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.

Structural Bioinformatics Pharm 201 UCSD Lecture 14

submitted by: Phil

This is lecture 14 from a graduate student class in structural bioinformatics offered at UCSD see http://www.sdsc.edu/pb/edu/pharm201/ The lecture covers the principles of assigning protein secondary structure using teh 3D structure as a starting point with a focus on the Kabsch-Sander algorithm as used in DSSP.

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 9

submitted by: Phil

This is lecture 9 from a graduate student class in structural bioinformatics offered at UCSD see http://www.sdsc.edu/pb/edu/pharm201/ The lecture covered the interrelationship between protein sequence-structure and function. This is a precursor to a study of data reduction and establishing a non-redundant set of information.

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.

Pascal Gaudet on the Biocurator Society at GSC8

submitted by: JGI

Pascal Gaudet of Northwestern University talks about "The Biocurator Society" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 11, 2009.

Tatiana Tatusova on "Annotations in Refseq" at GSC8

submitted by: JGI

Tatiana Tatusova of NCBI discusses "Annotations in Refseq" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009.

Nikos Kyrpides on Gene Calling Standards at GSC8

submitted by: JGI

Nikos Kyrpides of the DOE Joint Genome Institute discusses gene calling standards at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009.

Robert Cottingham on the DOE KnowledgeBase at GSC8

submitted by: JGI

Robert W. Cottingham of Oak Ridge National Laboratory discusses the DOE KnowledgeBase at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

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...