Mrr iti phar_mu

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Mrr iti phar_mu

  1. 1. PharMu Portal Bugs vs Drugs Database Graduation Project By: Mariam Reyad Rizkallah Open Source Technologies Department Information Technology Institute Intake 31
  2. 2. Presentation Outline <ul><li>Introduction </li></ul><ul><li>Scientific Problem and Technical Solution </li></ul><ul><li>PharMu Aim </li></ul><ul><li>Project Scope </li></ul><ul><li>Methodologies </li></ul><ul><li>Results: Delivered Features </li></ul><ul><li>Demo </li></ul><ul><li>Future Work </li></ul><ul><li>Acknowledgement </li></ul>
  3. 3. Introduction: EgyBio Network
  4. 4. Introduction: HGP (2001) <ul><li>Human Genome Project: </li></ul><ul><li>- To know how different we are! </li></ul><ul><li>- To assess how similar 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>Source: Science, 16 FEBRUARY 2001VOL 291, ISSUE 5507, PAGES 1145-1434 Result: Humans are 99% alike!
  5. 5. Introduction: HMP (2005) <ul><li>Human Microbiome Project: </li></ul><ul><li>- It's gotta be the microbes!! </li></ul><ul><li>Human cells 10^13 vs. microbial cells 10^14. </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: http://commonfund.nih.gov/hmp/
  6. 6. Introduction: Bugs vs Drugs <ul><li>Human-Microbiota Relationship: </li></ul><ul><li>It's complicated! </li></ul><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>
  7. 7. Introduction: Bugs vs Drugs <ul><li>Drug-Microbiome Relationship </li></ul>
  8. 8. PharMu Aim <ul><li>Explore how resident microbes change the behavior of drugs. </li></ul><ul><li>Introduce bioinformatics and microbial genomics to pharmacy students while benefiting the research community. </li></ul><ul><li>Build a knowledge base that allows interested students and scholars, in the future, to predict the behavior of untested members of drug classes or unstudied microbial species, and to design laboratory experiments for testing these predictions. </li></ul>
  9. 9. Scientific Problem and Technical Solution
  10. 10. PharMu Phases <ul><li>Step1: mining existing literature and extracting all known microbe-drug interactions. </li></ul><ul><li>Step2: manual curation of the extracted literature data(Pubmed) and their classification by drug classes (PubChem), microbial families (Taxonomy), and body systems (HMP). </li></ul><ul><li>Step3: creation of a relational database that includes the microbes at different body sites and their effects on drugs’ pharmacokinetic(fate) and pharmacodynamic(action) properties. </li></ul>
  11. 11. Scientific Problem and Technical Solution PharmacoMicrobiomics Body site Chemical ID Drug name Assay Drug class Effect (Increase/Decrease) Microbial ID Description Pathway/genes responsible Pubmed ID Classification hierarchy
  12. 12. Methodologies Powered by:
  13. 13. Methodologies: Database Diagram
  14. 14. Demo
  15. 15. Delivered Functionalities <ul><li>User module </li></ul><ul><li>Admin backend </li></ul><ul><li>Search engine </li></ul>
  16. 16. Future Work <ul><li>Deploment on Server (http://www.pharmacomicrobiomics.com) </li></ul><ul><li>Advanced search </li></ul><ul><li>Use of BioPython libraries to retrieve data from NCBI public database. </li></ul><ul><li>Deployment on Ubuntu Enterprise Cloud. </li></ul><ul><li>Integration with a content management system. </li></ul><ul><li>Annual update of data by designing a Perl script to parse MeSH tree of keywords binary files. </li></ul><ul><li>Addition of Chemical and pharmacological classification hierarchy (inclusion of >10 tables). </li></ul>
  17. 17. Acknowledgement <ul><li>I thank </li></ul><ul><li>Eng. Sherine Bahader, Head of OST Dept </li></ul><ul><li>Eng. Moataz Ahmed, TA at OST Dept </li></ul><ul><li>Eng. Ahmed Abdel-Khaleeq, E-Business Dept </li></ul><ul><li>Eng. Hany Safwat, Head of SD Dept </li></ul><ul><li>I thank ITI for giving me all the tools and knowledge necessary to solve my scientific problems. </li></ul>
  18. 18. Thank you

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