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Chemistry databases become much more interesting when combined with other kinds of data. Today's stop our continuing tour free chemistry databases and Web services is another case in point. STITCH allows you to visualize and explore relationships between small molecules and biomolecules. From the about page:

STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.

STITCH contains interactions for over 68,000 chemicals and over 1.5 million proteins in 373 species.

STITCH treats the interactions between small molecules and biomolecules as a network that can be interactively explored. Each biological or chemical entity is a hub that's connected to other entities through some form of evidence.

For example, let's say we'd like to learn something about the enzyme Fatty Acid Amide Hydrolase (FAAH). We'd start by typing a term "fatty acid amide hydrolase" into the field marked "name" in the top left of the screen. Pressing "go" takes us to screen in which we can select from a number of species. Keeping the selection on Homo sapiens and pressing "continue" takes us to a screen in which the centerpiece is an interactive biological-chemical network.

We can see from this network that the FAAH enzyme (in red) is related to a number of other biomolecules and small molecules. For example, we might want to get a closer look at one of FAAH's endogenous substrates, anandamide (AEA). Clicking the shape labelled "AEA" activate the pop-up from which one option is to re-center the network around this small molecule. Selecting our species interest (Homo sapiens) takes two another network view with a anandamide in the center. We can now see that anandamide interacts with a number of other biomolecules. We can continue exploring this way until we found everything were looking for.

We might be interested in knowing why it is that anandamide is associated with the 5-HT7 receptor. We can answer this question by hovering over the line connecting the two entities a clicking. This takes us to a page summarizing the evidence for a functional link. In this case the evidence consists of several simultaneous mentions in a PubMed abstracts (which is rated low by the system). We can find out what these abstracts are by clicking on the "show" button.

I found some minor problems with STITCH. For example, it was difficult to get to the evidence view because detection of a mouse hover over an evidence line was quite sensitive. Performing a substructure search was not as intuitive as it could be because I was also asked to select a species in addition to providing a SMILES string. Finally, the structure for anandamide given by STITCH was way off:

There's much more to STITCH than what's been covered here but this brief introduction gives you a feel for what's possible. For anyone interested in small molecules and how they interact with biomolecules STITCH is one of the better resources I've come across.

Kudos

• Interactive, engaging representation of complex data set.
• Step-by-step, interactive mini tutorial.
• Keep updated on new developments through STRING/STITCH blog.
• Assertions can easily be corroborated through the primary literature.

Ideas for Improvement

• Improve the usability of structure search by not requiring a species to be selected and by providing a chemical structure editor.
• Implement a convenient process for correcting errors such as the error in the structure of anandamide.

Chemistry databases have a way of building on top of one another to reveal new insights. In today's installment of our continuing series on free chemistry databases and Web services, we take a look at Side Effect Resource (SIDER).

SIDER is organized around the side-effects observed with marketed drugs, as determined primarily by product inserts. Relationships between drugs and side effects can be explored by browsing by the names of side effect or drugs. Text-based searching for either side effects or drug names is also possible.

Finding connections between side effects and drugs is especially easy due to the way these relationships are hyperlinked. For example, the entry for Gabapentin lists all known side effects of the drug, each of which are hyperlinked to a page dedicated to that side effect. Clicking on Ataxia, for example, I'm taken to a page that shows me that this side effect is shared by dozens of other drugs, one of which is Risperidone. Going back to Gabapentin, we can click within the colored data presentation to find the exact primary reference being cited. Simply beautiful.

A very interesting feature of SIDER is the visual presentation of side effect profiles. Again referring to the entry for Gabapentin, we see a color-coded map of the side effect profile that concisely summarizes a wealth of human clinical data.

SIDER has many applications, one of the most interesting of which is the prediction of drug-target correlations for non-analogous chemical structures. For those with an interest in data mining, SIDER's underlying dataset is freely downloadable under various forms of Creative Commons licenses.

One of the most interesting things about SIDER is how it was created: completely from information available to the public. One of those sources is the STITCH database, which maps interactions of small molecules and proteins. It should come as no surprise that STITCH itself uses PubChem. In other words, SIDER relies indirectly on PubChem for mapping drug label information onto chemical structure.

For those looking for information on side effects of marketed drugs, or ways to use that phenotypic information to discover new relationships, SIDER is an excellent resource.

Kudos

• Streamlined, elegant design.
• Color-coded information summary.
• Primary sources included for some data.
• Data freely downloadable.
• Global statistics and search interface on home page.

Ideas for Improvement

• More prominent display of chemical structures - side effect summary pages like this one are a good example of where this would be very helpful to medicinal chemists.
• Hyperlink to source of primary information.
• Add the name of side effects and drugs to URLs for better search engine discoverability.
• Feeds for new drug or side-effect entries.