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

Abstract

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.

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022

“…LncRNAWiki ( https://ngdc.cncb.ac.cn/lncrnawiki ) is a wiki-based database for community-curation of human long non-coding RNAs (lncRNAs) ( 27 , 28 ). The current version of LncRNAWiki 2.0 is significantly updated by (i) providing a new curation model with more informative and essential annotation items, (ii) developing a new web system based on MySQL/Java (instead of MediaWiki) that is capable of organizing all contents in a structured manner, (iii) improving the community-annotation submission functionality and providing more user-friendly web interfaces and (iv) equipping with online tools for ID conversion and functional prediction.…”

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023

“…Third, it integrates new omics features of lncRNA genes including sequence conservation across 40 vertebrates, small protein expression, and interaction with proteins. LncRNAWiki ( https://ngdc.cncb.ac.cn/lncrnawiki ), a knowledgebase of human lncRNAs, incorporates comprehensive annotations of functional lncRNAs based on a standardized curation model and provides user-friendly web interfaces to facilitate data curation, retrieval and visualization ( 54 , 55 ). This year, based on manual curation of 535 publications, we have expanded LncRNAWiki by adding 97 experiment-validated human lncRNAs, updating 191 existing lncRNAs and integrating 4761 newly-curated associations.…”

KaKs_Calculator 3.0: calculating selective pressure on coding and non-coding sequences

“…To test KaKs_Calculator 3.0, we choose three empirical lncRNA genes that are extensively studied according to LncRNAWiki [7] and collect their human-mouse orthologs as well as their adjacent coding orthologs from NGDC LncBook [31] and NCBI RefSeq [32].…”

“…Nowadays, a growing body of evidence have shown that non-coding sequences, historically thought as "junk" due to few knowledge on their function relative to coding sequences, are recognized as functional elements to play important regulation roles in multiple biological processes [4] and associate closely with various human diseases [5][6][7]. Albeit less conserved by comparison with coding sequences, a larger number of non-coding sequences have been identified highly conserved across mammalian genomes [8][9][10].…”

“…To test KaKs_Calculator 3.0, we choose three empirical lncRNA genes that are extensively studied according to LncRNAWiki [7] and collect their human-mouse orthologs as well as their adjacent coding orthologs from NGDC LncBook [31] and NCBI RefSeq [32]. Specifically, these non-coding and coding gene symbols with accession numbers are: (1) H19 (NR_002196.2 vs. NR_130973.1) and MRPL23 (NM_021134.4 vs. NM_011288.2); (2) MALAT1 (NR_002819.4 vs. NR_002847.3) and SCYL1 (NM_020680.4 vs. NM_001361921.1); and (3) HOTAIR (NR_003716.3 vs. NR_047528.1) and HOXC12 (NM_173860.3 vs. NM_010463.2).…”