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Mrr 05152011 pmdb_proposal

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  • 1. Mariam Rizkallah Open Source Technologies Department, Information Technology Institute, Egypt Pharmacomicrobiomics: The Drug-microbiome Database!
  • 2. PMDB:Outline
    • Introduction:
      • Human Genome Project (HGP 2001)
      • Drug Action and Fate
      • Human Microbiome Project (HMP 2005)
    • Pharmacomicrobiomics Database
    • What we are up to.
    • What we achieved.
  • 3. PMDB: Introduction - HGP
    • Target:
    • To know how different we are!
    • To predict susceptibility to diseases (e.g., heart disease and cancer)
    • To know if there is a certain population that is protected by its genes against certain diseases.
    • To use this information for tailoring medicine for patients based on their genetic profiles.
    Result: Humans are 99% alike! Source: Science, 16 FEBRUARY 2001VOL 291, ISSUE 5507, PAGES 1145-1434
  • 4. PMDB: Introduction - HMP
    • It's gotta be the microbes!!
    • “ Combined genomes of the human-associated microbes.“
    • Microbes freely live inside/on the surface of humans as their favorite place to live.
    Source: http://commonfund.nih.gov/hmp/
  • 5. Human-microbiota relationship: It's complicated!
    • Beneficial:
    • -Protective (against intruders)
    • -Productive (vitamins)
    • -Digestive (breakdown food)
    • Harmful:
    • -Imbalance (diarrhea)
    • -Invasion
    • -Become virulent
    Source: http://pharmacomicrobiomics.com/
  • 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. The Database Source: UT-ORNL-KBRIN Bioinformatics Summit 2011 http://citg.uthsc.edu/summit_11
  • 8. What do we need?
    • MySQL DB
    • Documentation: ERD, UML, Sequence diagram, use cases
    • PHP Interface (Joomla as a CMS)
    • Functionality:
    • -Insert in each table by field
    • -View tables
    • -View “views”
    • -Search by categories (Drug, Drug ID, Body site, pathway, publication..etc)
    • -Advanced: Connect with public DB through API (Eutils) either periodically, or per query requested (Perl script)
    • Cloud configuration
    • Community (Rally Agile, Assembla, SVN..etc.)
  • 9. Progress So Far
    • Domain: http://pharmacomicrobiomics.com/
    • A suggested structure of DB view.
    • One poster in an international conference.
    • One biological databases expert
    • Three pharmacy students for data curation.
    • Two publications:
    • - Rizkallah MR, Saad R, Aziz RK. "The Human Microbiome Project, Personalized Medicine, and the Birth of Pharmacomicrobiomics" Current Pharmacogenomics and Personalized Medicine, Volume 8, Number 3, September 2010 , pp. 182-193(12)
    • -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)