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“PharmacoMicrobiomics Database: The Drug-Microbiome Database”An educational web portal to explore the effects of human microbiome on drugsMariam ReyadRizkallahOpen Source Technologies Department, Information Technology Institute, EgyptSupervisors: Eng. Sherine M. Bahader, and Eng. Moataz Ahmed Results Modules: Registration module: Users handling, groups, and authentication/authorization. Database manipulation module: data entry backend provided by Django, and database views and search. Functionalities: Admin Utility: Users handling (Provided by Django) Database manipulation Search by drug class, publication ID, drug name, drug ID…etc. Project Aim The PharmacoMicrobiomics web portal is an initiative (http://pharmacomicrobiomics.org) launched by Dr. Ramy Aziz, PhD, Lecturer at Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University as a research-based educational web platform to explore how resident microbes change the behavior of drugs. The project aims to introduce bioinformatics and microbial genomics to pharmacy students while benefiting the research community. The project is expected to 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.  PharmacoMicrobiomics or How Bugs Modulate Drugs: An educational initiative to explore the effects of human microbiome on drugs”, Ramy K. Aziz, Rama Saad, Mariam Rizkallah. (Submitted to be published in Biomed Central Bioinformatics. Poster presented by the first author in the UT-ORNL-KBRIN 10th Bioinformatics Summit, March 2011, Tennessee, USA.) Methods Project Phases: Literature mining extraction of known microbe-drug interactions. Data collection and classification according to drug class, microbial family and body site. Creation of a relational database using MySQL Database management system and managed through Django, a secure python-based framework that implements MVC design pattern. PharmacoMicrobiomics examples: http://pharmacomicrobiomics.org/examples.html Drug-Microbiome Relational Database Directions for Future Research
On-site connection with NCBI public databases via BioPython Libraries
Annual update of data by designing a Perl script to parse MeSH tree of keywords binary files.
Addition of Chemical and pharmacological classification hierarchy (inclusion of >10 tables).
Integration of a template for a better design of the website in the production phase.
Setup of a private cloud using Ubuntu Enterprise Cloud operating system.
Background The Human Genome Project (HGP) - 2001: Sequencing all human genes to:
Know how different we are!
Predict susceptibility to diseases (e.g., heart disease and cancer)
Know if there is a certain population that is protected by its genes against certain diseases.
Use the information in tailoring medicine for patients based on their genetic profiles.
We are 99% alike!
Number of genes is much less than expected (20,000)
Pharmacogenomics: Study of the effect of all human genes on drugs fate and action . The Human Microbiome Project (HMP) - 2005:
“The combined genomes of the human-associated microbes.”
Microbes freely live inside/on the surface of humans as their favorite place to live.
A human body contains1014microbial cells vs. 1013 human cells.
Effective microbiome genes exceed effective human genes in number.
Human-Microbiota Relationship: It's Complicated! Beneficial: -Protective (e.g., against intruders) -Productive (e.g., vitamins production) -Digestive (e.g., food breakdown) Harmful: -Imbalance (e.g., diarrhea) -Invasion (e.g., fungal infection) -Become virulent Conclusion During the project phase of the 9-Month Diploma, we have been able to design, implement and test PharmacoMicrobiomics database, using open source database management system MySQL and Django python-based framework. PharmacoMicrobiomics is an ongoing project initiated and supervised by Dr. Ramy Aziz, Faculty of Pharmacy, Cairo University, that will be extended towards building an educational web portal that introduces bioinformatics to undergraduate pharmacy student. Science, 16 FEBRUARY 2001 VOL 291, ISSUE 5507 Figure1: Schematic representation of database sources of data Acknowledgement I thank, from ITI, Eng. Ahmed AbdelKhaleq for helpful database design tips, Eng. Moataz Ahmed for help with Django and BioPython implementation, and Eng. HanySafwat for guidance through UML documentation and design.I thank Eng, Ahmed Abdel-Aliemfor Django models implementation advice. I thank from AUC Teaching Assist. Rama Saad, and from FOPCU Teaching Assist.. RadwaSharaffor data entry and testing. HMP website: http://commonfund.nih.gov/hmp/ Figure2: Relational diagram generated by PHP-MyAdmin Utility. Powered by: