:  Caio Rafael do Nascimento Santiago; Renata de Almeida Barbosa Assis; Leandro Marcio Moreira; Luciano Antonio Digiampietri
Journal:  Front Genet       Date:  2019-08-26       Impact factor: 4.599

Review 10.  Taking Bioinformatics to Systems Medicine.

Authors:  Antoine H C van Kampen; Perry D Moerland
Journal:  Methods Mol Biol       Date:  2016
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