Tip of the Week: eGIFT, extracting gene information from text

submitted by: OpenHelix

This week's tip is on eGIFT, a tool that allows you to extract information from text. For more information, check out the post at http://blog.openhelix.eu/wp-admin/post.php?post=11293

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.

YeastMine: Using MyMine, Part 1

submitted by: yeastgenome

Describes how to create a MyMine account in YeastMine, allowing you to save Lists and Queries, and to create and save Templates. Part 1 describes saving Lists and Queries, Part 2 describes creating and saving Templates

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.

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...

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.

Structural Bioinformatics Pharm 201 UCSD Lecture 8

submitted by: Phil

This is lecture 8 from a graduate student class in structural bioinformatics offered at UCSD see http://www.sdsc.edu/pb/edu/pharm201/ The lecture covered two items. Prof Rik Belew described work he is doing on an HIVortal - a systems biology drill down of HIV. Prof Phil Bourne described the basics of the Gene Ontology.

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...