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.

Advertisement