Literature DB >> 16901222

A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group.

Susanna-Assunta Sansone1, Philippe Rocca-Serra, Weida Tong, Jennifer Fostel, Norman Morrison, Andrew R Jones.   

Abstract

In this article we present the Reporting Structure for Biological Investigation (RSBI), a working group under the Microarray Gene Expression Data (MGED) Society umbrella. RSBI brings together several communities to tackle the challenges associated with integrating data and representing complex biological investigations, employing multiple OMICS technologies. Currently, RSBI includes environmental genomics, nutrigenomics and toxicogenomics communities, where independent activities are underway to develop databases and establish data communication standards within their respective domains. The RSBI working group has been conceived as a "single point of focus" for these communities, conforming to general accepted view that duplication and incompatibility should be avoided where possible. This endeavour has aimed to synergize insular solutions into one common terminology between biologically driven standardisation efforts and has also resulted in strong collaborations and shared understanding between those in the technological domain. Through extensive liaisons with many standards efforts, several threads have been woven with the hope that ultimately technology-centered standards and their specific extensions into biological domains of interest will not only stand alone, but will also be able to function together, as interchangeable modules.

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Year:  2006        PMID: 16901222     DOI: 10.1089/omi.2006.10.164

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


  12 in total

Review 1.  Development of FuGO: an ontology for functional genomics investigations.

Authors:  Patricia L Whetzel; Ryan R Brinkman; Helen C Causton; Liju Fan; Dawn Field; Jennifer Fostel; Gilberto Fragoso; Tanya Gray; Mervi Heiskanen; Tina Hernandez-Boussard; Norman Morrison; Helen Parkinson; Philippe Rocca-Serra; Susanna-Assunta Sansone; Daniel Schober; Barry Smith; Robert Stevens; Christian J Stoeckert; Chris Taylor; Joe White; Andrew Wood
Journal:  OMICS       Date:  2006

2.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.

Authors:  Barry Smith; Michael Ashburner; Cornelius Rosse; Jonathan Bard; William Bug; Werner Ceusters; Louis J Goldberg; Karen Eilbeck; Amelia Ireland; Christopher J Mungall; Neocles Leontis; Philippe Rocca-Serra; Alan Ruttenberg; Susanna-Assunta Sansone; Richard H Scheuermann; Nigam Shah; Patricia L Whetzel; Suzanna Lewis
Journal:  Nat Biotechnol       Date:  2007-11       Impact factor: 54.908

3.  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

4.  Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network.

Authors:  Ulrich Harttig; Anthony J Travis; Philippe Rocca-Serra; Marten Renkema; Ben van Ommen; Heiner Boeing
Journal:  Genes Nutr       Date:  2009-04-30       Impact factor: 5.523

5.  Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.

Authors:  Chris F Taylor; Dawn Field; Susanna-Assunta Sansone; Jan Aerts; Rolf Apweiler; Michael Ashburner; Catherine A Ball; Pierre-Alain Binz; Molly Bogue; Tim Booth; Alvis Brazma; Ryan R Brinkman; Adam Michael Clark; Eric W Deutsch; Oliver Fiehn; Jennifer Fostel; Peter Ghazal; Frank Gibson; Tanya Gray; Graeme Grimes; John M Hancock; Nigel W Hardy; Henning Hermjakob; Randall K Julian; Matthew Kane; Carsten Kettner; Christopher Kinsinger; Eugene Kolker; Martin Kuiper; Nicolas Le Novère; Jim Leebens-Mack; Suzanna E Lewis; Phillip Lord; Ann-Marie Mallon; Nishanth Marthandan; Hiroshi Masuya; Ruth McNally; Alexander Mehrle; Norman Morrison; Sandra Orchard; John Quackenbush; James M Reecy; Donald G Robertson; Philippe Rocca-Serra; Henry Rodriguez; Heiko Rosenfelder; Javier Santoyo-Lopez; Richard H Scheuermann; Daniel Schober; Barry Smith; Jason Snape; Christian J Stoeckert; Keith Tipton; Peter Sterk; Andreas Untergasser; Jo Vandesompele; Stefan Wiemann
Journal:  Nat Biotechnol       Date:  2008-08       Impact factor: 54.908

Review 6.  Data standards for Omics data: the basis of data sharing and reuse.

Authors:  Stephen A Chervitz; 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
Journal:  Methods Mol Biol       Date:  2011

7.  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

8.  The use of concept maps during knowledge elicitation in ontology development processes--the nutrigenomics use case.

Authors:  Alexander Garcia Castro; Philippe Rocca-Serra; Robert Stevens; Chris Taylor; Karim Nashar; Mark A Ragan; Susanna-Assunta Sansone
Journal:  BMC Bioinformatics       Date:  2006-05-25       Impact factor: 3.169

9.  A minimum information standard for reproducing bench-scale bacterial cell growth and productivity.

Authors:  Ariel Hecht; James Filliben; Sarah A Munro; Marc Salit
Journal:  Commun Biol       Date:  2018-12-06

10.  Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research.

Authors:  Augustin Scalbert; Lorraine Brennan; Oliver Fiehn; Thomas Hankemeier; Bruce S Kristal; Ben van Ommen; Estelle Pujos-Guillot; Elwin Verheij; David Wishart; Suzan Wopereis
Journal:  Metabolomics       Date:  2009-06-12       Impact factor: 4.290

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