Omicseq: A web-based search engine for exploring omics datasets

Xiaobo Sun, William S. Pittard, Tianlei Xu, Li Chen, Michael E. Zwick, Xiaoqian Jiang, Fusheng Wang, Zhaohui S. Qin

Research output: Contribution to journalArticlepeer-review

9 Scopus citations

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 â € 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.

Original languageEnglish (US)
Pages (from-to)W445-W452
JournalNucleic acids research
Volume45
Issue numberW1
DOIs
StatePublished - Jul 3 2017
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Genetics

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