How good is Wikipedia's coverage of chemical compounds?

Wikipedia has an excellent coverage of chemical compounds, featuring above 20000 articles whose names match those PubChem compounds. After finding a few important chemicals not featured in Wikipedia, I wanted to quantify the coverage of Wikipedia and point out the gaps that should be filled.

I wondered how much coverage Wikipedia actually has for "important" chemicals. Here, I define importance as "number of hits in PubMed", since that is a thing that I can easily measure (and, in fact, already determined as part of working on STITCH and Reflect).

Missing chemicals
For each bin of 100 chemicals, the number of PubMed hits for all synonyms of this chemical is plotted against the fraction of the chemicals that have a Wikipedia article for any of the synonyms. (I exclude three-letter names as they are often ambiguous.) So, for compounds that occur more than 1000 times in PubMed, Wikipedia's coverage is above 80%. Here is the list of articles that should be added.

So, if you know something about one of the missing compounds, go right ahead and create an article! :)

Missing synonyms
The second question is if Wikipedia is missing important redirects, i.e. if there are widely-used names for chemicals that don't occur in Wikipedia even though an article exists for the chemical itself (just under another name). For very common names, the coverage is slightly lower, however, the abstracts in PubMed often contain chemical notation that people probably won't use when searching Wikipedia, e.g. "Ca(2+)" is the top hit on the list of redirects that could be added.

Announcing SIDER: a database of side effects

After using side effects to predict drug targets, we now created a public database of side effects with a total of 62269 side effects for 888 drugs. The database was created by doing text-mining on labels from various different public sources like the FDA. Furthermore, I developed rules to extract frequency information from the labels, this worked for about one third of the drug–side effect pairs.

We think that this database will make quite a bit of interesting research possible.

Negative controls and the police

Oh wow. In the last few years, the German police hunted a woman they only know from her DNA, which had been found at over 40 crime locations all over Germany and Austria (including the murder of a police officer in Heilbronn). Now, they slowly come to the conclusion that a charge of DNA collecting equipment got contaminated by a female employee... Running negative controls would have been really useful, no? (German source: stern.de, via: lawblog.de)

A little hack: "mark as read" for FriendFeed

FriendFeed is missing one important thing: the ability mark posts that didn't change since you last saw them as "read." Ideally, new posts or posts with new comments should be visually different from those that are unchanged.


I created a bookmarklet that lets you put a visual indicator of your last visit to FriendFeed into the stream of posts. (You should click the bookmarklet when you begin reading, because during reading you won't see posts that are posted while you read. New and updated posts will percolate to the top, and appear on top of the marker.) It works by using the FriendFeed API to create a post to a special room. As this is a hack, you'll have to adapt the bookmarklet.

Steps:

1. create a (private) room, e.g. USER-read
2. drag this link to your button bar: FFread (RSS readers might mangle this)
   
3. adapt the bookmarklet, substituting USER for your username (2x) and KEY for your remote key (1x)
   
4. go to FriendFeed and test it
5. optional: see how often you are visiting FriendFeed and calculate how much time you wasted :-)

Update: This worked in Firefox 3.0. I updated to the Firefox 3.1 / 3.5 beta, and it doesn't work anymore. :-/

Keine Experimente!

Lange habe ich diese Idee mit mir herumgetragen, jetzt habe ich sie dank Deutschem Historischen Museum und Vector Magic in die Tat umgesetzt. Den Vektorisierungs-Look finde ich sogar ziemlich passend.

Sollte der Witz unverstanden bleiben, hier die Auflösung. Andernfalls das ganze als PDF, zum Ausdrucken oder Editierien (statt Bioinformatik kann man ja auch Theoretische Physik favorisieren).

A seminar on Makefiles!

This blog, my tumblelog, and my Twitter stream are littered with examples of my use of Makefiles. So I was very happy to find this blog post about a whole seminar on Makefiles on FriendFeed. Go and check it out, I learned something new!

Want: Auto-adjust laptop fan speed with motion sensor

Someone should really integrate Fan Control with the MacBook's motion sensor. If the computer didn't move for a long time: It's sitting on a desk, so it can run hotter, but be silent. If the computer is being moved around: I have it on my lap, so turn the fan up and keep the case cool.