mrr 05152011 pmdb_proposal
TRANSCRIPT
Pharmacomicrobiomics: The Drug-microbiome
Database!
Mariam RizkallahOpen Source Technologies Department,Information Technology Institute, Egypt
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.
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
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/
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/
PMDB: The Birth of a Novel Discipline
HGPPharmacogenetics
&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
The Database
Source: UT-ORNL-KBRIN Bioinformatics Summit 2011 http://citg.uthsc.edu/summit_11
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.)
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)