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Mariam Reyad (OST) - PharMu Portal - June 2011
PharMu PortalBugs vs Drugs Database
Graduation Project By:Mariam Reyad Rizkallah
Open Source Technologies DepartmentInformation Technology Institute
Intake 31
Mariam Reyad (OST) - PharMu Portal - June 2011
Presentation Outline
Introduction Scientific Problem and Technical Solution PharMu Aim Project Scope Methodologies Results: Delivered Features Demo Future Work Acknowledgement
Mariam Reyad (OST) - PharMu Portal - June 2011
Introduction: EgyBio Network
Mariam Reyad (OST) - PharMu Portal - June 2011
Introduction: HGP (2001)Human Genome Project:- To know how different we are!
- To assess how similar 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. Source: Science, 16 FEBRUARY
2001VOL 291, ISSUE 5507, PAGES 1145-1434
Result: Humans are 99% alike!
Mariam Reyad (OST) - PharMu Portal - June 2011
Introduction: HMP (2005)
Human Microbiome Project:
- It's gotta be the microbes!!
Human cells 10^13 vs. microbial cells 10^14.
“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/
Mariam Reyad (OST) - PharMu Portal - June 2011
Introduction: Bugs vs DrugsHuman-Microbiota Relationship:
It's complicated! Beneficial:
-Protective (against intruders)
-Productive (vitamins)
-Digestive (breakdown food) Harmful:
-Imbalance (diarrhea)
-Invasion
-Become virulent
Mariam Reyad (OST) - PharMu Portal - June 2011
Introduction: Bugs vs Drugs
Drug-Microbiome Relationship
Mariam Reyad (OST) - PharMu Portal - June 2011
PharMu Aim
Explore how resident microbes change the behavior of drugs.
Introduce bioinformatics and microbial genomics to pharmacy students while benefiting the research community.
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.
Mariam Reyad (OST) - PharMu Portal - June 2011
Scientific Problem and Technical Solution
Mariam Reyad (OST) - PharMu Portal - June 2011
PharMu Phases
Step1: mining existing literature and extracting all known microbe-drug interactions.
Step2: manual curation of the extracted literature data(Pubmed) and their classification by drug classes (PubChem), microbial families (Taxonomy), and body systems (HMP).
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.
Mariam Reyad (OST) - PharMu Portal - June 2011
PharmacoMicrobiomics
Body site
Chemical ID
Drug name
Assay
Drug class
Effect (Increase/Decrease)
Microbial ID
Description
Pathway/genes responsiblePubmed ID
Classificationhierarchy
Scientific Problem and Technical Solution
Mariam Reyad (OST) - PharMu Portal - June 2011
Methodologies
Powered by:
Mariam Reyad (OST) - PharMu Portal - June 2011
Methodologies: Database Diagram
Mariam Reyad (OST) - PharMu Portal - June 2011
Delivered Functionalities
User module Admin backend Search engine
Mariam Reyad (OST) - PharMu Portal - June 2011
Future Work
Deploment on Server (http://www.pharmacomicrobiomics.com)
Advanced search Use of BioPython libraries to retrieve data from NCBI
public database. Deployment on Ubuntu Enterprise Cloud. Integration with a content management system. 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).
Mariam Reyad (OST) - PharMu Portal - June 2011
Acknowledgement
I thank
Eng. Sherine Bahader, Head of OST Dept
Eng. Moataz Ahmed, TA at OST Dept
Eng. Ahmed Abdel-Khaleeq, E-Business Dept
Eng. Hany Safwat, Head of SD Dept
I thank ITI for giving me all the tools and knowledge necessary to solve my scientific problems.
Mariam Reyad (OST) - PharMu Portal - June 2011
Thank you