YeastMine: List Operations

submitted by: yeastgenome

List operations (union, intersect, and subtract) allow you to combine results from previous YeastMine queries and thus provide a powerful way to build complex queries.

YeastMine Widgets: GO Term Enrichment

submitted by: yeastgenome

This tutorial demonstrates how to use YeastMine to obtain a GO Term Enrichment analysis for a gene list.

SPELL at SGD

submitted by: yeastgenome

Describes how to use SPELL (Serial Pattern of Expression Levels Locator), a query-driven search engine for large gene expression microarray compendia. Users will learn how to perform a search using a set of genes, download data, and show expression levels for a single gene.

YeastMine: Using Lists in a Template

submitted by: yeastgenome

This tutorial covers how to perform a template search using a pre-created list of genes in SGD's data retrieval tool YeastMine. Also covered is where to find some of the widgets and template search analyses automatically performed by YeastMine whenever you create a list of genes.

YeastMine: Creating and Using Lists

submitted by: yeastgenome

This tutorial covers how to create lists of genes and some of the list analysis options in SGD's data retrieval tool YeastMine.

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 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.