Improving Biocuration of MicroRNAs in Diseases: a Case Study in Idiopathic Pulmonary Fibrosis

Overview

Journal Database (Oxford)

Specialty Biology

Date 2017 Jun 13

PMID 28605770

Citations 3

Authors

Yalbi Itzel Balderas-Martinez

Fabio Rinaldi

Gabriela Contreras

Hilda Solano-Lira

Mishael Sanchez-Perez

Julio Collado-Vides

Moises Selman

Annie Pardo

Affiliations

Soon will be listed here.

Abstract

Database Url: http://odin.ccg.unam.mx/ODIN/bc2015-miRNA/.

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Statistical principle-based approach for recognizing and normalizing microRNAs described in scientific literature.

Dai H, Wang C, Chang N, Huang M, Jonnagaddala J, Wang F Database (Oxford). 2019; 2019.

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Strategies towards digital and semi-automated curation in RegulonDB.

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References

Li G, Ross K, Arighi C, Peng Y, Wu C, Vijay-Shanker K . miRTex: A Text Mining System for miRNA-Gene Relation Extraction. PLoS Comput Biol. 2015; 11(9):e1004391. PMC: 4583433. DOI: 10.1371/journal.pcbi.1004391. View

Rinaldi F, Clematide S, Garten Y, Whirl-Carrillo M, Gong L, Hebert J . Using ODIN for a PharmGKB revalidation experiment. Database (Oxford). 2012; 2012:bas021. PMC: 3332569. DOI: 10.1093/database/bas021. View

Gama-Castro S, Rinaldi F, Lopez-Fuentes A, Balderas-Martinez Y, Clematide S, Ellendorff T . Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12. Database (Oxford). 2014; 2014. PMC: 4207228. DOI: 10.1093/database/bau049. View

Wang Q, Abdul S, Almeida L, Ananiadou S, Balderas-Martinez Y, Batista-Navarro R . Overview of the interactive task in BioCreative V. Database (Oxford). 2016; 2016. PMC: 5009325. DOI: 10.1093/database/baw119. View

Hirschman L, Yeh A, Blaschke C, Valencia A . Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinformatics. 2005; 6 Suppl 1:S1. PMC: 1869002. DOI: 10.1186/1471-2105-6-S1-S1. View

Hinske L, Franca G, Torres H, Ohara D, Lopes-Ramos C, Heyn J . miRIAD-integrating microRNA inter- and intragenic data. Database (Oxford). 2014; 2014. PMC: 4186326. DOI: 10.1093/database/bau099. View

Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T . miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res. 2008; 37(Database issue):D105-10. PMC: 2686554. DOI: 10.1093/nar/gkn851. View

Rupani H, Sanchez-Elsner T, Howarth P . MicroRNAs and respiratory diseases. Eur Respir J. 2012; 41(3):695-705. DOI: 10.1183/09031936.00212011. View

Nam S, Kim B, Shin S, Lee S . miRGator: an integrated system for functional annotation of microRNAs. Nucleic Acids Res. 2007; 36(Database issue):D159-64. PMC: 2238850. DOI: 10.1093/nar/gkm829. View

10.

Yang S, Banerjee S, de Freitas A, Sanders Y, Ding Q, Matalon S . Participation of miR-200 in pulmonary fibrosis. Am J Pathol. 2011; 180(2):484-93. PMC: 3349843. DOI: 10.1016/j.ajpath.2011.10.005. View

11.

Wang P, Zhi H, Zhang Y, Liu Y, Zhang J, Gao Y . miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs. Database (Oxford). 2015; 2015. PMC: 4589693. DOI: 10.1093/database/bav098. View

12.

Murray B, Choe S, Woods M, Ryan T, Liu W . An in silico analysis of microRNAs: mining the miRNAome. Mol Biosyst. 2010; 6(10):1853-62. DOI: 10.1039/c003961f. View

13.

Hsu S, Chu C, Tsou A, Chen S, Chen H, Hsu P . miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. Nucleic Acids Res. 2007; 36(Database issue):D165-9. PMC: 2238982. DOI: 10.1093/nar/gkm1012. View

14.

Van Peer G, Lefever S, Anckaert J, Beckers A, Rihani A, Van Goethem A . miRBase Tracker: keeping track of microRNA annotation changes. Database (Oxford). 2014; 2014. PMC: 4142392. DOI: 10.1093/database/bau080. View

15.

Vlachos I, Paraskevopoulou M, Karagkouni D, Georgakilas G, Vergoulis T, Kanellos I . DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions. Nucleic Acids Res. 2014; 43(Database issue):D153-9. PMC: 4383989. DOI: 10.1093/nar/gku1215. View

16.

Mathelier A, Zhao X, Zhang A, Parcy F, Worsley-Hunt R, Arenillas D . JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 2013; 42(Database issue):D142-7. PMC: 3965086. DOI: 10.1093/nar/gkt997. View

17.

Chou C, Chang N, Shrestha S, Hsu S, Lin Y, Lee W . miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res. 2015; 44(D1):D239-47. PMC: 4702890. DOI: 10.1093/nar/gkv1258. View

18.

Friedman R, Farh K, Burge C, Bartel D . Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2008; 19(1):92-105. PMC: 2612969. DOI: 10.1101/gr.082701.108. View

19.

Pandit K, Milosevic J . MicroRNA regulatory networks in idiopathic pulmonary fibrosis. Biochem Cell Biol. 2015; 93(2):129-37. DOI: 10.1139/bcb-2014-0101. View

20.

King Jr T, Pardo A, Selman M . Idiopathic pulmonary fibrosis. Lancet. 2011; 378(9807):1949-61. DOI: 10.1016/S0140-6736(11)60052-4. View