MetaBase--the wiki-database of biological databases

Bolser, Dan; Chibon, Pierre-Yves; Palopoli, Nicolás; Gong, Sungsam; Jacob, Daniel; Angel, Victoria Domínguez Del; Swan, Daniel; Bassi, Sebastian; González, Virginia; Suravajhala, Prashanth; Hwang, Seungwoo; Romano, Paolo; Edwards, Robert A.; Bishop, Bryan M.; Eargle, John M.; Shtatland, Timur; Provart, Nicholas J.; Clements, D. L.; Renfro, Daniel P.; Bhak, Daeui; Bhak, Jong

doi:10.1093/nar/gkr1099

Cited by 43 publications

(25 citation statements)

References 33 publications

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“…For CHO-K1 analysis we used the Mus musculus genome. MetaCore™ analyses are based on MetaBase (http://metadatabase.org/), a 100% manually-curated integrated database of mammalian biology that contains over 6 million experimental findings on protein-protein, protein-DNA, protein-RNA, and protein-compound interactions; metabolic and signaling pathways; and other information (Bolser et al, 2012). …”

Section: Methodsmentioning

confidence: 99%

Regulation of miR-29b-1/a transcription and identification of target mRNAs in CHO-K1 cells

Muluhngwi

Richardson

Napier

et al. 2017

Molecular and Cellular Endocrinology

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miR-29b and miR-29a transcript levels were reported to increase in exponentially growing CHO-K1 cells. Here, we examine the regulation of miR-29b-1/a in CHO-K1 cells. We observed that 4-hydroxytamoxifen (4-OHT) increased pri-miR-29b-1 and pri-miR-29a transcription in CHO-K1 cells by activating endogenous estrogen receptor α (ERα). DICER, an established, bona fide target of miR-29b-1/a, was shown to be regulated by 4-OHT in CHO-K1 cells. We showed that miR-29b-1 and miR-29a serve a repressive role in cell proliferation, migration, invasion, and colony formation in CHO-K1 cells. To identify other targets of miR-29b-1 and miR-29a, RNA sequencing was performed by transfecting cells with anti-miR-29a, which inhibits both miR-29a and miR-29b-1, pre-miR-29b-1, and/or pre-miR-29a. In silico network analysis in MetaCore™ identified common and unique putative gene targets of miR-29b-1 and miR-29a. Pathway analysis of identified putative miR-29 targets were related to cell adhesion, cytoskeletal remodeling, and development. Further inquiry revealed regulation of pathways mediating responses to growth factor stimulus and cell cycle regulation.

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Section: Methodsmentioning

confidence: 99%

Regulation of miR-29b-1/a transcription and identification of target mRNAs in CHO-K1 cells

Muluhngwi

Richardson

Napier

et al. 2017

Molecular and Cellular Endocrinology

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“…The ever pressing need to organize, catalogue and rate these data resources, so that the information they contain can be most effectively exploited, is reflected by the existence of a special wiki for databases termed MetaBase (MB) (http://metadatabase.org/wiki/Main_Page). It is a community‐curated database containing more than 2000 commonly used biological databases 19. Even more Nucleic Acids Research releases every year a special database issue, recently featuring descriptions of 92 new online databases covering various areas of molecular biology and 100 papers describing recent updates to the databases previously described 20…”

Section: A New Era Of Open Innovationmentioning

confidence: 99%

Taking Open Innovation to the Molecular Level ‐ Strengths and Limitations

Zdrazil

Blomberg

Ecker

2012

Molecular Informatics

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The ever-growing availability of large-scale open data and its maturation is having a significant impact on industrial drug-discovery, as well as on academic and non-profit research. As industry is changing to an ‘open innovation’ business concept, precompetitive initiatives and strong public-private partnerships including academic research cooperation partners are gaining more and more importance. Now, the bioinformatics and cheminformatics communities are seeking for web tools which allow the integration of this large volume of life science datasets available in the public domain. Such a data exploitation tool would ideally be able to answer complex biological questions by formulating only one search query. In this short review/perspective, we outline the use of semantic web approaches for data and knowledge integration. Further, we discuss strengths and current limitations of public available data retrieval tools and integrated platforms.

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“…The idea of a wiki on gene function was first proposed based on the report that wikipedia comes close to Britannica in terms of the accuracy of its science entries [8]. Later on, there has been an significant increase in the construction domain-specific wiki-based databases [9–26]. However, none of the databases target human liver.…”

Section: Introductionmentioning

confidence: 99%

LiverWiki: a wiki-based database for human liver

Chen¹,

et al. 2017

BMC Bioinformatics

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BackgroundRecent advances in omics technology have produced a large amount of liver-related data. A comprehensive and up-to-date source of liver-related data is needed to allow biologists to access the latest data. However, current liver-related data sources each cover only a specific part of the liver. It is difficult for them to keep pace with the rapid increase of liver-related data available at those data resources. Integrating diverse liver-related data is a critical yet formidable challenge, as it requires sustained human effort.ResultsWe present LiverWiki, a first wiki-based database that integrates liver-related genes, homolog genes, gene expressions in microarray datasets and RNA-Seq datasets, proteins, protein interactions, post-translational modifications, associated pathways, diseases, metabolites identified in the metabolomics datasets, and literatures into an easily accessible and searchable resource for community-driven sharing. LiverWiki houses information in a total of 141,897 content pages, including 19,787 liver-related gene pages, 17,077 homolog gene pages, 50,251 liver-related protein pages, 36,122 gene expression pages, 2067 metabolites identified in the metabolomics datasets, 16,366 disease-related molecules, and 227 liver disease pages. Other than assisting users in searching, browsing, reviewing, refining the contents on LiverWiki, the most important contribution of LiverWiki is to allow the community to create and update biological data of liver in visible and editable tables. This integrates newly produced data with existing knowledge. Implemented in mediawiki, LiverWiki provides powerful extensions to support community contributions.ConclusionsThe main goal of LiverWiki is to provide the research community with comprehensive liver-related data, as well as to allow the research community to share their liver-related data flexibly and efficiently. It also enables rapid sharing new discoveries by allowing the discoveries to be integrated and shared immediately, rather than relying on expert curators. The database is available online at http://liverwiki.hupo.org.cn/.

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MetaBase--the wiki-database of biological databases

Cited by 43 publications

References 33 publications

Regulation of miR-29b-1/a transcription and identification of target mRNAs in CHO-K1 cells

Regulation of miR-29b-1/a transcription and identification of target mRNAs in CHO-K1 cells

Taking Open Innovation to the Molecular Level ‐ Strengths and Limitations

LiverWiki: a wiki-based database for human liver

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