One year!

It is now one year since the PharmacoMicrobiomics Portal was officially launched. We feel like providing a sort-of-informal progress report.

First of all, we are really happy and proud that the portal is still up and running. The initiative started with a few dedicated undergraduate students, but soon after they all graduated and started on their own career paths. At this moment, the PI is on long-term travel, following up the project remotely. The main players have joined graduate school (in four different universities spanning three continents: MRR at the American University in Cairo; RSA in USA; RRS in Germany; and SG at Cairo University in Egypt). This is partly why we are thankful that the website is not just running, but also—slowly but surely—growing.


It is always hard to properly measure progress, notably in the case of a project run by volunteers; however, we can look at a few criteria that are often used to evaluate web portals.

1) Stability:
Since its launch, PharmacoMicrobiomics has been up and running without any interruption, of course except for server down times, which we cannot fully control; yet, we have been running with two different domain names and located on two different servers (although one redirects to another).

2) Utility/ Access statistics:
The purpose of a public database is simply to be used by the community and to reach all users who might benefit from it. This is one of the hardest goals of all databases. It requires publication, promotion, advertisement, and lot of travel. Unfortunately, most of the above is not available to us at the moment; however, we published about the database (initially as a paragraph within an abstract then as a full article) and we attempt to spread the news via a Twitter and a Mendeley profile. Again the purpose is to get those interested into using the database, and we cannot really know this until we’re “officially cited”; however, from the access statistics we can see some positive patterns (nothing like the giant databases of course). Having filtered out our own computers/IPs, we estimate the users of the account to be ~600 unique visits in the first year (since officially launched on 11/11/11), with 77 returning users. This is very modest of course, but given that a few laboratories are interested in drug-microbiome interactions, and from manually checking the access data we see that we are often visited by top laboratories & companies in the US and UK (e.g., Harvard, Glaxo, Cambridge, NIH in Maryland, Pfizer, see below). This is not a bad pattern of course.

3) Data growth:
Another sign of progress is the growth of the submitted data. So far, we have not started crowdsourcing data submission yet, and we count on our 4-5 curators. During the past year, we started with about ten records at the time of launch. Today, we’re almost at 70 records. That is great progress given the scarcity and sparsity of data in literature.

In conclusion, we find the signs of progress in the first year promising. The coming challenges are on three axes:
1) Adding data (the more we have the harder we can add; but as the Human Microbiome Project is booming, we have to expect loads of publications in the next 2-3 years).
2) Adding functionality (microbiome mining tools, connecting the current data to enzyme and pathway databases, etc.)
3) Adding users and soliciting crowdsourcing & crowdfunding.

Let’s hope for the best. Please let us know how we can do better and how you can help.

Posted in Uncategorized | 1 Comment

PharmacoMicrobiomics Web Portal (what we believe is) Release 1.0.

Today, what we believe is Release 1.0 of the PharmacoMicrobiomics web portal is done, on 11/11/11 as scheduled. What a relief!

We just released a test-version of this site on Nov 1, and it looked as if it were near complete; but, under the hood, there were many problems. There were many URL issues; the domain name wasn’t properly set; curators were practically unable to add or modify data records; the data were missing major information.

Now, there are enough entries for users to test, and most of the entries are complete (or that’s what we hope).

For example, you can browse the drug-microbe interactions, select one of them and see some natural language interpretation of the effect of microbes on drugs, e.g.,

Summary Gut microbes (species: Eggerthella lenta) decrease digoxin‘s metabolic processing.

[Here all you see in red is retrieved from the database].

In many instances, where the actual microbes are unknown (e.g., gut microbiota’s effects on baicalin, you see an adapted text–see below).

Summary Gut microbes (currently unknown members) increase baicalin‘s hydrolysis.

We think this is quite an achievement for the non-experts, although it might look trivial to many. But those of you who have skimmed through drug interaction databases know that such trivial options are not always available.

We’re enthusiastic about this release but know that we need to manually curate dozens of articles to get a good feel for the available data and explore their potential applications. We also look for more serious features in the next release, such as adding reactions, linking them to genes and pathways, and perhaps in the future trying to predict similar interactions.

At this point, we hope you can find the data useful. You can still browse the old Google Docs, notably the information-rich literature table and some of the old examples. This release also includes a literature feed that retrieves the latest related entries from PubMed. It is not a very fancy one and we’re looking for a major improvement that allows us to keep all the entries and to be able to add them to our publications database with one click.

As always, we welcome feedback, reports about bugs and broken links, and suggestions for future development.

Posted in Announcements, Development | 2 Comments

The PharmacoMicrobiomics Database is now live!

Today marks the first major upgrade of the PharmacoMicrobiomics web portal since its launch about 15 months ago.

It is a major upgrade because we finally have a functional relational database to replace the old GoogleDoc spreadsheet tables, thanks to the amazing efforts of the pharmacy-graduate-who-also-became-an-IT-expert in less than a year, Mariam Rizkallah, who is also a co-author of this blog.

Please check the new site; play with the database; make suggestions; do everything possible to break it and report it to us so we can have a good stable release by 11/11/11 (our fancy deadline for the first release).

Yes, the database is missing a major thing: data! Hmmm. I mean we just uploaded a few examples now to test the system, but more examples are expected to be uploaded soon… very soon!

Posted in Announcements | Tagged , , | 2 Comments

Graduation Ceremony Poster Session!

I get this call from my supervisor at ITI telling me that I have to prepare a poster about my project to be presented in the graduation ceremony. She did encourage me to break the ice and start typing.

I did it! I acknowledged many supporters. I thank them all, along with my colleagues, for helping me out.

Posted in Publications or Presentations | Tagged , , | Leave a comment

BioPython Me!

“I am quite concerned about the API [NCBI’s EUtils] that you’re planning to use! I think we should give it a try before start working on the database and the interface! Give me the URL! ‘Pypi’s EUtils‘?” Those words were from my supervisor at ITI as you might have guessed!

We started EUtils in python setup, tried the example in the README file, a very sticky error faced us, “File “/usr/local/lib/python2.6/dist-packages/EUtils/”, line 25, in _load_module mod = __import__(name) ImportError: No module named DTDs.pubmed_020114″.

>>> from EUtils import DBIdsClient
>>> import EUtils
>>> from EUtils import DBIdsClient #repeated line
>>> import EUtils #repeated line
>>> dbids = EUtils.DBIds("pubmed", ["9390282"])
>>> pom = DBIdsClient.from_dbids(dbids).fetch() #efetch() is the correction
>>> print pom #print is the correction

My supervisor refused to give up and gave it a shot by using efetch() and printing pom, and a logical error hit us “<addinfourl at 142981388 whose fp = <socket._fileobject object at 0x8827f2c>>”!

After that, I tried to summarize the “central dogma” to him, and to a colleague “Imagine a class “rhodopsin”, you can say: new rhodopsin() in eye or just don’t create new instance in the heart!”. Then, we decided to install BioPython, happiest moment in my day! I would like to say that Biopython is not just an API for NCBI databases.. it’s way more than that.


We downloaded Biopython-1.57 source code and ran our first test before even reading the documentation! It’s amazing! You can connect to NCBI databases anytime, anyquery, to grab data using ID or keywords and insert it into our database. You may want to install BioSql (to create database for biological data with different DBMS) and have to install NumPy packages.

My script (compiled form the tutorial):

#!/usr/bin/python #magic line suggested by my supervisor
from Bio import Entrez = '' #one reason to write script was to avoid writing email each time I run something
#handle = Entrez.esearch(db="pubmed", term="biopython")
#record =
#print record["IdList"]
handle = Entrez.einfo(db="pubmed")
record =
#print record["DbInfo"].keys()
##Returns: [u'Count', u'LastUpdate', u'MenuName', u'Description', u'LinkList', u'FieldList', u'DbName']
for field in record["DbInfo"]["FieldList"]:
	print "%(Name)s, %(FullName)s, %(Description)s" % field

Further readings:

-Biopython: freely available Python tools for computational molecular biology and bioinformatics [PMID: 19304878]:

Posted in Bioinformatics, Development | Tagged , , , , , , , , | Leave a comment

Pharmacomicrobiomics for Engineers!

As we start the IT-based phase of the project Pharmacomicrobiomics, I decided to make this slideshow to market the project to my supervisors at the Information Technology Institute, and –honestly– to organize my ideas to create an action plan for the project. I have to say that the poster that Dr. Ramy Aziz has presented in UT-ORNL-KBRIN Bioinformatics Summit 2011 did help big time.

Actually, my supervisor loved it and he found it beneficial to scientific community.

Posted in Development | Tagged , , | Leave a comment

How bugs modulate acetaminophen’s metabolism and toxicity?

From Microbe World: Metabolomics and the Microbiome (MWV45)

An interview with Dr. Jeremy Nicholson, Head of the Department of Surgery & Cancer at Imperial College London by Dr. Stanley Maloy, Dean, College of Sciences, SDSU

Posted in Pharmacokinetics | Tagged , , , | Leave a comment