Literature DB >> 33196130

Towards a unified data infrastructure to support European and global microbiome research: a call to action.

Matthew J Ryan1, Michael Schloter2, Gabriele Berg3, Linda L Kinkel4, Kellye Eversole5,6, James A Macklin7, Daria Rybakova3, Angela Sessitsch8.   

Abstract

High-quality microbiome research relies on the integrity, management and quality of supporting data. Currently biobanks and culture collections have different formats and approaches to data management. This necessitates a standard data format to underpin research, particularly in line with the FAIR data standards of findability, accessibility, interoperability and reusability. We address the importance of a unified, coordinated approach that ensures compatibility of data between that needed by biobanks and culture collections, but also to ensure linkage between bioinformatic databases and the wider research community.
© 2020 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Entities:  

Mesh:

Year:  2020        PMID: 33196130      PMCID: PMC7898335          DOI: 10.1111/1462-2920.15323

Source DB:  PubMed          Journal:  Environ Microbiol        ISSN: 1462-2912            Impact factor:   5.491


  10 in total

1.  Standard PREanalytical Codes: A New Paradigm for Environmental Biobanking Sectors Explored in Algal Culture Collections.

Authors:  Erica E Benson; Fotini Betsou; Raquel Amaral; Lília M A Santos; Keith Harding
Journal:  Biopreserv Biobank       Date:  2011-11-17       Impact factor: 2.300

2.  Standard preanalytical coding for biospecimens: review and implementation of the Sample PREanalytical Code (SPREC).

Authors:  Sabine Lehmann; Fiorella Guadagni; Helen Moore; Garry Ashton; Michael Barnes; Erica Benson; Judith Clements; Iren Koppandi; Domenico Coppola; Sara Yasemin Demiroglu; Yvonne DeSouza; Annemieke De Wilde; Jacko Duker; James Eliason; Barbara Glazer; Keith Harding; Jae Pil Jeon; Joseph Kessler; Theresa Kokkat; Umberto Nanni; Kathi Shea; Amy Skubitz; Stella Somiari; Gunnel Tybring; Elaine Gunter; Fotini Betsou
Journal:  Biopreserv Biobank       Date:  2012-08       Impact factor: 2.300

3.  Development of Microbiome Biobanks - Challenges and Opportunities.

Authors:  M J Ryan; M Schloter; G Berg; T Kostic; L L Kinkel; K Eversole; J A Macklin; B Schelkle; M Kazou; I Sarand; B K Singh; D Fischer; E Maguin; I Ferrocino; N Lima; R S McClure; T C Charles; R S C de Souza; G S Kiran; H L Krug; J Taffner; H Roume; J Selvin; D Smith; D Rybakova; A Sessitsch
Journal:  Trends Microbiol       Date:  2020-08-13       Impact factor: 17.079

4.  Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

Authors:  Pelin Yilmaz; Renzo Kottmann; Dawn Field; Rob Knight; James R Cole; Linda Amaral-Zettler; Jack A Gilbert; Ilene Karsch-Mizrachi; Anjanette Johnston; Guy Cochrane; Robert Vaughan; Christopher Hunter; Joonhong Park; Norman Morrison; Philippe Rocca-Serra; Peter Sterk; Manimozhiyan Arumugam; Mark Bailey; Laura Baumgartner; Bruce W Birren; Martin J Blaser; Vivien Bonazzi; Tim Booth; Peer Bork; Frederic D Bushman; Pier Luigi Buttigieg; Patrick S G Chain; Emily Charlson; Elizabeth K Costello; Heather Huot-Creasy; Peter Dawyndt; Todd DeSantis; Noah Fierer; Jed A Fuhrman; Rachel E Gallery; Dirk Gevers; Richard A Gibbs; Inigo San Gil; Antonio Gonzalez; Jeffrey I Gordon; Robert Guralnick; Wolfgang Hankeln; Sarah Highlander; Philip Hugenholtz; Janet Jansson; Andrew L Kau; Scott T Kelley; Jerry Kennedy; Dan Knights; Omry Koren; Justin Kuczynski; Nikos Kyrpides; Robert Larsen; Christian L Lauber; Teresa Legg; Ruth E Ley; Catherine A Lozupone; Wolfgang Ludwig; Donna Lyons; Eamonn Maguire; Barbara A Methé; Folker Meyer; Brian Muegge; Sara Nakielny; Karen E Nelson; Diana Nemergut; Josh D Neufeld; Lindsay K Newbold; Anna E Oliver; Norman R Pace; Giriprakash Palanisamy; Jörg Peplies; Joseph Petrosino; Lita Proctor; Elmar Pruesse; Christian Quast; Jeroen Raes; Sujeevan Ratnasingham; Jacques Ravel; David A Relman; Susanna Assunta-Sansone; Patrick D Schloss; Lynn Schriml; Rohini Sinha; Michelle I Smith; Erica Sodergren; Aymé Spo; Jesse Stombaugh; James M Tiedje; Doyle V Ward; George M Weinstock; Doug Wendel; Owen White; Andrew Whiteley; Andreas Wilke; Jennifer R Wortman; Tanya Yatsunenko; Frank Oliver Glöckner
Journal:  Nat Biotechnol       Date:  2011-05       Impact factor: 54.908

5.  The Genomic Standards Consortium.

Authors:  Dawn Field; Linda Amaral-Zettler; Guy Cochrane; James R Cole; Peter Dawyndt; George M Garrity; Jack Gilbert; Frank Oliver Glöckner; Lynette Hirschman; Ilene Karsch-Mizrachi; Hans-Peter Klenk; Rob Knight; Renzo Kottmann; Nikos Kyrpides; Folker Meyer; Inigo San Gil; Susanna-Assunta Sansone; Lynn M Schriml; Peter Sterk; Tatiana Tatusova; David W Ussery; Owen White; John Wooley
Journal:  PLoS Biol       Date:  2011-06-21       Impact factor: 8.029

6.  Open resource metagenomics: a model for sharing metagenomic libraries.

Authors:  J D Neufeld; K Engel; J Cheng; G Moreno-Hagelsieb; D R Rose; T C Charles
Journal:  Stand Genomic Sci       Date:  2011-11-23

7.  Microbiome definition re-visited: old concepts and new challenges.

Authors:  Gabriele Berg; Daria Rybakova; Doreen Fischer; Tomislav Cernava; Marie-Christine Champomier Vergès; Trevor Charles; Xiaoyulong Chen; Luca Cocolin; Kellye Eversole; Gema Herrero Corral; Maria Kazou; Linda Kinkel; Lene Lange; Nelson Lima; Alexander Loy; James A Macklin; Emmanuelle Maguin; Tim Mauchline; Ryan McClure; Birgit Mitter; Matthew Ryan; Inga Sarand; Hauke Smidt; Bettina Schelkle; Hugo Roume; G Seghal Kiran; Joseph Selvin; Rafael Soares Correa de Souza; Leo van Overbeek; Brajesh K Singh; Michael Wagner; Aaron Walsh; Angela Sessitsch; Michael Schloter
Journal:  Microbiome       Date:  2020-06-30       Impact factor: 14.650

8.  Global catalogue of microorganisms (gcm): a comprehensive database and information retrieval, analysis, and visualization system for microbial resources.

Authors:  Linhuan Wu; Qinglan Sun; Hideaki Sugawara; Song Yang; Yuguang Zhou; Kevin McCluskey; Alexander Vasilenko; Ken-Ichiro Suzuki; Moriya Ohkuma; Yeonhee Lee; Vincent Robert; Supawadee Ingsriswang; François Guissart; Desmeth Philippe; Juncai Ma
Journal:  BMC Genomics       Date:  2013-12-30       Impact factor: 3.969

9.  The FAIR Guiding Principles for scientific data management and stewardship.

Authors:  Mark D Wilkinson; Michel Dumontier; I Jsbrand Jan Aalbersberg; Gabrielle Appleton; Myles Axton; Arie Baak; Niklas Blomberg; Jan-Willem Boiten; Luiz Bonino da Silva Santos; Philip E Bourne; Jildau Bouwman; Anthony J Brookes; Tim Clark; Mercè Crosas; Ingrid Dillo; Olivier Dumon; Scott Edmunds; Chris T Evelo; Richard Finkers; Alejandra Gonzalez-Beltran; Alasdair J G Gray; Paul Groth; Carole Goble; Jeffrey S Grethe; Jaap Heringa; Peter A C 't Hoen; Rob Hooft; Tobias Kuhn; Ruben Kok; Joost Kok; Scott J Lusher; Maryann E Martone; Albert Mons; Abel L Packer; Bengt Persson; Philippe Rocca-Serra; Marco Roos; Rene van Schaik; Susanna-Assunta Sansone; Erik Schultes; Thierry Sengstag; Ted Slater; George Strawn; Morris A Swertz; Mark Thompson; Johan van der Lei; Erik van Mulligen; Jan Velterop; Andra Waagmeester; Peter Wittenburg; Katherine Wolstencroft; Jun Zhao; Barend Mons
Journal:  Sci Data       Date:  2016-03-15       Impact factor: 6.444

10.  IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes.

Authors:  I-Min A Chen; Ken Chu; Krishna Palaniappan; Manoj Pillay; Anna Ratner; Jinghua Huang; Marcel Huntemann; Neha Varghese; James R White; Rekha Seshadri; Tatyana Smirnova; Edward Kirton; Sean P Jungbluth; Tanja Woyke; Emiley A Eloe-Fadrosh; Natalia N Ivanova; Nikos C Kyrpides
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

  10 in total
  3 in total

Review 1.  Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research.

Authors:  Ethan W Morgan; Gary H Perdew; Andrew D Patterson
Journal:  Toxicol Sci       Date:  2022-05-26       Impact factor: 4.109

Review 2.  Microbiome Research as an Effective Driver of Success Stories in Agrifood Systems - A Selection of Case Studies.

Authors:  Rocío Olmo; Stefanie Urimare Wetzels; Jaderson Silveira Leite Armanhi; Paulo Arruda; Gabriele Berg; Tomislav Cernava; Paul D Cotter; Solon Cordeiro Araujo; Rafael Soares Correa de Souza; Ilario Ferrocino; Jens C Frisvad; Marina Georgalaki; Hanne Helene Hansen; Maria Kazou; George Seghal Kiran; Tanja Kostic; Susanne Krauss-Etschmann; Aicha Kriaa; Lene Lange; Emmanuelle Maguin; Birgit Mitter; Mette Olaf Nielsen; Marta Olivares; Narciso Martín Quijada; Marina Romaní-Pérez; Yolanda Sanz; Michael Schloter; Philippe Schmitt-Kopplin; Sarah Craven Seaton; Joseph Selvin; Angela Sessitsch; Mengcen Wang; Benjamin Zwirzitz; Evelyne Selberherr; Martin Wagner
Journal:  Front Microbiol       Date:  2022-07-04       Impact factor: 6.064

Review 3.  The microbiota-gut-brain axis: pathways to better brain health. Perspectives on what we know, what we need to investigate and how to put knowledge into practice.

Authors:  Anirikh Chakrabarti; Lucie Geurts; Lesley Hoyles; Patricia Iozzo; Aletta D Kraneveld; Giorgio La Fata; Michela Miani; Elaine Patterson; Bruno Pot; Colette Shortt; David Vauzour
Journal:  Cell Mol Life Sci       Date:  2022-01-19       Impact factor: 9.261

  3 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.