The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework.

Authors:
Emily Merrill
Emily Merrill
Texas Tech University Health Sciences Center
United States
Nils Gehlenborg
Nils Gehlenborg
Harvard Medical School
United States
Psalm Haseley
Psalm Haseley
Harvard Medical School
United States
Ilya Sytchev
Ilya Sytchev
USA ; Harvard Stem Cell Institute
United States
Richard Park
Richard Park
Colorado State University
United States
Philippe Rocca-Serra
Philippe Rocca-Serra
European Bioinformatics Institute
United Kingdom
Stephane Corlosquet
Stephane Corlosquet
USA ; Harvard Stem Cell Institute
United States

AMIA Jt Summits Transl Sci Proc 2013 18;2013:70. Epub 2013 Mar 18.

Harvard School of Public Health, Biostatistics, Boston, MA, USA ; Harvard Stem Cell Institute, Cambridge, MA, USA.

Comparisons of stem cell experiments at both molecular and semantic levels remain challenging due to inconsistencies in results, data formats, and descriptions among biomedical research discoveries. The Harvard Stem Cell Institute (HSCI) has created the Stem Cell Commons (stemcellcommons.org), an open, community-based approach to data sharing. Experimental information is integrated using the Investigation-Study-Assay tabular format (ISA-Tab) used by over 30 organizations (ISA Commons, isacommons.org). The early adoption of this format permitted the novel integration of three independent systems to facilitate stem cell data storage, exchange and analysis: the Blood Genomics Repository, the Stem Cell Discovery Engine, and the new Refinery platform that links the Galaxy analytical engine to data repositories.
December 2013
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