Cheminfo Retrieval Class 9th FA09

submitted by: jcbradley

A final overview of student assignments for the class, mainly about finding and reporting on sources of molecular properties.

Cheminfo Retrieval Class 8th FA09

submitted by: jcbradley
This is the lecture from the 8th Chemical Information Retrieval class at Drexel University on November 12, 2009. It starts with a demonstration of how to use of ChemSketch and Chemspider to display and manipulate chemical structures, especially those with complicated stereochemistry. Technical issues with using SMILES between the two platforms are addressed, as are optimization of 3D structures and inverting chiral centers. Microsoft Paint is used to process screen captures to images that...

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.

Cheminfo Retrieval Class Six FA09

submitted by: jcbradley
This is the lecture from the sixth Chemical Information Retrieval class at Drexel University on October 29, 2009. It starts with a review of some of the new questions answered by students from the chemistry publishing FAQ, which covers patent information and accessing electronic journals at Drexel. Tony Williams submitted a puzzle to resolve conflicting structures in ChemSpider, which is too difficult to be a regular assignment. It requires re-analyzing spectroscopic data in papers where...

Cheminfo Retrieval Fourth Class FA09

submitted by: jcbradley
This is a recording of the fourth class on Chemical Information Retrieval on Oct 15, 2009 at Drexel University. It starts with some tips on removing formatting from Wikispaces pages, the Drexel Cisco VPN client for accessing paid subscriptions off campus and how to link to a DOI. The first two assignments for the class are then described. The first involves summarizing each paragraph of an article and an option to use AcaWiki is demonstrated. The second involves filling in an FAQ for...

AMGA Metadata Catalog

submitted by: lciuffo

Presentation given at the 2nd EELA-2 Grid School

Chemical Information Retrieval class 1 FA09

submitted by: jcbradley

Jean-Claude Bradley introduces Chemical Information Retrieval (CHEM 367 and CHEM 767) at Drexel University with an overview of topics to be covered. See class wiki at http://getcheminfo.wikispaces.com for details.

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.

Data Curation in Biology – Past, Present and Future

submitted by: simont
This is an audio recording of Janet Thornton's keynote presentation at the Third International BioCurator Society meeting held in Berlin, April 2009. Abstract: Data curation has been critical in the development of biology from Darwin and Linnaeus to UniProt, the careful collection and organisation of data has been the spring from which new hypotheses and understanding have emerged. In this presentation, I will describe how we have used data curation in my own research group - and also...