NCBO/DBP
Using ontologies to annotate and mine the GEO microarray db
In a collaboration with the National Center for Biomedical Ontology (NCBO) we are building software tools to explore the use of ontology annotations as a way to extract useful data out of the GEO microarray database at NCBI. This project is a Driving Biological Project (DBP) for the NCBO and our role is to work with the NCBO to drive their technology development, specifically their web service tools and APIs.
As the project progresses we’ll be adding content to this page. Currently there are slides and a video of our presentation available from the NCBO All Hands meeting (December 2008). We do have an early prototype ruby on rails application that we used to access the NCBO webservices, the source code is available via GitHub.
We have started to make the early results of our GEO data mining available via the Gminer website: http://gminer.mcw.edu This site is also our development environment as we explore the data and the indexing results from the NCBO tools so its liable to change without warning.
The Rat Strain ontology developed by Rajni Nigam at the Rat Genome Database is available via the NCBO BioPortal.
People currently involved in this project @ MCW:
- Simon Twigger (PI)
- Jennifer Smith (Curation, ontology and annotation review)
- Joey Geiger (RubyOnRails developer)
