http://precedings.nature.com/users/bc5f8bd91bd56d6f133a79b920a7d08e/ Documents posted by Rajarshi Guha Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://dx.doi.org/10.1038/npre.2009.3176.1 OBJECTIVES: We report on a experiment to functionally annotate PubChem assays using the Gene Ontology Categorizer (GOCat). METHODS and MATERIALS: The assays are processed to filter out non functional information, then the textual content is sent to the categorizer, which provide a ranked list of GO descriptors based on a GOA-learned association model. RESULTS: The GO descriptors are regarded as irrelevant for only 18% of the assays. CONCLUSION: Semantic enrichment of PubChem assays with functional genomics categories seems effective at least to navigate PubChem assays. AVAILABILITIES: the database is hosted by the University of Indiana at http://goassay.rguha.net/index.html the GO categorizer interface and service is available at the University of Geneva http://eagl.unige.ch/EAGLi/. http://dx.doi.org/10.1038/npre.2009.3176.1 Tue, 28 Apr 2009 08:47:47 UTC GOAssay: from Gene Ontology to Assays IDentifiers – Towards Automatic Functional Annotation of PubChem BioAssays doi:10.1038/npre.2009.3176.1 2009-04-28 Patrick Ruch Nature Precedings 2009-04-28T08:47:47Z Poster Chemistry Genetics & Genomics Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.2216.1 This talk was presented by Jean-Claude Bradley at the American Chemical Society meeting in Philadelphia on August 20, 2008. An introduction to Open Notebook Science is presented followed by an illustration of how ONS can be used in drug discovery. New data relating to the anti-malarial activity of Ugi products on 2 falcipain-2 docking sites is detailed. The docking calculations were provided by Rajarshi Guha and the enzyme and in vitro assays on Plasmodium falciparum were provided by Phil Rosenthal and Jiri Gut. Most of the syntheses were carried out by Khalid Mirza in the Bradley group.Screencast available at: http://video.google.com/videoplay?docid=3251406956070376532&hl=en http://dx.doi.org/10.1038/npre.2008.2216.1 Tue, 26 Aug 2008 17:09:10 UTC Open Notebook Science – Falcipain-2 Preliminary Results doi:10.1038/npre.2008.2216.1 2008-08-26 Jean-Claude Bradley Nature Precedings 2008-08-26T17:09:10Z Presentation Chemistry Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2007.104.1 This presentation combines 2 blog posts explaining the CombiUgi project and the predicted anti-tumor activity of a virtual library of 68,000 compounds. http://dx.doi.org/10.1038/npre.2007.104.1 Wed, 20 Jun 2007 12:43:38 UTC The CombiUgi Project and Closing the Open Science Loop doi:10.1038/npre.2007.104.1 2007-06-20 Jean-Claude Bradley Nature Precedings 2007-06-20T12:43:38Z Presentation Cancer Chemistry Bioinformatics http://creativecommons.org/licenses/by/2.5/