Led by researchers at University of Oxford (UK) and
the Harvard Stem Cell Institute (HSCI) at Harvard University, (USA), more than
50 collaborators at over 30 scientific organizations around the globe have
agreed on a common standard that will make possible the consistent description
of enormous and radically different databases compiled in fields ranging from
genetics to stem cell science, to environmental studies.
This collaborative effort provides a way for
scientists in widely disparate life science fields to co-ordinate each other’s
findings by allowing behind-the-scenes combination of the mountains of data
produced by modern, technology driven science.
“We are now working together to provide the means
to manage enormous quantities of otherwise incompatible data, ranging from the
biomedical to the environmental,” says Dr. Susanna-Assunta Sansone, Team
Leader of the project at the University of Oxford’s e-Research Centre.
An ecosystem of standard-compliant data curation and
sharing solutions and the establishment of its on-line presence, the ISA Commons, is described in a Commentary published today in the
journal Nature Genetics. The BioSharing initiatives is also introduced,
extending on the MIBBI effort.
The commentary is signed by all the collaborators.
"Sansone and colleagues also list a set of
participant communities that can pioneer the approach and teach by example"
says the Nature Genetics' Editorial.
This emerging commons depends on its participants’ use
of the ‘Investigation’, ‘Study’, and ‘Assay’ (ISA) metadata tracking framework.
“The ISA system is the ideal solution for managing experimental metadata
from diverse groups and is now a core solution at the NERC Environmental
Bioinformatics Centre. We look forward in the future to being able to exchange
data with other ISA-compliant projects,” says
Dawn Field, director of NERC NEBC, and
visiting Professor at the Oxford e-Research Centre, noting that “this is the
type of data sharing that should underpin ELIXIR”.
“An example of how this works at the Harvard Stem
Cell Institute is that we can now find a relationship between experiments
involving normal blood stem cells in fish and cancers in children”, says
Winston Hide, director of HSCI’s new Center for Stem Cell Bioinformatics, and an
associate Professor of Bioinformatics at the Harvard School of Public Health.
ISA Commons is also being used at Harvard Medical
School (HMS) by the HMS LINCS (Library
of Integrated Network-based Cellular Signatures) project led by Professors
Peter Sorger and Timothy Mitchison.
“Understanding biology requires data from multiple
fields, laboratories and experiments to work together. That not only requires
commons standards, but tools that enable scientists to work with those
standards without additional overheads. ISA is a great example of these
principles in action" says Lee
Harland, CTO at ConnectedDiscovery, London, UK
"One of the things that I find most empowering
about this effort is that now small research groups can begin to store
laboratory data using this framework, complying with community standards,
without their own dedicated bioinformatics support. It is a bit like Facebook
allowing everyone to create their own website pages - suddenly you don't need
to be an expert in computing to get your data out to the rest of the world",
says Jules Griffin, of the University of Cambridge.
"It also
has the potential to work for large centers too”, says Scott Edmunds,
editor of the journal published by open-access publisher BioMedCentral and BGI Shenzhen (previously known as the Beijing Genomics Institute)
the world’s largest genomics institute, “We are working with this framework
to help harmonizing and presenting may large-data types as possible in a common
standardized and usable form, publishing it in the associated GigaScience journal.”
"What we like about the ISA framework is its
unifying nature across different bioscience fields and institutions”, notes
Dr. Christoph Steinbeck of the European Molecular Biology Laboratory, The European Bioinformatics Institute (EBI), who
uses the ISA framework to power MetaboLights, the BBSRC-funded public repository for metabolomics
experiments at EBI developed in collaboration with Griffin.
It was necessary to establish common data standards,
say the commentary’s authors, because of the tsunami of data and technologies
washing over the sciences. “There are hundreds of new technologies coming
along but also many ways to describe the information produced” said
Sansone, noting that "we can take a jigsaw puzzle of different sciences
and now fit the many pieces together to form a complete picture".
The work was funded, by among
others, the Harvard Stem Cell Institute, the U.S. National Institutes of
Health, and the UK's Biotechnology and Biological Sciences Research Council
(BBSRC) and Natural Environment Research Council (NERC).
Source article:
Sansone, S-A. et
al. Toward interoperable bioscience data. Nature
Genetics 44, 2
(2012). ISA Commons: isacommons.org
The Oxford e-Research Centre
(http://www.oerc.ox.ac.uk) works across the University of Oxford, and at
national and international level, to accelerate research through development of
innovative computational and information technologies in multidisciplinary
collaborations.
The Harvard Stem Cell Institute
(http://www.hsci.harvard.edu) is a collaboration of more than 100 Harvard and
Harvard-affiliated scientists dedicated to using the power of stem cell biology
to advance basic understanding of human development in order to develop
treatments and cures for a host of degenerative conditions and diseases.
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