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Precision annotation of digital samples in NCBI?s gene expression omnibus #MMPMID28925997
Hadley D; Pan J; El-Sayed O; Aljabban J; Aljabban I; Azad TD; Hadied MO; Raza S; Rayikanti BA; Chen B; Paik H; Aran D; Spatz J; Himmelstein D; Panahiazar M; Bhattacharya S; Sirota M; Musen MA; Butte AJ
Sci Data 2017[]; 4 (ä): ä PMID28925997show ga
The Gene Expression Omnibus (GEO) contains more than two million digital samples from functional genomics experiments amassed over almost two decades. However, individual sample meta-data remains poorly described by unstructured free text attributes preventing its largescale reanalysis. We introduce the Search Tag Analyze Resource for GEO as a web application (http://STARGEO.org) to curate better annotations of sample phenotypes uniformly across different studies, and to use these sample annotations to define robust genomic signatures of disease pathology by meta-analysis. In this paper, we target a small group of biomedical graduate students to show rapid crowd-curation of precise sample annotations across all phenotypes, and we demonstrate the biological validity of these crowd-curated annotations for breast cancer. STARGEO.org makes GEO data findable, accessible, interoperable and reusable (i.e., FAIR) to ultimately facilitate knowledge discovery. Our work demonstrates the utility of crowd-curation and interpretation of open ?big data? under FAIR principles as a first step towards realizing an ideal paradigm of precision medicine.