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Phenotypes and Models Help

The “Phenotypes and Models” portal contains data related to rat strains,phenotypes,and disease models and is accessed through the “Phenotypes and Models” tab at the top of most RGD web pages or through the link in the right center of the RGD home page. Below is a description of the different sections found in “Phenotypes and Models”.

Jump to help for:

The Phenotypes and Models Home Page
Meet Joe Rat
Strains & Models
Strain Medical Records

To view the “Introduction to the RGD Phenotypes and Models Portal” tutorial video, click here.

Phenotypes and Models Home Page

This is the home page for “Phenotypes and Models”. The different types of information can be accessed by the image links in the middle of the page and some of those links are also available via the menu bar at the top of the page.  The five subsections of the “Phenotypes and Models” are:

  1. Meet Joe Rat – divided into four sections: Photos and Images, Rats 101, Phylogenetics, and Portals
  2. Phenotypes
  3. PhenoMiner – A tool to mine phenotypic data
  4. Strains & Models
  5. Strain Medical records


Meet Joe Rat

Photos and Images
1.  PhysGen Photo archive: This link leads to a page of images for rat strains that were subjects of the PhysGen Program for Genomic Applications. In turn the image page has links to phenotypic data for each of the strains.

2.  Ratday: This link leads to an online PDF version of the RGD Rat Calendar.

3.  Community Submissions: This link leads to a page where links for photo submission and strain registration can be found.

4.  For Sale: This link returns a page containing a chart showing rat strain availability by vendors and repositories, with links for each source.


Rats 101
This section of Meet Joe Rat provides two resources for experiments using rats:

1. Methods and Techniques: This resource allows the user to browse the Measurement Method Ontology, and then to access references specific for the methods chosen.

2. Strain development:  This resource provides descriptions of techniques to develop a variety of rat models, with appropriate references which provide more detail.

This section of Meet Joe Rat provides brief descriptions and links to three different phylogenetic trees for inbred strains of the laboratory rat.
This last section of Meet Joe Rat is under construction.  The first “Mini-Portal” will focus on development and aging.

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The phenotypes section of the Phenotypes & Models portal provides access to PGA (PhysGen Program for Genomic Applications) and NBRP (National BioResource Project in Japan) data from a wide variety of  phenotyping experiments.  Access to experimental methods for most of the data is also provided.

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Strains & Models

The Strains and Models page provides access to four main sections:

  1. RGD Strain Search
  2. Strain Availability
  3. Disease Models
  4. Animal Husbandry

Each section heading is a link to a page with further information and links.  Additionally, on the Strains and Models page there is a list of links for literature reviews relevant to particular rat strains.  There is also a general information section with links to more strain-related information at both RGD and external sources. 



RGD Strain Search – The RGD strain-specific search can also be found by selecting the “Data” tab at the top of most RGD web pages. Search here by symbol, ontology term, or keyword.
Strain Availability –  This is a chart listing available strains with a link to the respective sources. A click on the parental strain symbol leads to a detailed list of different types of strains generated from the parental strain and their availability. Interested individuals can order rat strains through the commercial vendor or non-commercial sources.
Disease Models – Rats serve as excellent models for human diseases as they have similar phenotypes during the progression of selected diseases. This page lists categories of disease for which certain rat strains serve as models for human disease. Each category title links to a page containing lists of strains used for modeling specific diseases and specific disease-related phenotypes.

Animal Husbandry – This page provides vendor/source and protocol links in five different categories relevant to the laboratory care of rats:

  1. Breeding
  2. Cages
  3. Colony Management Software
  4. Diagnostic and Genetic Testing
  5. Rat Food


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 This is the home page of the PhenoMiner tool which is accessed through the Phenotypes & Models portal.  A separate help page for PhenoMiner can be found here.

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Strain Medical Records

The Strain Medical Records page provides links to pages containing standard phenotypic data for various rat strains.  Both the rounded symbol/name squares and the text below are links to the page specific for that strain.

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