Literature DB >> 18447634

The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".

Susanna-Assunta Sansone1, Philippe Rocca-Serra, Marco Brandizi, Alvis Brazma, Dawn Field, Jennifer Fostel, Andrew G Garrow, Jack Gilbert, Federico Goodsaid, Nigel Hardy, Phil Jones, Allyson Lister, Michael Miller, Norman Morrison, Tim Rayner, Nataliya Sklyar, Chris Taylor, Weida Tong, Guy Warner, Stefan Wiemann.   

Abstract

This article summarizes the motivation for, and the proceedings of, the first ISA-TAB workshop held December 6-8, 2007, at the EBI, Cambridge, UK. This exploratory workshop, organized by members of the Microarray Gene Expression Data (MGED) Society's Reporting Structure for Biological Investigations (RSBI) working group, brought together a group of developers of a range of collaborative systems to discuss the use of a common format to address the pressing need of reporting and communicating data and metadata from biological, biomedical, and environmental studies employing combinations of genomics, transcriptomics, proteomics, and metabolomics technologies along with more conventional methodologies. The expertise of the participants comprised database development, data management, and hands-on experience in the development of data communication standards. The workshop's outcomes are set to help formalize the proposed Investigation, Study, Assay (ISA)-TAB tab-delimited format for representing and communicating experimental metadata. This article is part of the special issue of OMICS on the activities of the Genomics Standards Consortium (GSC).

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Year:  2008        PMID: 18447634     DOI: 10.1089/omi.2008.0019

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


  44 in total

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Review 2.  Informatics and standards for nanomedicine technology.

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Journal:  Wiley Interdiscip Rev Nanomed Nanobiotechnol       Date:  2011-06-30

Review 3.  Biomarkers in autism spectrum disorder: the old and the new.

Authors:  Barbara Ruggeri; Ugis Sarkans; Gunter Schumann; Antonio M Persico
Journal:  Psychopharmacology (Berl)       Date:  2013-10-06       Impact factor: 4.530

4.  FuGEFlow: data model and markup language for flow cytometry.

Authors:  Yu Qian; Olga Tchuvatkina; Josef Spidlen; Peter Wilkinson; Maura Gasparetto; Andrew R Jones; Frank J Manion; Richard H Scheuermann; Rafick-Pierre Sekaly; Ryan R Brinkman
Journal:  BMC Bioinformatics       Date:  2009-06-16       Impact factor: 3.169

5.  Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies.

Authors:  Ben van Ommen; Jildau Bouwman; Lars O Dragsted; Christian A Drevon; Ruan Elliott; Philip de Groot; Jim Kaput; John C Mathers; Michael Müller; Fre Pepping; Jahn Saito; Augustin Scalbert; Marijana Radonjic; Philippe Rocca-Serra; Anthony Travis; Suzan Wopereis; Chris T Evelo
Journal:  Genes Nutr       Date:  2010-02-03       Impact factor: 5.523

6.  ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level.

Authors:  Philippe Rocca-Serra; Marco Brandizi; Eamonn Maguire; Nataliya Sklyar; Chris Taylor; Kimberly Begley; Dawn Field; Stephen Harris; Winston Hide; Oliver Hofmann; Steffen Neumann; Peter Sterk; Weida Tong; Susanna-Assunta Sansone
Journal:  Bioinformatics       Date:  2010-08-02       Impact factor: 6.937

7.  The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.

Authors:  Hideya Kawaji; Jessica Severin; Marina Lizio; Andrew Waterhouse; Shintaro Katayama; Katharine M Irvine; David A Hume; Alistair R R Forrest; Harukazu Suzuki; Piero Carninci; Yoshihide Hayashizaki; Carsten O Daub
Journal:  Genome Biol       Date:  2009-04-19       Impact factor: 13.583

8.  SDRF2GRAPH: a visualization tool of a spreadsheet-based description of experimental processes.

Authors:  Hideya Kawaji; Yoshihide Hayashizaki; Carsten O Daub
Journal:  BMC Bioinformatics       Date:  2009-05-07       Impact factor: 3.169

9.  A System for Information Management in BioMedical Studies--SIMBioMS.

Authors:  Maria Krestyaninova; Andris Zarins; Juris Viksna; Natalja Kurbatova; Peteris Rucevskis; Sudeshna Guha Neogi; Mike Gostev; Teemu Perheentupa; Juha Knuuttila; Amy Barrett; Ilkka Lappalainen; Johan Rung; Karlis Podnieks; Ugis Sarkans; Mark I McCarthy; Alvis Brazma
Journal:  Bioinformatics       Date:  2009-07-24       Impact factor: 6.937

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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