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Poster De Conférence Année : 2009

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.
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Dates et versions

hal-04300504 , version 1 (22-11-2023)

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  • HAL Id : hal-04300504 , version 1

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Simon N. Twigger, Jennifer Smith, Rajni Nigam, Clement Jonquet, Mark A. Musen. Billion Data Points Trapped in International Data Repository Daring rescue Planned!. 3rd International Biocuration Conference (Biocuration 2009), Poster session, Apr 2009, Berlin, Germany. ⟨hal-04300504⟩
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