The Nutritional Phenotype Database (DbNP) helps biologists to interpret the results of biology studies which involve multiple 'omics' techniques. Initially, it was aimed at medium sized nutrigenomics intervention studies (hence the name), but it is now also used for storing studies from different biology areas, such as environmental plant studies. DbNP can be used for different purposes:

• Store detailed information about the design of your studies
• Link those study designs to actual 'omics' data
• Interpret the measured data along the axes of your study design

Current status

The development of DbNP software was started in December 2009.

• As of September 2010, we have completed the first version of the main 'module' of DbNP, called GSCF. It allows users to create or import study design information, and link that to 'omics' data in other DbNP-compliant software modules.
• Also, a number of modules are being developed, for clinical chemistry (Simple Assay Module), for metabolomics and for transcriptomics.

Who is behind it?

• The project was initated by the European Nutrigenomics Organization (NuGO)
• The Netherlands Metabolomics Centre (NMC) devotes developers to it, especially to the metabolomics module
• The Netherlands Bioinformatics Centre (NBIC) supplies development infrastructure and project management
• European Micronutrient Recommendations Aligned (EURECCA) gives academic input on the GSCF and SAM modules
• TNO Quality of Life (TNO) supplies first-time test users and also hosts some of our activities
• The Nutrition, Metabolism and Genomics (Nutrigenomics) Group @ WUR and the Netherlands Nutrigenomics Centre built the Clean Transcriptome Database module
  
• The Netherlands Toxicogenomics Centre (NTC) are among our first-time end users and supply import/export to ArrayTrack
• Plant Research International (PRI @ Wageningen University) also are in our pool of early test users
• The National Centre for Toxicological Research (NCTR @ FDA) and the Human Nutrition Research Centre of Aging (HNRCA @ Tufts) are our international partners in the development of a genetics module
• The Hyve has contributed to the program code of some of the modules

Relation to other projects

There are quite a few open source projects which focus on storing study design, multiple types of omics data or even both (such as ISATAB - see our supported exchange formats, LabKey, XGAP, OpenBIS, caBIG). All these initatives have more or less the same goals, but differ in focus, programming platform and user base. The unique focus points of DbNP are:

• DbNP has been from the very start of the project a collaboration of biologists, bioinformaticians and computer scientists, but it's focused on usability by biologists as end users.
• DbNP makes organization-wide or even consortium-wide standardization as easy as possible, by providing easy access to ontologies, so-called (study description) 'templates' and SOPs
• DbNP links to external webservices/websites hosting the actual omics data, rather than storing everything in one place (although it is possible to host all these services on one server)

Related Publications

The core of dbNP is formed by a module called GSCF, which stands for Generic Study Capture Framework. It is a web application that is designed to store the design of the biological studies in the database. This information is small in terms of disk size, but very valuable. GSCF serves as a linking hub for the other dbNP modules: it links to the data in the various assay modules. The data in these assay modules tends to be large in terms of disk space, but generally has a low information density.

Data model

The data in GSCF, the study capture module, forms the top layer of this graph. In GSCF, studies are defined. On a study level, meta-information about the study is defined, such as the people involved, study code, description, aim, associated publications etc. Also, the subjects (humans, mice, plants, cell cultures) of the study are defined. After that, the events are indicated that take place in the study. These can be treatments (such as medicine treatment), nutritional challenges, but also e.g. adverse effects can be described with an event. (See templates below on how to customize event descriptions for a particular area of biology). Also, a special type of event, called a 'sampling event', results in associated samples. For example, a sampling event 'Blood sampling' could lead to a blood sample for each subject on which this sampling event is applied. Events can be grouped in so-called 'event groups', which couple a group of subjects to a specific group of events. For example, a medicine intervention study in which one half of the subjects gets the actual medicine and the other half gets a placebo, could be described by two event groups, one with an associated medicine intervention event with the substance set to the actual medicine, and an event group with a medicine intervention event of which the substance is set to placebo. Finally, the samples are normally generated from the specified sampling events, but these can be customized if necessary, and then added to one or more assays, which reside in assay modules.

GSCF Data Model Overview

The following picture gives an overview of the main GSCF data entities. Most of them extend TemplateEntity, allowing them to store multiple custom field types. These field types form 'templates', which are editable from within the user interface using the 'template editor'.

Screenshot of the template editor:

Also, a study links to a number of other entities, such a persons and publications. Those are highlighted in the image below. Also, here is shown how a particular study has a particular template which contains the custom fields.

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