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Phenotype database: what is it?
Peter Kok, Jolanda Strubel 04-APR-2017
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Contents
1.
Background
2.
What does Phenotype DB do?
3.
Who is it for?
4.
How does it work?
5.
Conclusion
Phenotype database: what is it? Peter Kok, Jolanda Strubel - - PowerPoint PPT Presentation
Phenotype database: what is it? Peter Kok, Jolanda Strubel - - PowerPoint PPT Presentation
Phenotype database: what is it? Peter Kok, Jolanda Strubel 04-APR-2017 Contents Background 1. What does Phenotype DB do? 2. Who is it for? 3. How does it work? 4. Conclusion 5. 2 A little history: Collaborators (early days and now)
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A little history: Collaborators (early days and now)
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Nutritional Phenotype database
Genotype Environment Phenotype
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Background
Developed to: empower scientists, within various communities of practice, with standardized software and knowledge stores to store, manage, and retrieve information and data on genotypes and phenotypes.
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How to reach this goal
❖ Standardization of study data capture (templates and ontologies) ❖ Make it possible to share study design and actual data (e.g. for reproducing)
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What does Phenotype DB do
❖ Store data ○ Meta data (study setup/design) using templates and ontologies ○ Measurements data ❖ Share data ❖ Quick visualization of data
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Who is it for?
❖ Current users: TNO TraIT Researchers at Maastricht University ❖ In general:
- rganisations who want to share study set up and data
internally or externally ❖ ...
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How does it work?
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Templates for everything
Template TemplateF ield
- Study
- Subject
- Event
(sample and treatment group)
- Sampling
event
- Sample
- Assay
- Platform
- Feature
*
entity type
- short text (< 255
chars)
- long text
- selection from list of
terms
- selection from
extendible list of terms
- decimal number
(double)
- natural number (long)
- term from ontology
- file
- boolean
- date
- relative time
- template
- module
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Using ontologies in template fields
- Uses BioPortal (National Center for Biomedical Ontology),
a repository of ontologies. https://bioportal.bioontology.org/
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Technical details
❖ Grails 2.5.1 + PostgreSQL ❖ Server-side rendering of pages ❖ JavaScript with a lot of jQuery ❖ Database tables automatically generated from domain model
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What’s new in version 2?
❖ Redesign of front-end (style) ❖ Test plan ❖ Lots and lots of bug fixes (work-in-progress) ❖ Optimization (database queries, importer) ❖ Improved documentation
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Summary
Phenotype database has a lot going for it: ❖ standardization of study setup and data ❖ easily customizable using templates ❖ open source ❖ ontologies integrated
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