Rat Genome Database

The Introduction to Biomedical Ontologies Video Series

Are you new to the field of Biomedical Ontologies, or just want to become more savvy about their use? Then this video series is a great place to start:

What is an Ontology?

Anatomy of an Ontology Annotation, part 1

Anatomy of an Ontology Annotation, part 2

Ontology Term Enrichment Using RatMine

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.

Even if you know something about biomedical ontologies, you might have wondered where the ontology “annotations”–that is, the assignments of specific ontology terms to genes, proteins, QTLs, animal strains, etc–come from. How are terms assigned to data objects? What are the assignments based on? And is there a way to tell just by looking at an annotation what kind of evidence it’s based on? This video is the first of a pair of companion tutorials that answer these questions.

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 pay attention to is the term itself, you could be skipping over valuable information that the other components of annotations supply. This video is the second of a pair of companion tutorials that will give you insight into what that “valuable information” is and how to interpret what you see when you examine ontology annotations.

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 and other InterMine-based tools to quickly and easily extract enrichment data for your list of genes or proteins.

To access other RGD tutorial videos, visit the Rat Community Videos page.

This work was supported in part by a Driving Biological Project Grant from the National Center for Biomedical Ontology (NCBO).

For more information about NCBO, click here. To explore any of the more than 200 biomedical ontologies found in the NCBO BioPortal tool, click here.

RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.

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The Introduction to Biomedical Ontologies Video Series

What is an Ontology?

Anatomy of an Ontology Annotation, part 1

Anatomy of an Ontology Annotation, part 2

Ontology Term Enrichment Using RatMine