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LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs.

Ma L, Li A, Zou D, Xu X, Xia L, Yu J, Bajic VB, Zhang Z - Nucleic Acids Res. (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.

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Screenshots of the lncRNAWiki page for the lncRNA transcript MALAT-1, available at http://lncrna.big.ac.cn/index.php/ENST00000534336.1. This lncRNA was collaboratively curated by four researchers, yielding 125 versions as of October11, 2014. (A) Whole page, containing multiple different sections. (B) Brief authorship information in reward for community curation and a one-sentence summary for the description of this lncRNA. (C) Annotated information. It is organized as free text and links to several sub-sections. (D) Labs working on this lncRNA. It is a list of laboratories working on this lncRNA derived from references and provided by the community. (E) References, which are automatically generated and formatted with the help of the ‘Cite’ extension. (F) Basic Information. It is organized structurally in the form of a table, including transcript ID, source, transcript structure, genome context, sequence information, etc. (G) Authorship details generated by the ‘AuthorReward’ extension that quantifies researchers’ contributions and provides explicit authorship according to their quantitative contributions. The cutoff core for awarding authorship is configurable and set to 1 (by default) in lncRNAWiki.
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Figure 3: Screenshots of the lncRNAWiki page for the lncRNA transcript MALAT-1, available at http://lncrna.big.ac.cn/index.php/ENST00000534336.1. This lncRNA was collaboratively curated by four researchers, yielding 125 versions as of October11, 2014. (A) Whole page, containing multiple different sections. (B) Brief authorship information in reward for community curation and a one-sentence summary for the description of this lncRNA. (C) Annotated information. It is organized as free text and links to several sub-sections. (D) Labs working on this lncRNA. It is a list of laboratories working on this lncRNA derived from references and provided by the community. (E) References, which are automatically generated and formatted with the help of the ‘Cite’ extension. (F) Basic Information. It is organized structurally in the form of a table, including transcript ID, source, transcript structure, genome context, sequence information, etc. (G) Authorship details generated by the ‘AuthorReward’ extension that quantifies researchers’ contributions and provides explicit authorship according to their quantitative contributions. The cutoff core for awarding authorship is configurable and set to 1 (by default) in lncRNAWiki.

Mentions: The central entities of lncRNAWiki are human lncRNA transcripts. Thus, each transcript has a corresponding wiki page (Figure 3). Meanwhile, transcripts are grouped together by classification categories, as well as by genes. This information can be accessed at the homepage and at the bottom of the transcript page. Transcript-specific pages are generated based on transcript identifiers. The content of every transcript in lncRNAWiki is structured into two parts: ‘user-edit’ part and ‘Basic Information’ part. The ‘user-edit’ part allows users to add or delete annotations. On the contrary, the ‘Basic Information’ portion is organized as a table and will be regularly updated by the lncRNAWiki team based on the annotation information integrated from multiple different lncRNA-associated sources. The lncRNA information in lncRNAWiki was seeded from GENCODE, NONCODE and LNCipedia, yielding a comprehensive integration of 105 255 non-redundant lncRNA transcripts (Figure 1).


LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs.

Ma L, Li A, Zou D, Xu X, Xia L, Yu J, Bajic VB, Zhang Z - Nucleic Acids Res. (2014)

Screenshots of the lncRNAWiki page for the lncRNA transcript MALAT-1, available at http://lncrna.big.ac.cn/index.php/ENST00000534336.1. This lncRNA was collaboratively curated by four researchers, yielding 125 versions as of October11, 2014. (A) Whole page, containing multiple different sections. (B) Brief authorship information in reward for community curation and a one-sentence summary for the description of this lncRNA. (C) Annotated information. It is organized as free text and links to several sub-sections. (D) Labs working on this lncRNA. It is a list of laboratories working on this lncRNA derived from references and provided by the community. (E) References, which are automatically generated and formatted with the help of the ‘Cite’ extension. (F) Basic Information. It is organized structurally in the form of a table, including transcript ID, source, transcript structure, genome context, sequence information, etc. (G) Authorship details generated by the ‘AuthorReward’ extension that quantifies researchers’ contributions and provides explicit authorship according to their quantitative contributions. The cutoff core for awarding authorship is configurable and set to 1 (by default) in lncRNAWiki.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4383965&req=5

Figure 3: Screenshots of the lncRNAWiki page for the lncRNA transcript MALAT-1, available at http://lncrna.big.ac.cn/index.php/ENST00000534336.1. This lncRNA was collaboratively curated by four researchers, yielding 125 versions as of October11, 2014. (A) Whole page, containing multiple different sections. (B) Brief authorship information in reward for community curation and a one-sentence summary for the description of this lncRNA. (C) Annotated information. It is organized as free text and links to several sub-sections. (D) Labs working on this lncRNA. It is a list of laboratories working on this lncRNA derived from references and provided by the community. (E) References, which are automatically generated and formatted with the help of the ‘Cite’ extension. (F) Basic Information. It is organized structurally in the form of a table, including transcript ID, source, transcript structure, genome context, sequence information, etc. (G) Authorship details generated by the ‘AuthorReward’ extension that quantifies researchers’ contributions and provides explicit authorship according to their quantitative contributions. The cutoff core for awarding authorship is configurable and set to 1 (by default) in lncRNAWiki.
Mentions: The central entities of lncRNAWiki are human lncRNA transcripts. Thus, each transcript has a corresponding wiki page (Figure 3). Meanwhile, transcripts are grouped together by classification categories, as well as by genes. This information can be accessed at the homepage and at the bottom of the transcript page. Transcript-specific pages are generated based on transcript identifiers. The content of every transcript in lncRNAWiki is structured into two parts: ‘user-edit’ part and ‘Basic Information’ part. The ‘user-edit’ part allows users to add or delete annotations. On the contrary, the ‘Basic Information’ portion is organized as a table and will be regularly updated by the lncRNAWiki team based on the annotation information integrated from multiple different lncRNA-associated sources. The lncRNA information in lncRNAWiki was seeded from GENCODE, NONCODE and LNCipedia, yielding a comprehensive integration of 105 255 non-redundant lncRNA transcripts (Figure 1).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.

Show MeSH