DbNPFAQ

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This webpage is no longer maintained and only here for archive purposes. Please refer to https://trac.nbic.nl/gscf and http://dbnp.org for up to date information on this project.


Frequently Asked Questions

1. What's with the weird name?

dbNP is a shorthand for Nutritional Phenotype Database. The project was initially kickstarted by NuGO, the European Nutrigenomics Organisation, hence the term 'Nutritional'. However, there is nothing stopping you from putting data into dbNP from biological studies that have a totally different focus. Also, to make things more complicated, the name of the actual software application is GSCF (General Study Capture Framework).

2. What is this project really about?

There have been several initiatives in the bioinformatics community worldwide to standardize the storage of data from so called 'omics studies', biological studies which involve gathering different types of 'omics'. A number of these initiatives are covered on DbNPInspiration. This project is yet one other initiative to standardize data storage of multi(omics) studies. However, we go beyond the current initiatives in two ways: first, we try to clearly separate study 'metadata' such as study design, information about the organisms and compounds involved etc. from all kinds of omics data (such as microarray expression data), and second, we focus not only on storage but also on querying: we want to be able to answer biological questions over multiple studies and multiple omics techniques, taking into account the study metadata. And the good news is: we are making a web interface for all this.

3. I'm still lost. What is it exactly that you are building?

The dbNP project is structured in software modules, which you can download and run on your own server if you like. The core part is a web interface with a database underneath which stores the metadata of your studies, and enables you (via the web interface) to modify and query your studies. This part is built in Grails and named GSCF. Furthermore, 'omics assay data', such as gene expressions in the case of transcriptomics, are stored in submodules, which are linked to the core part via a 'clean data layer'. A list of known submodules can be found on the DbNPModules page.

4. Can I download dbNP?

Yes, you can download the source code and host your own private instance of the core part (see GSCF Quickstart and DbNPDeveloperQuickstart for details). Also, you can download and add any submodules you might need (see DbNPModules). You can check out the source code by using the Subversion client:

svn checkout https://trac.nbic.nl/svn/gscf/trunk

Alternatively, you can Download the binary WAR file.

5. Can I contribute to dbNP?

Of course. We are an open source project and welcome collaboration. Please contact Kees van Bochove (User:keesvb) or Jildau Bouwman (User:Jildau). Also, if you have specific omics data you want to add, you could consider building your own 'clean data module' (see DbNPModules).

6. Is this initiative published in a scientific journal?

An article is published in the 5th volume of Genes & Nutrition, with the title: 'The Nutritional Phenotype database to store, share and evaluate nutritional systems biology studies'.

7. I found a bug in dbNP. Where can I submit it?

Bugs can be submitted to the bug tracker of the module involved. Also, feature request can be placed in the feature tracker of the module. See DbNPTrackers for a list of those trackers.