Article ; Online: Knowledge-guided analysis of "omics" data using the KnowEnG cloud platform.
2020 Volume 18, Issue 1, Page(s) e3000583
Abstract: We present Knowledge Engine for Genomics (KnowEnG), a free-to-use computational system for analysis of genomics data sets, designed to accelerate biomedical discovery. It includes tools for popular bioinformatics tasks such as gene prioritization, sample ...
| Abstract | We present Knowledge Engine for Genomics (KnowEnG), a free-to-use computational system for analysis of genomics data sets, designed to accelerate biomedical discovery. It includes tools for popular bioinformatics tasks such as gene prioritization, sample clustering, gene set analysis, and expression signature analysis. The system specializes in "knowledge-guided" data mining and machine learning algorithms, in which user-provided data are analyzed in light of prior information about genes, aggregated from numerous knowledge bases and encoded in a massive "Knowledge Network." KnowEnG adheres to "FAIR" principles (findable, accessible, interoperable, and reuseable): its tools are easily portable to diverse computing environments, run on the cloud for scalable and cost-effective execution, and are interoperable with other computing platforms. The analysis tools are made available through multiple access modes, including a web portal with specialized visualization modules. We demonstrate the KnowEnG system's potential value in democratization of advanced tools for the modern genomics era through several case studies that use its tools to recreate and expand upon the published analysis of cancer data sets. |
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| MeSH term(s) | Algorithms ; Cloud Computing ; Cluster Analysis ; Computational Biology/methods ; Data Analysis ; Data Mining/methods ; Datasets as Topic ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Knowledge ; Machine Learning ; Metabolomics/methods ; Software | |||||
| Language | English | |||||
| Publishing date | 2020-01-23 | |||||
| Publishing country | United States | |||||
| Document type | Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't | |||||
| ZDB-ID | 2126776-5 | |||||
| ISSN | 1545-7885 ; 1544-9173 | |||||
| ISSN (online) | 1545-7885 | |||||
| ISSN | 1544-9173 | |||||
| DOI | 10.1371/journal.pbio.3000583 | |||||
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| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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