Literature DB >> 16901212

Data standards: a call to action.

Cath Brooksbank1, John Quackenbush.   

Abstract

Access to data is something that every molecular biologist takes for granted nowadays, but data alone is of little use unless it is made available in a useable form through the development and global uptake of data standards. The challenge of standards development has been taken up by grass-roots movements working within several different branches of the biomedical research community. Many of these initiatives are proving extremely successful; for example, the Gene Ontology, which provides a controlled vocabulary for describing the properties of gene products, the Microarray Gene Expression Data Society's standards for describing microarray experiments, and the emerging standards developed by the Proteomics Standards Initiative are gaining broad acceptance. Standards development now faces its greatest ever challenge--the integration of diverse data types to fulfill the goals of systems biology. Now is the time for the communities that are developing these standards, the funding bodies that have invested so heavily in high-throughput data generation, and the publishers of biomedical research papers to cooperate fully to make the goals of integrated data analysis a reality.

Mesh:

Year:  2006        PMID: 16901212     DOI: 10.1089/omi.2006.10.94

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


  14 in total

Review 1.  Standardization and omics science: technical and social dimensions are inseparable and demand symmetrical study.

Authors:  Christina Holmes; Fiona McDonald; Mavis Jones; Vural Ozdemir; Janice E Graham
Journal:  OMICS       Date:  2010-06

2.  Biomedical ontologies in action: role in knowledge management, data integration and decision support.

Authors:  O Bodenreider
Journal:  Yearb Med Inform       Date:  2008

3.  The case for developing consensus standards for research in microbial pathogenesis: Bacillus anthracis toxins as an example.

Authors:  Molly A Hughes; Drusilla L Burns; Stephen J Juris; Wei-Jen Tang; Kristin H Clement; Linda J Eaton; Cassandra D Kelly-Cirino; Marian L McKee; Bradford S Powell; Brian L Bishop; Thomas L Rudge; Nancy Shine; Anita Verma; Melissa Swope Willis; Stephen A Morse
Journal:  Infect Immun       Date:  2009-08-03       Impact factor: 3.441

4.  In silico research in the era of cloud computing.

Authors:  Joel T Dudley; Atul J Butte
Journal:  Nat Biotechnol       Date:  2010-11       Impact factor: 54.908

5.  The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process.

Authors:  Erick Antezana; Mikel Egaña; Ward Blondé; Aitzol Illarramendi; Iñaki Bilbao; Bernard De Baets; Robert Stevens; Vladimir Mironov; Martin Kuiper
Journal:  Genome Biol       Date:  2009-05-29       Impact factor: 13.583

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.  Top-level categories of constitutively organized material entities--suggestions for a formal top-level ontology.

Authors:  Lars Vogt; Peter Grobe; Björn Quast; Thomas Bartolomaeus
Journal:  PLoS One       Date:  2011-04-21       Impact factor: 3.240

8.  Spatio-structural granularity of biological material entities.

Authors:  Lars Vogt
Journal:  BMC Bioinformatics       Date:  2010-05-28       Impact factor: 3.169

9.  ONTO-ToolKit: enabling bio-ontology engineering via Galaxy.

Authors:  Erick Antezana; Aravind Venkatesan; Chris Mungall; Vladimir Mironov; Martin Kuiper
Journal:  BMC Bioinformatics       Date:  2010-12-21       Impact factor: 3.169

10.  Megascience. 'Omics data sharing.

Authors:  Dawn Field; Susanna-Assunta Sansone; Amanda Collis; Tim Booth; Peter Dukes; Susan K Gregurick; Karen Kennedy; Patrik Kolar; Eugene Kolker; Mary Maxon; Siân Millard; Alexis-Michel Mugabushaka; Nicola Perrin; Jacques E Remacle; Karin Remington; Philippe Rocca-Serra; Chris F Taylor; Mark Thorley; Bela Tiwari; John Wilbanks
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

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