Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: https://ngdc.cncb.ac.cn/lncrnawiki
Full name: a wiki-based platform for community curation of human lncRNAs
Description: LncRNAWiki, a knowledgebase of human long non-coding RNAs (lncRNAs), has been rapidly expanded by incorporating more experimentally validated lncRNAs. In LncRNAWiki 2.0, all contents are organized in a structured manner powered by MySQL/Java and curators are able to submit/edit annotations based on the curation model that includes a wider range of annotation items. The new version incorporates a total of 2512 lncRNAs and 106 242 associations for disease, function, drug, interacting partner, molecular signature, experimental sample, CRISPR design, etc.
Year founded: 2014
Last update: 2021-6-15
Version: v2.0
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: China

Classification and Labelling

Data type:
RNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Beijing Institute of Genomics, Chinese Academy of Sciences
Address: No.1 Beichen West Road, Chaoyang District
City: Beijing
Province/State: Beijing
Country/Region: China
Contact name (PI/Team): Lina Ma
Contact email (PI/Helpdesk): malina@big.ac.cn

Publications

34751395
LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system. [PMID: 34751395]
Liu L, Li Z, Liu C, Zou D, Li Q, Feng C, Jing W, Luo S, Zhang Z, Ma L.

LncRNAWiki, a knowledgebase of human long non-coding RNAs (lncRNAs), has been rapidly expanded by incorporating more experimentally validated lncRNAs. Since it was built based on MediaWiki as its database system, it fails to manage data in a structured way and is ineffective to support systematic exploration of lncRNAs. Here we present LncRNAWiki 2.0 (https://ngdc.cncb.ac.cn/lncrnawiki), which is significantly improved with enhanced database system and curation model. In LncRNAWiki 2.0, all contents are organized in a structured manner powered by MySQL/Java and curators are able to submit/edit annotations based on the curation model that includes a wider range of annotation items. Moreover, it is equipped with popular online tools to help users identify lncRNAs with potentially important functions, and provides more user-friendly web interfaces to facilitate data curation, retrieval and visualization. Consequently, LncRNAWiki 2.0 incorporates a total of 2512 lncRNAs and 106 242 associations for disease, function, drug, interacting partner, molecular signature, experimental sample, CRISPR design, etc., thus providing a comprehensive and up-to-date resource of functionally annotated lncRNAs in human.

Nucleic Acids Res. 2022:50(D1) | 1 Citations (from Europe PMC, 2022-05-14)
31524988
Community Curation and Expert Curation of Human Long Noncoding RNAs with LncRNAWiki and LncBook. [PMID: 31524988]
Lina Ma, Jiabao Cao, Lin Liu, Zhao Li, Huma Shireen, Nashaiman Pervaiz, Fatima Batool, Rabail Z Raza, Dong Zou, Yiming Bao, Amir A Abbasi, Zhang Zhang

In recent years, the number of human long noncoding RNAs (lncRNAs) that have been identified has increased exponentially. However, these lncRNAs are poorly annotated compared to protein-coding genes, posing great challenges for a better understanding of their functional significance and elucidating their complex functioning molecular mechanisms. Here we employ both community and expert curation to yield a comprehensive collection of human lncRNAs and their annotations. Specifically, LncRNAWiki (http://lncrna.big.ac.cn/index.php/Main_Page) uses a wiki-based community curation model, thus showing great promise in dealing with the flood of biological knowledge, while LncBook (http://bigd.big.ac.cn/lncbook) is an expert curation-based database that provides a complement to LncRNAWiki. LncBook features a comprehensive collection of human lncRNAs and a systematic curation of lncRNAs by multi-omics data integration, functional annotation, and disease association. These protocols provide step-by-step instructions on how to browse and search a specific lncRNA and how to obtain a range of related information including expression, methylation, variation, function, and disease association. © 2019 by John Wiley & Sons, Inc.

Curr Protoc Bioinformatics. 2019:67(1) | 4 Citations (from Europe PMC, 2022-05-14)
25399417
LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. [PMID: 25399417]
Ma L, Li A, Zou D, Xu X, Xia L, Yu J, Bajic VB, Zhang Z.

Long non-coding RNAs (lncRNAs) perform a diversity of functions in numerous important biological processes and are implicated in many human diseases. In this report we present lncRNAWiki (http://lncrna.big.ac.cn), a wiki-based platform that is open-content and publicly editable and aimed at community-based curation and collection of information on human lncRNAs. Current related databases are dependent primarily on curation by experts, making it laborious to annotate the exponentially accumulated information on lncRNAs, which inevitably requires collective efforts in community-based curation of lncRNAs. Unlike existing databases, lncRNAWiki features comprehensive integration of information on human lncRNAs obtained from multiple different resources and allows not only existing lncRNAs to be edited, updated and curated by different users but also the addition of newly identified lncRNAs by any user. It harnesses community collective knowledge in collecting, editing and annotating human lncRNAs and rewards community-curated efforts by providing explicit authorship based on quantified contributions. LncRNAWiki relies on the underling knowledge of scientific community for collective and collaborative curation of human lncRNAs and thus has the potential to serve as an up-to-date and comprehensive knowledgebase for human lncRNAs. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2015:43(Database issue) | 71 Citations (from Europe PMC, 2022-05-14)

Ranking

All databases:
836/5177 (83.871%)
Gene genome and annotation:
274/1407 (80.597%)
Health and medicine:
182/1164 (84.45%)
Literature:
76/435 (82.759%)
836
Total Rank
76
Citations
10.857
z-index

Community reviews

5 Stars (1)
Data quality & quantity:
Content organization & presentation
System accessibility & reliability:

Word cloud

Related Databases

Citing
Cited by

Record metadata

Created on: 2015-06-20
Curated by:
Lina Ma [2022-04-26]
Lina Ma [2021-06-23]
Lina Ma [2018-11-27]
Lina Ma [2018-11-26]
Lina Ma [2018-11-23]
Lina Ma [2018-11-22]
Dong Zou [2018-11-22]
Dong Zou [2018-11-02]
Lina Ma [2018-07-10]
Lina Ma [2018-04-26]
Dong Zou [2018-03-05]
Lina Ma [2016-10-31]
Lina Ma [2016-07-18]
Zhang Zhang [2016-02-06]
Lina Ma [2015-06-26]