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. 2019 Oct 10;48(D1):D204–D219. doi: 10.1093/nar/gkz869

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© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 1. — SEAweb system architecture. SEAweb system was developed using the modular system design approach (model-view-controller). The system has a presentation layer for user interface and visualization of search results. Presentation layer is followed by a business layer which transform complex user queries and distribute particular requests to the data access layer REST API services. There is a semantic data layer, to store and access primary and derived data together with annotations and links to secondary data. Annotation-DB stores metadata for experiments, samples, corresponding ontological terms as well as relations between dataset/sample, sample/term and term/term. Association-DB contains information about sRNAs and genes chromosomal locations, miRNA target genes and miRNA disease associations. Expression-DB stores sRNA expression profiles, sRNA differential expression; sRNA based classification as well as pathogen detection and pathogen differential expression. It also store details about dataset processing pipeline and parameters. Oasis-DB was used to store novel predicted miRNA information. User DB contains in-house data uploaded by the end users from Oasis 2 pipeline. Semantic data integration layer integrates primary and secondary data into the mentioned databases. Microservices were implemented in order to achieve strong encapsulation and well-defined interfaces via REST APIs.