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Mrr 05152011 pmdb_proposal


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Mrr 05152011 pmdb_proposal

  1. 1. Mariam Rizkallah Open Source Technologies Department, Information Technology Institute, Egypt Pharmacomicrobiomics: The Drug-microbiome Database!
  2. 2. PMDB:Outline <ul><li>Introduction: </li></ul><ul><ul><li>Human Genome Project (HGP 2001) </li></ul></ul><ul><ul><li>Drug Action and Fate </li></ul></ul><ul><ul><li>Human Microbiome Project (HMP 2005) </li></ul></ul><ul><li>Pharmacomicrobiomics Database </li></ul><ul><li>What we are up to. </li></ul><ul><li>What we achieved. </li></ul>
  3. 3. PMDB: Introduction - HGP <ul><li>Target: </li></ul><ul><li>To know how different we are! </li></ul><ul><li>To predict susceptibility to diseases (e.g., heart disease and cancer) </li></ul><ul><li>To know if there is a certain population that is protected by its genes against certain diseases. </li></ul><ul><li>To use this information for tailoring medicine for patients based on their genetic profiles. </li></ul>Result: Humans are 99% alike! Source: Science, 16 FEBRUARY 2001VOL 291, ISSUE 5507, PAGES 1145-1434
  4. 4. PMDB: Introduction - HMP <ul><li>It's gotta be the microbes!! </li></ul><ul><li>“ Combined genomes of the human-associated microbes.“ </li></ul><ul><li>Microbes freely live inside/on the surface of humans as their favorite place to live. </li></ul>Source:
  5. 5. Human-microbiota relationship: It's complicated! <ul><li>Beneficial: </li></ul><ul><li>-Protective (against intruders) </li></ul><ul><li>-Productive (vitamins) </li></ul><ul><li>-Digestive (breakdown food) </li></ul><ul><li>Harmful: </li></ul><ul><li>-Imbalance (diarrhea) </li></ul><ul><li>-Invasion </li></ul><ul><li>-Become virulent </li></ul>Source:
  6. 6. PMDB: The Birth of a Novel Discipline HGP Pharmacogenetics & Pharmacogenomics HMP Pharmacomicrobiomics Body site Pathway: genes responsible Chemical ID Drug name Assay Drug class Effect (Increase/Decrease level) Microbial ID Publications DB Description Pubmed ID
  7. 7. The Database Source: UT-ORNL-KBRIN Bioinformatics Summit 2011
  8. 8. What do we need? <ul><li>MySQL DB </li></ul><ul><li>Documentation: ERD, UML, Sequence diagram, use cases </li></ul><ul><li>PHP Interface (Joomla as a CMS) </li></ul><ul><li>Functionality: </li></ul><ul><li>-Insert in each table by field </li></ul><ul><li>-View tables </li></ul><ul><li>-View “views” </li></ul><ul><li>-Search by categories (Drug, Drug ID, Body site, pathway, publication..etc) </li></ul><ul><li>-Advanced: Connect with public DB through API (Eutils) either periodically, or per query requested (Perl script) </li></ul><ul><li>Cloud configuration </li></ul><ul><li>Community (Rally Agile, Assembla, SVN..etc.) </li></ul>
  9. 9. Progress So Far <ul><li>Domain: </li></ul><ul><li>A suggested structure of DB view. </li></ul><ul><li>One poster in an international conference. </li></ul><ul><li>One biological databases expert </li></ul><ul><li>Three pharmacy students for data curation. </li></ul><ul><li>Two publications: </li></ul><ul><li>- Rizkallah MR, Saad R, Aziz RK. &quot;The Human Microbiome Project, Personalized Medicine, and the Birth of Pharmacomicrobiomics&quot; Current Pharmacogenomics and Personalized Medicine, Volume 8, Number 3, September 2010 , pp. 182-193(12) </li></ul><ul><li>-Aziz RK, Saad R, Rizkallah MR. “PharmacoMicrobiomics: How Bugs Modulate Drugs.” An educational initiative to explore the effects of human microbiome on drugs, BioMedCentral Bioinformatics (Ahead of print) </li></ul>