| URL: | http://targetmine.mizuguchilab.org/ |
| Full name: | |
| Description: | an integrated data warehouse system which has been primarily developed for the purpose of target prioritisation and for broad-based biological knowledge discovery |
| Year founded: | 2011 |
| Last update: | 2017-03-02 |
| Version: | |
| Accessibility: |
Accessible
|
| Country/Region: | Japan |
| Data type: | |
| Data object: | |
| Database category: | |
| Major species: | |
| Keywords: |
| University/Institution: | National Institutes of Biomedical Innovation, Health and Nutrition |
| Address: | 7-6-8 Saito-Asagi, Ibaraki |
| City: | Osaka |
| Province/State: | |
| Country/Region: | Japan |
| Contact name (PI/Team): | Kenji Mizuguchi |
| Contact email (PI/Helpdesk): | kenji@nibiohn.go.jp |
|
An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. [PMID: 26989145]
Data analysis is one of the most critical and challenging steps in drug discovery and disease biology. A user-friendly resource to visualize and analyse high-throughput data provides a powerful medium for both experimental and computational biologists to understand vastly different biological data types and obtain a concise, simplified and meaningful output for better knowledge discovery. We have previously developed TargetMine, an integrated data warehouse optimized for target prioritization. Here we describe how upgraded and newly modelled data types in TargetMine can now survey the wider biological and chemical data space, relevant to drug discovery and development. To enhance the scope of TargetMine from target prioritization to broad-based knowledge discovery, we have also developed a new auxiliary toolkit to assist with data analysis and visualization in TargetMine. This toolkit features interactive data analysis tools to query and analyse the biological data compiled within the TargetMine data warehouse. The enhanced system enables users to discover new hypotheses interactively by performing complicated searches with no programming and obtaining the results in an easy to comprehend output format. Database URL: http://targetmine.mizuguchilab.org. © The Author(s) 2016. Published by Oxford University Press. |
|
TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery. [PMID: 21408081]
Prioritising candidate genes for further experimental characterisation is a non-trivial challenge in drug discovery and biomedical research in general. An integrated approach that combines results from multiple data types is best suited for optimal target selection. We developed TargetMine, a data warehouse for efficient target prioritisation. TargetMine utilises the InterMine framework, with new data models such as protein-DNA interactions integrated in a novel way. It enables complicated searches that are difficult to perform with existing tools and it also offers integration of custom annotations and in-house experimental data. We proposed an objective protocol for target prioritisation using TargetMine and set up a benchmarking procedure to evaluate its performance. The results show that the protocol can identify known disease-associated genes with high precision and coverage. A demonstration version of TargetMine is available at http://targetmine.nibio.go.jp/. |