EcoliWiki: a wiki-based community resource for Escherichia coli

McIntosh, Brenley K.; Renfro, Daniel P.; Knapp, Gwendowlyn S.; Lairikyengbam, Chanchala R.; Liles, Nathan; Niu, Lili; Supak, Amanda M.; Venkatraman, Anand; Zweifel, Adrienne E.; Siegele, Deborah A.; Hu, James C.

doi:10.1093/nar/gkr880

Cited by 27 publications

(20 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Currently, we have curators that review the new pages/tables to ensure the accuracy of the information because the user group is relatively small at the moment. As the user group continues to grow, user participation is be included to ensure the accuracy of the information on LiverWiki following the wiki model: the quality of information is ensured and improved by multiple users reviewing and refining the same content [21]. When the user group grows bigger, pages/tables created by users are to be reviewed by peers in co-editing manners to ensure the accuracy of the information on the pages/tables.…”

Section: Utility and Discussionmentioning

confidence: 99%

LiverWiki: a wiki-based database for human liver

Chen¹,

et al. 2017

BMC Bioinformatics

View full text Add to dashboard Cite

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/.

show abstract

Section: Utility and Discussionmentioning

confidence: 99%

LiverWiki: a wiki-based database for human liver

Chen¹,

et al. 2017

BMC Bioinformatics

View full text Add to dashboard Cite

show abstract

“…What is unusual is the specificity of YdjG for NAD(H) as a cofactor, which represents the first example of an AKR which is not able to use NADP(H). The ydjG gene is located in an uncharacterised operon which includes a putative sugar kinase (ydjH), aldolase (ydjI) and a major facilitator superfamily transporter (ydjK) [23] (Figure 4a). These types of enzyme are consistent with a sugar metabolism pathway (exemplified by rhamnose degradation) with the AKR called upon to reduce the aldehyde produced by the aldolase.…”

Section: A Nadh Specific Akr Akr11b2 (Ydjg B1771)mentioning

confidence: 99%

The diversity of microbial aldo/keto reductases from Escherichia coli K12

Lapthorn

Zhu

Ellis

2013

Chemico-Biological Interactions

View full text Add to dashboard Cite

reductase, tyrosine auxotrophy suppressor protein, L-glyceraldehyde 3-phosphate reductase, AKR quaternary structure. AbstractThe genome of Escherichia coli K12 contains 9 open reading frames encoding aldo/keto reductases (AKR) that are differentially regulated and sequence diverse. A significant amount of data is available for the E. coli AKRs through the availability of gene knockouts and gene expression studies, which adds to the biochemical and kinetic data.This together with the availability of crystal structures for nearly half of the E. coli AKRs and homologues of several others provides an opportunity to look at the diversity of these representative bacterial AKRs. Based around the common AKR fold of (β/α) 8 barrel with two additional α-helices, the E. coli AKRs have a loop structure that is more diverse than their mammalian counterparts, creating a variety of active site architectures. Nearly half of the AKRs are expected to be monomeric, but there are examples of dimeric, trimeric and octameric enzymes, as well as diversity in specificity for NAD as well as NADP as a cofactor. However in functional assignments and characterisation of enzyme activities there is a paucity of data when compared to the mammalian AKR enzymes. 1.

show abstract

“…56,57 Such collections are increasingly being digitized as corresponding whole-genome sequences are fed into reference sequence databases. 37 Construction of comprehensive databases for the many organisms that can be considered as relevant in a microbial forensic context will take time.…”

Section: Reference Strain Collectionsmentioning

confidence: 99%

The Need for High-Quality Whole-Genome Sequence Databases in Microbial Forensics

Sjödin¹,

Broman²,

Melefors³

et al. 2013

Biosecurity and Bioterrorism: Biodefense Strategy, Practice, an

View full text Add to dashboard Cite

Microbial forensics is an important part of a strengthened capability to respond to biocrime and bioterrorism incidents to aid in the complex task of distinguishing between natural outbreaks and deliberate acts. The goal of a microbial forensic investigation is to identify and criminally prosecute those responsible for a biological attack, and it involves a detailed analysis of the weapon-that is, the pathogen. The recent development of next-generation sequencing (NGS) technologies has greatly increased the resolution that can be achieved in microbial forensic analyses. It is now possible to identify, quickly and in an unbiased manner, previously undetectable genome differences between closely related isolates. This development is particularly relevant for the most deadly bacterial diseases that are caused by bacterial lineages with extremely low levels of genetic diversity. Whole-genome analysis of pathogens is envisaged to be increasingly essential for this purpose. In a microbial forensic context, whole-genome sequence analysis is the ultimate method for strain comparisons as it is informative during identification, characterization, and attribution-all 3 major stages of the investigation-and at all levels of microbial strain identity resolution (ie, it resolves the full spectrum from family to isolate). Given these capabilities, one bottleneck in microbial forensics investigations is the availability of high-quality reference databases of bacterial whole-genome sequences. To be of high quality, databases need to be curated and accurate in terms of sequences, metadata, and genetic diversity coverage. The development of whole-genome sequence databases will be instrumental in successfully tracing pathogens in the future.

show abstract

EcoliWiki: a wiki-based community resource for Escherichia coli

Cited by 27 publications

References 46 publications

LiverWiki: a wiki-based database for human liver

LiverWiki: a wiki-based database for human liver

The diversity of microbial aldo/keto reductases from Escherichia coli K12

The Need for High-Quality Whole-Genome Sequence Databases in Microbial Forensics

Contact Info

Product

Resources

About