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EuPathDB –Eukaryotic Pathogen Database Resources

EuPathDB –Eukaryotic Pathogen Database Resources. Chris Stoeckert, Ph.D. Dept of Genetics and Penn Center for Bioinformatics, University of Pennsylvania School of Medicine IDO Workshop Dec. 8, 2010 BWI. EuPathDB supports genomic research on Eukaryotic Protozoan Parasites.

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EuPathDB –Eukaryotic Pathogen Database Resources

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  1. EuPathDB –Eukaryotic Pathogen Database Resources Chris Stoeckert, Ph.D. Dept of Genetics and Penn Center for Bioinformatics, University of Pennsylvania School of Medicine IDO Workshop Dec. 8, 2010 BWI

  2. EuPathDB supports genomic research on Eukaryotic Protozoan Parasites EuPathDB: a portal to eukaryotic pathogen databases.Aurrecoechea C, Brestelli J, Brunk BP, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer ET, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Srinivasamoorthy G, Stoeckert CJ Jr, Thibodeau R, Treatman C, Wang H.Nucleic Acids Res. 2010

  3. EuPathDB retreat Athens, Georgia June 2009 EuPathDB: a portal to eukaryotic pathogen databases.Aurrecoechea C, Brestelli J, Brunk BP, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer ET, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Srinivasamoorthy G, Stoeckert CJ Jr, Thibodeau R, Treatman C, Wang H.Nucleic Acids Res. 2010

  4. EuPathDB metadata associated with genomic and post-genomic data is mostly free text with some structure • Gene annotations • User comments • Data sources • Study descriptions • Submission forms

  5. EuPathDB metadata associated with genomic and post-genomic data is mostly free text with some structure • Gene annotations • User comments • Data sources • Study descriptions • Submission forms

  6. EuPathDB metadata associated with genomic and post-genomic data is mostly free text with some structure • Gene annotations • User comments • Data sources • Study descriptions • Submission forms

  7. EuPathDB metadata associated with genomic and post-genomic data is mostly free text with some structure • Gene annotations • User comments • Data sources • Study descriptions • Submission forms Opportunity for cross study integration and analysis if descriptions were standardized.

  8. EuPathDB metadata associated with genomic and post-genomic data is mostly free text with some structure • Gene annotations • User comments • Data sources • Study descriptions • Submission forms Opportunity for cross study integration and analysis if descriptions were standardized.

  9. EuPathDB metadata associated with genomic and post-genomic data is mostly free text with some structure • Gene annotations • User comments • Data sources • Study descriptions • Submission forms

  10. Ontology-driven Isolate Submission Form

  11. Find T. brucei genes by phenotype based on RNAi knockdown and insufficiency studies. TriTrypDB: a functional genomic resource for the Trypanosomatidae.Aslett M, Aurrecoechea C, Berriman M, Brestelli J, Brunk BP, Carrington M, Depledge DP, Fischer S, Gajria B, Gao X, Gardner MJ, Gingle A, Grant G, Harb OS, Heiges M, Hertz-Fowler C, Houston R, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Logan FJ, Miller JA, Mitra S, Myler PJ, Nayak V, Pennington C, Phan I, Pinney DF, Ramasamy G, Rogers MB, Roos DS, Ross C, Sivam D, Smith DF, Srinivasamoorthy G, Stoeckert CJ Jr, Subramanian S, Thibodeau R, Tivey A, Treatman C, Velarde G, Wang H.Nucleic Acids Res. 2010

  12. Using OBI and other OBO Foundry ontologies to capture phenotype data JieZheng, Omar Harb

  13. EuPathDB and IDO • Using IDO (and other OBO Foundry ontologies) to capture phenotypes • manifestations of disease • severity • occurrences • smears of parasites • pathology • Other use cases • host-parasite interactions • specific host response • drug resistance and regimens • location(s) in host • parasite biology • adhesion molecules • metabolic states • developmental stage(s) • Synergy with other BRCs D. Wirth

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