RNAInter


34718726	RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility. [PMID: 34718726] Juanjuan Kang, Qiang Tang, Jun He, Le Li, Nianling Yang, Shuiyan Yu, Mengyao Wang, Yuchen Zhang, Jiahao Lin, Tianyu Cui, Yongfei Hu, Puwen Tan, Jun Cheng, Hailong Zheng, Dong Wang, Xi Su, Wei Chen, Yan Huang Abstract Establishing an RNA-associated interaction repository facilitates the system-level understanding of RNA functions. However, as these interactions are distributed throughout various resources, an essential prerequisite for effectively applying these data requires that they are deposited together and annotated with confidence scores. Hence, we have updated the RNA-associated interaction database RNAInter (RNA Interactome Database) to version 4.0, which is freely accessible at http://www.rnainter.org or http://www.rna-society.org/rnainter/. Compared with previous versions, the current RNAInter not only contains an enlarged data set, but also an updated confidence scoring system. The merits of this 4.0 version can be summarized in the following points: (i) a redefined confidence scoring system as achieved by integrating the trust of experimental evidence, the trust of the scientific community and the types of tissues/cells, (ii) a redesigned fully functional database that enables for a more rapid retrieval and browsing of interactions via an upgraded user-friendly interface and (iii) an update of entries to >47 million by manually mining the literature and integrating six database resources with evidence from experimental and computational sources. Overall, RNAInter will provide a more comprehensive and readily accessible RNA interactome platform to investigate the regulatory landscape of cellular RNAs. Nucleic Acids Res. 2022:50(D1) \| 96 Citations (from Europe PMC, 2025-03-15)
31906603	RNAInter in 2020: RNA interactome repository with increased coverage and annotation. [PMID: 31906603] Lin Y, Liu T, Cui T, Wang Z, Zhang Y, Tan P, Huang Y, Yu J, Wang D. Abstract Research on RNA-associated interactions has exploded in recent years, and increasing numbers of studies are not limited to RNA-RNA and RNA-protein interactions but also include RNA-DNA/compound interactions. To facilitate the development of the interactome and promote understanding of the biological functions and molecular mechanisms of RNA, we updated RAID v2.0 to RNAInter (RNA Interactome Database), a repository for RNA-associated interactions that is freely accessible at http://www.rna-society.org/rnainter/ or http://www.rna-society.org/raid/. Compared to RAID v2.0, new features in RNAInter include (i) 8-fold more interaction data and 94 additional species; (ii) more definite annotations organized, including RNA editing/localization/modification/structure and homology interaction; (iii) advanced functions including fuzzy/batch search, interaction network and RNA dynamic expression and (iv) four embedded RNA interactome tools: RIscoper, IntaRNA, PRIdictor and DeepBind. Consequently, RNAInter contains >41 million RNA-associated interaction entries, involving more than 450 thousand unique molecules, including RNA, protein, DNA and compound. Overall, RNAInter provides a comprehensive RNA interactome resource for researchers and paves the way to investigate the regulatory landscape of cellular RNAs. Nucleic Acids Res. 2020:48(D1) \| 132 Citations (from Europe PMC, 2025-03-15)
30668649	RIscoper: a tool for RNA-RNA interaction extraction from the literature. [PMID: 30668649] Zhang Y, Liu T, Chen L, Yang J, Yin J, Zhang Y, Yun Z, Xu H, Ning L, Guo F, Jiang Y, Lin H, Wang D, Huang Y, Huang J. Abstract Motivation Numerous experimental and computational studies in the biomedical literature have provided considerable amounts of data on diverse RNA-RNA interactions (RRIs). However, few text mining systems for RRIs information extraction are available. Results RNA Interactome Scoper (RIscoper) represents the first tool for full-scale RNA interactome scanning and was developed for extracting RRIs from the literature based on the N-gram model. Notably, a reliable RRI corpus was integrated in RIscoper, and more than 13 300 manually curated sentences with RRI information were recruited. RIscoper allows users to upload full texts or abstracts, and provides an online search tool that is connected with PubMed (PMID and keyword input), and these capabilities are useful for biologists. RIscoper has a strong performance (90.4% precision and 93.9% recall), integrates natural language processing techniques and has a reliable RRI corpus. Availability and implementation The standalone software and web server of RIscoper are freely available at www.rna-society.org/riscoper/. Supplementary information Supplementary data are available at Bioinformatics online. Bioinformatics. 2019:35(17) \| 12 Citations (from Europe PMC, 2025-03-15)
27899615	RAID v2.0: an updated resource of RNA-associated interactions across organisms. [PMID: 27899615] Yi Y, Zhao Y, Li C, Zhang L, Huang H, Li Y, Liu L, Hou P, Cui T, Tan P, Hu Y, Zhang T, Huang Y, Li X, Yu J, Wang D, Wang D. Abstract With the development of biotechnologies and computational prediction algorithms, the number of experimental and computational prediction RNA-associated interactions has grown rapidly in recent years. However, diverse RNA-associated interactions are scattered over a wide variety of resources and organisms, whereas a fully comprehensive view of diverse RNA-associated interactions is still not available for any species. Hence, we have updated the RAID database to version 2.0 (RAID v2.0, www.rna-society.org/raid/) by integrating experimental and computational prediction interactions from manually reading literature and other database resources under one common framework. The new developments in RAID v2.0 include (i) over 850-fold RNA-associated interactions, an enhancement compared to the previous version; (ii) numerous resources integrated with experimental or computational prediction evidence for each RNA-associated interaction; (iii) a reliability assessment for each RNA-associated interaction based on an integrative confidence score; and (iv) an increase of species coverage to 60. Consequently, RAID v2.0 recruits more than 5.27 million RNA-associated interactions, including more than 4 million RNA-RNA interactions and more than 1.2 million RNA-protein interactions, referring to nearly 130 000 RNA/protein symbols across 60 species. Nucleic Acids Res. 2017:45(D1) \| 119 Citations (from Europe PMC, 2025-03-15)
24803509	RAID: a comprehensive resource for human RNA-associated (RNA-RNA/RNA-protein) interaction. [PMID: 24803509] Zhang X, Wu D, Chen L, Li X, Yang J, Fan D, Dong T, Liu M, Tan P, Xu J, Yi Y, Wang Y, Zou H, Hu Y, Fan K, Kang J, Huang Y, Miao Z, Bi M, Jin N, Li K, Li X, Xu J, Wang D. Abstract Transcriptomic analyses have revealed an unexpected complexity in the eukaryote transcriptome, which includes not only protein-coding transcripts but also an expanding catalog of noncoding RNAs (ncRNAs). Diverse coding and noncoding RNAs (ncRNAs) perform functions through interaction with each other in various cellular processes. In this project, we have developed RAID (http://www.rna-society.org/raid), an RNA-associated (RNA-RNA/RNA-protein) interaction database. RAID intends to provide the scientific community with all-in-one resources for efficient browsing and extraction of the RNA-associated interactions in human. This version of RAID contains more than 6100 RNA-associated interactions obtained by manually reviewing more than 2100 published papers, including 4493 RNA-RNA interactions and 1619 RNA-protein interactions. Each entry contains detailed information on an RNA-associated interaction, including RAID ID, RNA/protein symbol, RNA/protein categories, validated method, expressing tissue, literature references (Pubmed IDs), and detailed functional description. Users can query, browse, analyze, and manipulate RNA-associated (RNA-RNA/RNA-protein) interaction. RAID provides a comprehensive resource of human RNA-associated (RNA-RNA/RNA-protein) interaction network. Furthermore, this resource will help in uncovering the generic organizing principles of cellular function network. RNA. 2014:20(7) \| 39 Citations (from Europe PMC, 2025-03-15)

RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility. [PMID: 34718726]

Juanjuan Kang, Qiang Tang, Jun He, Le Li, Nianling Yang, Shuiyan Yu, Mengyao Wang, Yuchen Zhang, Jiahao Lin, Tianyu Cui, Yongfei Hu, Puwen Tan, Jun Cheng, Hailong Zheng, Dong Wang, Xi Su, Wei Chen, Yan Huang

Abstract

Establishing an RNA-associated interaction repository facilitates the system-level understanding of RNA functions. However, as these interactions are distributed throughout various resources, an essential prerequisite for effectively applying these data requires that they are deposited together and annotated with confidence scores. Hence, we have updated the RNA-associated interaction database RNAInter (RNA Interactome Database) to version 4.0, which is freely accessible at http://www.rnainter.org or http://www.rna-society.org/rnainter/. Compared with previous versions, the current RNAInter not only contains an enlarged data set, but also an updated confidence scoring system. The merits of this 4.0 version can be summarized in the following points: (i) a redefined confidence scoring system as achieved by integrating the trust of experimental evidence, the trust of the scientific community and the types of tissues/cells, (ii) a redesigned fully functional database that enables for a more rapid retrieval and browsing of interactions via an upgraded user-friendly interface and (iii) an update of entries to >47 million by manually mining the literature and integrating six database resources with evidence from experimental and computational sources. Overall, RNAInter will provide a more comprehensive and readily accessible RNA interactome platform to investigate the regulatory landscape of cellular RNAs.

Nucleic Acids Res. 2022:50(D1) | 96 Citations (from Europe PMC, 2025-03-15)

RNAInter in 2020: RNA interactome repository with increased coverage and annotation. [PMID: 31906603]

Lin Y, Liu T, Cui T, Wang Z, Zhang Y, Tan P, Huang Y, Yu J, Wang D.

Abstract

Research on RNA-associated interactions has exploded in recent years, and increasing numbers of studies are not limited to RNA-RNA and RNA-protein interactions but also include RNA-DNA/compound interactions. To facilitate the development of the interactome and promote understanding of the biological functions and molecular mechanisms of RNA, we updated RAID v2.0 to RNAInter (RNA Interactome Database), a repository for RNA-associated interactions that is freely accessible at http://www.rna-society.org/rnainter/ or http://www.rna-society.org/raid/. Compared to RAID v2.0, new features in RNAInter include (i) 8-fold more interaction data and 94 additional species; (ii) more definite annotations organized, including RNA editing/localization/modification/structure and homology interaction; (iii) advanced functions including fuzzy/batch search, interaction network and RNA dynamic expression and (iv) four embedded RNA interactome tools: RIscoper, IntaRNA, PRIdictor and DeepBind. Consequently, RNAInter contains >41 million RNA-associated interaction entries, involving more than 450 thousand unique molecules, including RNA, protein, DNA and compound. Overall, RNAInter provides a comprehensive RNA interactome resource for researchers and paves the way to investigate the regulatory landscape of cellular RNAs.

Nucleic Acids Res. 2020:48(D1) | 132 Citations (from Europe PMC, 2025-03-15)

RIscoper: a tool for RNA-RNA interaction extraction from the literature. [PMID: 30668649]

Zhang Y, Liu T, Chen L, Yang J, Yin J, Zhang Y, Yun Z, Xu H, Ning L, Guo F, Jiang Y, Lin H, Wang D, Huang Y, Huang J.

Abstract

Motivation

Numerous experimental and computational studies in the biomedical literature have provided considerable amounts of data on diverse RNA-RNA interactions (RRIs). However, few text mining systems for RRIs information extraction are available.

Results

RNA Interactome Scoper (RIscoper) represents the first tool for full-scale RNA interactome scanning and was developed for extracting RRIs from the literature based on the N-gram model. Notably, a reliable RRI corpus was integrated in RIscoper, and more than 13 300 manually curated sentences with RRI information were recruited. RIscoper allows users to upload full texts or abstracts, and provides an online search tool that is connected with PubMed (PMID and keyword input), and these capabilities are useful for biologists. RIscoper has a strong performance (90.4% precision and 93.9% recall), integrates natural language processing techniques and has a reliable RRI corpus.

Availability and implementation

The standalone software and web server of RIscoper are freely available at www.rna-society.org/riscoper/.

Supplementary information

Supplementary data are available at Bioinformatics online.

Bioinformatics. 2019:35(17) | 12 Citations (from Europe PMC, 2025-03-15)

RAID v2.0: an updated resource of RNA-associated interactions across organisms. [PMID: 27899615]

Yi Y, Zhao Y, Li C, Zhang L, Huang H, Li Y, Liu L, Hou P, Cui T, Tan P, Hu Y, Zhang T, Huang Y, Li X, Yu J, Wang D, Wang D.

Abstract

With the development of biotechnologies and computational prediction algorithms, the number of experimental and computational prediction RNA-associated interactions has grown rapidly in recent years. However, diverse RNA-associated interactions are scattered over a wide variety of resources and organisms, whereas a fully comprehensive view of diverse RNA-associated interactions is still not available for any species. Hence, we have updated the RAID database to version 2.0 (RAID v2.0, www.rna-society.org/raid/) by integrating experimental and computational prediction interactions from manually reading literature and other database resources under one common framework. The new developments in RAID v2.0 include (i) over 850-fold RNA-associated interactions, an enhancement compared to the previous version; (ii) numerous resources integrated with experimental or computational prediction evidence for each RNA-associated interaction; (iii) a reliability assessment for each RNA-associated interaction based on an integrative confidence score; and (iv) an increase of species coverage to 60. Consequently, RAID v2.0 recruits more than 5.27 million RNA-associated interactions, including more than 4 million RNA-RNA interactions and more than 1.2 million RNA-protein interactions, referring to nearly 130 000 RNA/protein symbols across 60 species.

Nucleic Acids Res. 2017:45(D1) | 119 Citations (from Europe PMC, 2025-03-15)

RAID: a comprehensive resource for human RNA-associated (RNA-RNA/RNA-protein) interaction. [PMID: 24803509]

Zhang X, Wu D, Chen L, Li X, Yang J, Fan D, Dong T, Liu M, Tan P, Xu J, Yi Y, Wang Y, Zou H, Hu Y, Fan K, Kang J, Huang Y, Miao Z, Bi M, Jin N, Li K, Li X, Xu J, Wang D.

Abstract

Transcriptomic analyses have revealed an unexpected complexity in the eukaryote transcriptome, which includes not only protein-coding transcripts but also an expanding catalog of noncoding RNAs (ncRNAs). Diverse coding and noncoding RNAs (ncRNAs) perform functions through interaction with each other in various cellular processes. In this project, we have developed RAID (http://www.rna-society.org/raid), an RNA-associated (RNA-RNA/RNA-protein) interaction database. RAID intends to provide the scientific community with all-in-one resources for efficient browsing and extraction of the RNA-associated interactions in human. This version of RAID contains more than 6100 RNA-associated interactions obtained by manually reviewing more than 2100 published papers, including 4493 RNA-RNA interactions and 1619 RNA-protein interactions. Each entry contains detailed information on an RNA-associated interaction, including RAID ID, RNA/protein symbol, RNA/protein categories, validated method, expressing tissue, literature references (Pubmed IDs), and detailed functional description. Users can query, browse, analyze, and manipulate RNA-associated (RNA-RNA/RNA-protein) interaction. RAID provides a comprehensive resource of human RNA-associated (RNA-RNA/RNA-protein) interaction network. Furthermore, this resource will help in uncovering the generic organizing principles of cellular function network.

RNA. 2014:20(7) | 39 Citations (from Europe PMC, 2025-03-15)

URL:	http://www.rnainter.org
Full name:	RNA interactome database
Description:	RNAInter is a repository for RNA-associated interactions, and it is updated based on the database RAID. The current version RNAInter 4.0 not only contains an enlarged data set, but also an updated confidence scoring system. RNAInter 4.0 houses more than 47 million interactions for more than 530 thousand moleculars across 156 species.
Year founded:	2014
Last update:	2021
Version:	v4.0
Accessibility:	Accessible
Country/Region:	China

Data type:	RNA
Data object:	Animal Bacteria Fungi Virus
Database category:	Interaction Literature
Major species:	Drosophila melanogaster Homo sapiens Mus musculus Human alphaherpesvirus 1
Keywords:	mRNA lncRNA miRNA pseudogene RNA-RNA interaction

University/Institution:	Southern Medical University
Address:	Southern Medical University, Guangzhou 510515, China.
City:
Province/State:
Country/Region:	China
Contact name (PI/Team):	Dong Wang
Contact email (PI/Helpdesk):	wangdong79@smu.edu.cn

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Database Commons a catalog of worldwide biological databases

a catalog of worldwide biological databases

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RNAInter

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Classification & Tag

Contact information

Publications

Motivation

Results

Availability and implementation

Supplementary information

Ranking

Community reviews

Word cloud

Tags

Related Databases

Record metadata

Database Commons
a catalog of worldwide biological databases