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)