Miare mibbi 2010-12-01

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  • INFOBIOMED: Promote adoption of the methods, tools and technologies of Medical Informatics and Bioinformatics by the emerging and unifying discipline of Biomedical Informatics. edikt: produces new knowledge by using computational science to extract information from vast datasets, and generate models through simulation.
  • Miare mibbi 2010-12-01

    1. 1. MIARE MIBBI Portal Project Update 2 nd MIBBI Workshop Nigel Binns 1-2 December 2010
    2. 2. MIARE : Biology and Scope <ul><li>MIARE (www.miare.org) </li></ul><ul><ul><li>M inimum I nformation A bout an R NAi E xperiment </li></ul></ul><ul><li>RNA interference (RNAi) </li></ul><ul><ul><li>natural post-transcriptional gene-silencing </li></ul></ul><ul><li>High-throughput genome-wide gene knockdown screens </li></ul><ul><ul><li>small interfering RNA (siRNA) or expressed small hairpin RNA (shRNA) </li></ul></ul><ul><li>High content phenotypic screens (phenome) </li></ul>
    3. 3. MIARE : Implementation <ul><li>Status of specification: </li></ul><ul><ul><li>transitioning from draft to mature guidelines </li></ul></ul><ul><li>Tools: </li></ul><ul><ul><li>MIARE-Tab: simple Microsoft Excel-based data exchange format </li></ul></ul><ul><ul><li>PubChem Deposition Template and guidance notes: deposit MIARE-compliant RNAi screening data into PubChem (http://pubchem.ncbi.nlm.nih.gov) </li></ul></ul><ul><li>Database support: </li></ul><ul><ul><li>NCBI/PubChem RNAi Deposition Gateway implements MIARE-compliance via a flexible tag/value pair container </li></ul></ul><ul><li>Controlled Vocabulary: </li></ul><ul><ul><li>Defines a number of reporting requirements contained in the MIARE reporting guidelines </li></ul></ul>
    4. 4. MIARE : Status and Support <ul><li>Project status: </li></ul><ul><ul><li>PubChem RNAi deposition gateway is actively being developed </li></ul></ul><ul><li>Contributors: </li></ul><ul><ul><li>Division of Pathway Medicine (www.ed.ac.uk/pathway-medicine) </li></ul></ul><ul><ul><ul><li>Peter Ghazal, Graeme Grimes, Javier Santoyo-Lopez, Nigel Binns </li></ul></ul></ul><ul><ul><li>RNAi Global Initiative (www.rnaiglobal.org) </li></ul></ul><ul><ul><ul><li>Amanda Birmingham, Queta Smith </li></ul></ul></ul><ul><ul><li>PubChem developers (http://pubchem.ncbi.nlm.nih.gov) </li></ul></ul><ul><ul><ul><li>Yanli Wang, Steve Bryant </li></ul></ul></ul><ul><li>This work is/was supported by: </li></ul><ul><ul><li>INFOBIOMED (www.infobiomed.org) - EC-IST 2001-35024 </li></ul></ul><ul><ul><li>eScience Data Information & Knowledge Transformation (www.edikt.org.uk) - SFC HR04019 </li></ul></ul><ul><li>Publications: </li></ul><ul><ul><li>Statistical methods for analysis of high-throughput RNA interference screens </li></ul></ul><ul><ul><ul><li>Birmingham, A. et al Nat Methods 6 (2009) p569-75 </li></ul></ul></ul>

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