Physiological Pathway Diagrams

submitted by: RGD.Videos
Are you looking for a more intuitive way to visualize pathway information? RGD's newest video tutorial about the Physiological Pathway diagrams will help you navigate these interactive diagrams for use as either a research or study tool. In this video, we will: • Locate the Physiological Pathway Diagrams on RGD’s website • Walk through a particular pathway diagram • View relationships between levels of organization • Learn every one of the controls attached to the diagrams

Introduction to Biomedical Ontologies #4: Ontology Term Enrichment Using RatMine

submitted by: jennifer.r.smith
You've done your experiments and you have a list of genes that might be of interest, but…what now? Or you keep seeing the term "ontology term enrichment analysis" in the papers you're reading and, well, you have a vague idea of what that means, but you aren't really sure. Whether you're interested in information about gene functions, diseases, phenotypes or pathways, this video provides an overview of what ontology term enrichment analysis is and how you can use the "widgets" in RatMine...

Introduction to the RGD Phenotypes and Models Portal

submitted by: jennifer.r.smith

Despite what our name might imply, the Rat Genome Database contains much more than just genomic and genetic data for the rat. This video will give you an overview of the RGD Phenotypes and Models portal—a rich resource of information on topics including animal husbandry, identifying what rat strains are good models for certain human diseases, and normal physiological measurements for a variety of rat strains.

An introduction to the Ratmine database

submitted by: simont

This video provides a brief introduction to the new Ratmine ( data warehouse and data mining tool released as part of the Rat Genome Database. It highlights some of Ratmine's key features and shows how to use Ratmine's Templates and Lists to find disease genes, common pathways and display protein-protein interactions and more.

Introduction to Biomedical Ontologies 3: Anatomy of an Ontology Annotation, part 2

submitted by: jennifer.r.smith
Are you missing the added value that you could be getting from ontology annotations? You know what ontologies are—maybe you've even used them on occasion. But if the only part of an ontology annotation that you take into account is the term itself, you could be skipping over valuable information that the other components of annotations supply. This video will give you insight into what that "valuable information" is and how to interpret what you see when you examine ontology annotations.

Introduction to Biomedical Ontologies #2: Anatomy of an Ontology Annotation, part 1

submitted by: jennifer.r.smith
Do you find that, like many who use biomedical ontologies, the only part of an ontology "annotation" you use is the ontology term itself? Perhaps you've noticed from time to time that there are some other things that seem to tag along with the ontology term but never really paid attention to those. Or perhaps you are just learning about ontologies and you want to know where the ontology "annotations" come from and what they are based on. This video gives a general overview of how ontology...

Introduction to Biomedical Ontologies 1: What is an Ontology?

submitted by: jennifer.r.smith

While reading an article or looking at a website, have you ever seen the term “ontology” and wondered what that meant? Do you hear people talking about using ontologies and ask yourself what the hubbub is about? This video is designed to help answer those questions. Here is a beginner’s look at what an ontology is and why ontologies are an important tool in the scientist’s toolbox.

Getting Started with GBrowse

submitted by: jennifer.r.smith

So you've heard people talking about "Genome Browsers" but you've never used one and you're not quite sure where to start. This video is just what you've been looking for! We use the Rat Genome Browser at the Rat Genome Database as an example, but this information is applicable to any similar "GBrowse" tool. Check this out for a quick look at "Getting started with GBrowse".

Finding polymorphic Rat SNPs using RGD's SNPlotyper tool

submitted by: simont

This screencast shows how to identify polymorphic SNPs between different rat strains using RGD's SNPlotyper tool and the STAR consortium SNP genotype dataset. SNPlotyper is available at the Rat Genome Database ( and contains SNP genotype data produced by the european STAR consortium (

When it Comes to the Rat Genome, Bigger is Better

submitted by: dabraham
The rat genome comes to life through the use of the Gviewer tool. This video will show you how to use this helpful tool within the RGD website at . Genes, QTLs, and species syntenies of interest can all be visualized with ease as the Gviewer zooms in and navigates through the rat genome with a few clicks. See our website at for more tools for rat researchers.