Cargando…

LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system

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 ex...

Descripción completa

Detalles Bibliográficos
Autores principales: Liu, Lin, Li, Zhao, Liu, Chang, Zou, Dong, Li, Qianpeng, Feng, Changrui, Jing, Wei, Luo, Sicheng, Zhang, Zhang, Ma, Lina
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728265/
https://www.ncbi.nlm.nih.gov/pubmed/34751395
http://dx.doi.org/10.1093/nar/gkab998
_version_ 1784626700075663360
author Liu, Lin
Li, Zhao
Liu, Chang
Zou, Dong
Li, Qianpeng
Feng, Changrui
Jing, Wei
Luo, Sicheng
Zhang, Zhang
Ma, Lina
author_facet Liu, Lin
Li, Zhao
Liu, Chang
Zou, Dong
Li, Qianpeng
Feng, Changrui
Jing, Wei
Luo, Sicheng
Zhang, Zhang
Ma, Lina
author_sort Liu, Lin
collection PubMed
description 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.
format Online
Article
Text
id pubmed-8728265
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-87282652022-01-05 LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system Liu, Lin Li, Zhao Liu, Chang Zou, Dong Li, Qianpeng Feng, Changrui Jing, Wei Luo, Sicheng Zhang, Zhang Ma, Lina Nucleic Acids Res Database Issue 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. Oxford University Press 2021-11-09 /pmc/articles/PMC8728265/ /pubmed/34751395 http://dx.doi.org/10.1093/nar/gkab998 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Database Issue
Liu, Lin
Li, Zhao
Liu, Chang
Zou, Dong
Li, Qianpeng
Feng, Changrui
Jing, Wei
Luo, Sicheng
Zhang, Zhang
Ma, Lina
LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system
title LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system
title_full LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system
title_fullStr LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system
title_full_unstemmed LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system
title_short LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system
title_sort lncrnawiki 2.0: a knowledgebase of human long non-coding rnas with enhanced curation model and database system
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728265/
https://www.ncbi.nlm.nih.gov/pubmed/34751395
http://dx.doi.org/10.1093/nar/gkab998
work_keys_str_mv AT liulin lncrnawiki20aknowledgebaseofhumanlongnoncodingrnaswithenhancedcurationmodelanddatabasesystem
AT lizhao lncrnawiki20aknowledgebaseofhumanlongnoncodingrnaswithenhancedcurationmodelanddatabasesystem
AT liuchang lncrnawiki20aknowledgebaseofhumanlongnoncodingrnaswithenhancedcurationmodelanddatabasesystem
AT zoudong lncrnawiki20aknowledgebaseofhumanlongnoncodingrnaswithenhancedcurationmodelanddatabasesystem
AT liqianpeng lncrnawiki20aknowledgebaseofhumanlongnoncodingrnaswithenhancedcurationmodelanddatabasesystem
AT fengchangrui lncrnawiki20aknowledgebaseofhumanlongnoncodingrnaswithenhancedcurationmodelanddatabasesystem
AT jingwei lncrnawiki20aknowledgebaseofhumanlongnoncodingrnaswithenhancedcurationmodelanddatabasesystem
AT luosicheng lncrnawiki20aknowledgebaseofhumanlongnoncodingrnaswithenhancedcurationmodelanddatabasesystem
AT zhangzhang lncrnawiki20aknowledgebaseofhumanlongnoncodingrnaswithenhancedcurationmodelanddatabasesystem
AT malina lncrnawiki20aknowledgebaseofhumanlongnoncodingrnaswithenhancedcurationmodelanddatabasesystem