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Open Access Database

PASmiR: a literature-curated database for miRNA molecular regulation in plant response to abiotic stress

Shihua Zhang12, Yi Yue3, Liang Sheng2, Yunzhi Wu3, Guohua Fan3, Ao Li4, Xiaoyi Hu2, Mingzhu ShangGuan2 and Chaoling Wei2*

Author affiliations

1 School of life sciences, Anhui Agricultural University, Hefei 230036, China

2 Key laboratory of Tea Biochemistry and Biotechnology, Ministry of Education, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China

3 College of information and computer science, Anhui Agricultural University, Hefei 230036, China

4 Department of Electronic Science and Technology, University of Science and Technology of China, Hefei, China

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Citation and License

BMC Plant Biology 2013, 13:33  doi:10.1186/1471-2229-13-33

Published: 1 March 2013

Abstract

Background

Over 200 published studies of more than 30 plant species have reported a role for miRNAs in regulating responses to abiotic stresses. However, data from these individual reports has not been collected into a single database. The lack of a curated database of stress-related miRNAs limits research in this field, and thus a cohesive database system should necessarily be constructed for data deposit and further application.

Description

PASmiR, a literature-curated and web-accessible database, was developed to provide detailed, searchable descriptions of miRNA molecular regulation in different plant abiotic stresses. PASmiR currently includes data from ~200 published studies, representing 1038 regulatory relationships between 682 miRNAs and 35 abiotic stresses in 33 plant species. PASmiR’s interface allows users to retrieve miRNA-stress regulatory entries by keyword search using plant species, abiotic stress, and miRNA identifier. Each entry upon keyword query contains detailed regulation information for a specific miRNA, including species name, miRNA identifier, stress name, miRNA expression pattern, detection method for miRNA expression, a reference literature, and target gene(s) of the miRNA extracted from the corresponding reference or miRBase. Users can also contribute novel regulatory entries by using a web-based submission page. The PASmiR database is freely accessible from the two URLs of http://hi.ustc.edu.cn:8080/PASmiR webcite, and http://pcsb.ahau.edu.cn:8080/PASmiR webcite.

Conclusion

The PASmiR database provides a solid platform for collection, standardization, and searching of miRNA-abiotic stress regulation data in plants. As such this database will be a comprehensive repository for miRNA regulatory mechanisms involved in plant response to abiotic stresses for the plant stress physiology community.