Using the NCBO Web Services for Concept Recognition and Ontology Annotation of Expression Datasets
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This is the introductory slides for our poster at the 2009 Semantic Web Applications and Tools for Life Sciences workshop.
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Using the NCBO Web Services for Concept Recognition and Ontology Annotation of Expression Datasets
- 1. Using the NCBO Web Services for Concept Recognition and Ontology Annotation of Expression Datasets Simon N. Twigger 1,2 , Joey F. Geiger 2 and Jennifer R. Smith 1 1 Human and Molecular Genetics Center and 2 Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
- 2. Rat Genome Database http://rgd.mcw.edu
- 3. The Problem
- 4. GEO + Ontologies + OBA
- 7. Link to Genes? Probeset 1369048_at (Gabrd) was P resent in sample GSM132484 which was from hippocampus . Can we compile all such results for Gabrd, for the Hippocampus, etc?
- 8. RDF
Editor's Notes
- This is an intro to the poster presented at SWAT4LS, Amsterdam 2009. This work is done at MCW as part of a driving biological project collaboration with the National Center for Biomedical Ontology
- One our main areas is Rats as a model system. We maintain the Rat Genome Database, the MOD for the laboratory rat. Lots of useful information connecting genes to phenotypes and disease. Note the video tutorials on ontologies - I wanted to mention these are also being produced as part of this project, Id love feedback from these from anyone who has watched them. We’re also looking for suggestions for new ontology-related topics.
- Here’s the problem that many rat researchers face...
- GEO has a lot of relevant data, either as text or raw data. Can we start to capture some of this informaiton in an informatically-tractable fashion using ontologies and the OBA tools at NCBO in an annotation pipeline?
- We built a (ruby on rails) web app to help us manage this annotation process, curate the results and ultimately to provide a place for other users to start to access and explore this data.
- Initial results focusing on GEO rat datasets has provided a lot of great information and allowed us to create some handy navigational interfaces to the data, enabling queries that were not possible on any other site.
- Based on the annotations connecting GEO datasets and samples to specific tissues which were analyzed, can we use the Affy detection call combined with the tissue annotations to assert some information about the specific genes that were tested in that tissue?
- We’d like to share our results and the broader set of data from RGD with the community as RDF, here’s some example RDF we’ve been thinking about. We would really love to have some basic guidelines and information on some of the core elements needed and how to name them.