Billion Data Points Trapped in International Data Repository Daring rescue Planned!
Résumé
Researchers from the Medical College of Wisconsin released plans today to
rescue over 1.5 billion data points currently trapped inside NCBIʼs Gene
Expression Omnibus (GEO) data repository. In a collaboration with the National
Center for Biomedical Ontology (NCBO), the Wisconsin team lead by Dr Simon
Twigger intends to use the NCBOʼs extensive ontological indexing of the GEO
data to gain access to the wealth of expression data currently stored in this vital
public database. “The data just wants to be free, we have to find ways to make
this happen!” Twigger told reporters in a recent interview.
Building on the needs of researchers using the Rat as model system, the MCW
team will explore the use of automated ontological indexing of the GEO database
as a framework for subsequent data mining. The NCBO already indexes a variety
of data resources with a large number of biomedical ontologies as part of its
Open Biomedical Resource project. This has good coverage in the areas of
disease and anatomy and will allow the identification of expression datasets
measured under relevant physiological conditions or from specific organs or
tissues. By itself this has great value to researchers but the MCW team hopes to
do more than provide improved searching. By combining ontological annotations
from the expression datasets and samples with the gene-level expression data
contained in the database it should be possible to create many millions of new
functional annotations. These will capture the tissues and organs where genes
have been shown to be expressed and allow this information to be used in many
other settings.
Discussing the project, Twigger was enthusiastic, “Thereʼs clearly a lot of work to
be done and its not going to be easy but thereʼs a huge amount of data in these
types of repositories and if we can find effective ways to set it free then the
benefits could be enormous!”. More details of the project along with preliminary
data and progress to date will be presented at the 3rd International BioCurator
meeting in Berlin in April.