An Introduction to Biomedical Nomenclature: Part IV, Strain Nomenclature

submitted by: RGD.Videos
Learn how to use biomedical nomenclature to name to strains that you or your research group develop or to find a strain that meets your research needs with this informative tutorial. Using effective nomenclature will help to disambiguate your data will help you to present it to your colleagues in a clear and meaningful way. For a copy of RGNC’s complete set of rules on nomenclature, visit: http://rgd.mcw.edu/nomen/nomen.shtml Or contact us at: rgd.data@mcw.edu

An Introduction to Biomedical Nomenclature: Part III, QTL and Marker Nomenclature

submitted by: RGD.Videos
Biomedical nomenclature is a valuable and ever-expanding tool that researchers can use in order to more easily learn about, refer to or retrieve any particular parts of the genome using the literature or through the use of curated data and a variety of tools, such as the ones available in RGD. This video showcases both QTL and marker nomenclature. For a copy of RGNC’s complete set of rules on nomenclature, visit: http://rgd.mcw.edu/nomen/nomen.shtml Or contact us at:...

An Introduction to Biomedical Nomenclature: Part II, Genetic Nomenclature

submitted by: RGD.Videos
This video focuses on rat gene nomenclature, noting how it is formed and where you can go to seek help when naming your genes. Biomedical nomenclature is a valuable and ever-expanding tool that researchers can use in order to more reliably retrieve data on any particular part of the genome through analysis tools, such as the ones available in RGD. Learn more about this vital mechanism. For a copy of RGNC’s complete set of rules on nomenclature, visit:...

An Introduction to Biomedical Nomenclature: Part I, The History and Reasoning behind Biomedical Nomenclature

submitted by: RGD.Videos
The recent emphasis on standardization of nomenclature is not just a trend, but a necessary way to disambiguate the identification of biological objects such as genes, QTLs, markers, and strains. This video will give you some background on the history of standardized genetic nomenclature and the reason for why it’s important in order to strengthen your understanding of genetic nomenclature. For a copy of the complete set of guidelines for nomenclature, visit:...

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...

Tip of the Week: YeastMine

submitted by: OpenHelix

For more information about this resource see our blog post at http://blog.openhelix.eu/?p=4968. In this tip we introduce YeastMine (beta) and show you how to make gene lists and link to other model organism information using InterMine's interoperability.

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 (http://ratmine.mcw.edu) 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...