title: Omicseq: a web-based search engine for exploring omics datasets.
abstract: The development and application of high-throughput genomics technologies has resulted in massive quantities of diverse omics data that continue to accumulate rapidly. These rich datasets offer unprecedented and exciting opportunities to address long standing questions in biomedical research. However, our ability to explore and query the content of diverse omics data is very limited. Existing dataset search tools rely almost exclusively on the metadata. A text-based query for gene name(s) does not work well on datasets wherein the vast majority of their content is numeric. To overcome this barrier, we have developed Omicseq, a novel web-based platform that facilitates the easy interrogation of omics datasets holistically to improve 'findability' of relevant data. The core component of Omicseq is trackRank, a novel algorithm for ranking omics datasets that fully uses the numerical content of the dataset to determine relevance to the query entity. The Omicseq system is supported by a scalable and elastic, NoSQL database that hosts a large collection of processed omics datasets. In the front end, a simple, web-based interface allows users to enter queries and instantly receive search results as a list of ranked datasets deemed to be the most relevant. Omicseq is freely available at http://www.omicseq.org.
authors.affiliation: Department of Mathematics and Computer Science, Emory University, 400 Dowman Drive, Atlanta, GA 30322, USA.
authors.forename: Xiaobo
authors.initials: X
authors.lastname: Sun
authors.affiliation: Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA 30322, USA.
authors.forename: William S
authors.initials: WS
authors.lastname: Pittard
authors.affiliation: Department of Mathematics and Computer Science, Emory University, 400 Dowman Drive, Atlanta, GA 30322, USA.
authors.forename: Tianlei
authors.initials: T
authors.lastname: Xu
authors.affiliation: Department of Mathematics and Computer Science, Emory University, 400 Dowman Drive, Atlanta, GA 30322, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Chen
authors.affiliation: Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Zwick
authors.affiliation: Health Science Department of Biomedical Informatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
authors.forename: Xiaoqian
authors.initials: X
authors.lastname: Jiang
authors.affiliation: Department of Biomedical Informatics, Stony Brook University, HSC L3-043, Stony Brook, NY 11794, USA.|Department of Computer Science, Stony Brook University, Computer Science Building, Stony Brook, NY 11794, USA.
authors.forename: Fusheng
authors.initials: F
authors.lastname: Wang
authors.affiliation: Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA 30322, USA.|Department of Biomedical Informatics, Emory University School of Medicine, 36 Eagle Row, Atlanta, GA 30322, USA.
authors.forename: Zhaohui S
authors.initials: ZS
authors.lastname: Qin
mesh_terms: D000465:Algorithms; D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism; D001943:Breast Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D030541:Databases, Genetic; D030562:Databases, Protein; D066264:Datasets as Topic; D005260:Female; D015870:Gene Expression; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D007610:Kallikreins / Q000235:genetics / Q000378:metabolism; D008297:Male; D000071253:Metadata / Q000706:statistics & numerical data; D051059:PTEN Phosphohydrolase / Q000235:genetics / Q000378:metabolism; D017430:Prostate-Specific Antigen / Q000235:genetics / Q000378:metabolism; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000235:genetics / Q000378:metabolism; D057386:Search Engine; D014584:User-Computer Interface
chemical_list: D014408:Biomarkers, Tumor; D007610:Kallikreins; D051059:PTEN Phosphohydrolase; D017430:Prostate-Specific Antigen; D018719:Erb-b2 Receptor Tyrosine Kinases; C508053:ERBB2 protein, human; C494929:PTEN protein, human; C549870:KLK3 protein, human