Zusammen

Spectroscopy databases are useful in a number of situations - from tracking down impurities to identifying unknowns. Although we've previously covered other spectra databases, today's stop on our continuing tour of free chemistry databases an Web services offers something different still. Spectra Online hosts a diverse collection of spectral data of various types. From the about page:

Spectra Online is a FREE web-based spectral database service for the chemical research community. The spectra in the database are comprised of collections of public domain and other data generously submitted by various institutions and individuals. The database spans many different classes of compounds including drugs, common chemicals, polymers, petroleum products among others. It includes spectral data from many different instrument types such as FT-IR, UV-Vis, NIR, Raman, MS, NMR (13C, 1H and others), XRD and more. Please note that Thermo Electron Corporation does not review the data in the collections; all spectra and related compound information are presented "as-is" in the form they we received.

You'll need to create a free account before viewing any of the spectra on Spectra Online. I found the process to be relatively painless.

Spectra Online's dataset consists mainly of mass- and FT-IR spectra and associated structural data. Spectra have been assembled from a variety of free and proprietary sources. Records can be searched by compound name, CAS Number, molecular formula, and by molecular weight.

A potentially very useful way to search Spectra Online is through a spectrum match. By uploading your own spectrum, it's possible to perform a match based on a variety of criteria such as correlation and Euclidean distance. With such a large assortment of searching methods, an brief explanation of each would be helfpul. When browsing the search results, both the search spectrum and the target spectrum are shown with overlapping x-axes, making identification straightforward.

One thing to be aware of: at various times in my testing, the service seemed to malfunction during queries, giving repeated error messages. Each instance was resolved within a few hours.

Spectra Online hosts many spectra that may be of use. If you're ever looking for match to a chemical unknown, or trying to track down an impurity in your sample, Spectra Online makes a good resource.

Kudos

• Large collection of spectra viewable in graphical format online.
• Spectra referenced to original source collection.

Ideas for Improvement

• Add structure search.
• Enable spectra and structure browsing.
• Promote offline use by offering spectra in JCAMP-DX format.
• Encourage use by eliminating login requirement for viewing spectra.

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.

One of the things chemistry is known for is creating very long names. Acronyms offer a solution, but sometimes at the expense of clarity. Today stop on our continuing tour of free chemistry databases and Web services takes us to Acronyms, a service focused on answering one simple question: what does this chemical abbreviation stand for?

From the about page:

This list of common acronyms contains more than 800 acronyms of chemical substances or fragments which have been collected from about 100 chemical journals. In view of the thousands of acronyms devised by authors in the chemical literature, this list is certainly not comprehensive, but it is useful for the identification of the more common abbreviations.

Acronyms is organized around the association between a chemical acronym and a chemical substance, structure fragment, or process. The service can be used either through a search interface in which the acronym (or an acronym fragment) is entered, or through alphabetically arranged index in which acronyms can be browsed by starting letter.

I found the service extremely easy to use and was able to locate many chemical acronym I've come to know and love, including such favorites as BARF, BINAP, AIBN, THF, TMEDA, and DABCO.

One area in which Acronyms does not seem to perform well is with locating the numerous phosphine ligands developed in the last few decades. For example I was unable to find DuPHOS, DPPF, or DIOP. It turned out that the latter was located with a substring search.

If an acronym you're looking for doesn't appear in their search results, a feedback form offers the opportunity to suggest it be added.

Acronyms, offered by publisher FIZ CHEMIE Berlin, is yet another good example of how good scientific marketing can actually be useful. The next time you find yourself drawing a blank when encountering a cryptic four letter abbreviation in chemistry, consider using Acronyms.

Kudos

• Simple, focused interface for searching and browsing.
• Large collection of useful acronyms.

Ideas for Improvement

• Make it easier to submit a new acronym through a dedicated form rather than a general-purpose e-mail contact form.
• Implement auto complete for the search field.
• Use substring searching by default (so, for example, 'DIOP' will return a usable result). Rank direct hits at the top and substring matches below.
• Link results to external sources such as PubChem, Wikipedia, eMolecules, or ChemSpider.
• Make it easy to bookmark, share, and link to acronyms by giving each acronym a dedicated page.

Of all the forms of data generated by chemists today, one of the most important consists of NMR spectra. Our continuing series on free chemistry databases and Web services has previously reviewed Spectral Database of Organic Compounds, nmrdb.org, and mylims.org, three services oriented toward the management of NMR spectral data. Today we'll take a look at NMRShiftDB which approaches the problem from a different perspective. From the about page:

NMRShiftDB is a NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. Last [but] not least, it features peer-reviewed submission of datasets by its users. The NMRShiftDB software is open source, the data is published under an open content license. ...

NMRShiftDB is organized around the concept of one or more NMR spectra associated with a chemical structure. Each entry lists a chemical structure and the chemical shifts for each spectrum associated with it. Clicking on the "additional data" tab lists general information such as chemical formula and molecular weight in addition to the conditions under which spectrum was recorded. Some entries even contain a reference to the primary literature from which the spectrum was drawn. Each spectrum can be exported in a variety of formats including PNG and SVG for use in reports and other documents.

An innovative and useful feature is the way chemical structures and spectral data are interactively linked. For example, hovering over an atom in a structure not only highlights the peak listing, but also highlights the peak in a graphical representation below it.

What sets NMRShiftDB apart from most public-facing chemistry databases is the way it solicits and incorporates contributions from the scientific community. For example the home page lists the top 20 contributors by name and the number of contributions each is made. All that's needed to begin contributing (and reviewing) is to create a free account.

A particularly interesting feature of NMRShiftDB is the "wish list" tab, through which users can submit structures and the kind of spectrum they're looking for - anonymously if they wish. Although it doesn't look like this feature gets much use, given the right adjustments it has great potential to bring together those seeking NMR spectral information with those who have it.

Although the community-driven approach used by NMRShiftDB sets apart from most other services reviewed here, there's much more that could be done. For example, the home page lists contributors names and numbers of contributions; this could be hyperlinked to enable visitors to see all contributions made by a particular user. Additionally, each spectrum submission could have a link to the user who contributed it. Each of these features could provide anonymity for users desiring it at the time of submission is made.

I ran into several technical difficulties when using the NMRShiftDB site. For example, when logged in, clicking on one of the latest additions links on the right-hand sidebar returned me to the home page rather than directing me to the entry for that structure. However, this feature did work work when I was logged out. I also found it difficult to discover how to perform a structure search. The trick, it appears, is to click the small circular icon with the "J" in the center from the search page under the search by structure heading. Be prepared to wait though; after almost 2 1/2 minutes of apparent inactivity, a structure editor appeared.

There's a great deal more to NMRShiftDB than what's been reviewed here. If you're at all involved in creating or using NMR data, NMRShiftDB is an excellent resource.

Kudos

• Community-driven NMR data collection and aggregation.
• Interactively linked chemical structures and spectral data.
• Free multi-nucleus NMR prediction (not reviewed here).

Ideas for Improvement

• Hyperlink contributions and contributors in Hall of Fame and spectral record detail.
• Make sure all features work when using site as both guest and user.
• Increase the usability of structure search by decreasing download time for structure editor.
• Enable structures, spectra, and users to be browsed.
• Create a separate page for each structure, each spectrum, and each user so that these items can be bookmarked, shared and discussed.
• Improve usability of bookmarks by removing session ID from URIs.

Chemistry databases take a wide variety of forms and serve a variety of purposes. A case in point is ChemWiki, today's stop on our continuing tour of free chemistry databases and Web services. ChemWiki is an attempt to create a free chemistry textbook using a model similar to Wikipedia. From the about page:

The ChemWiki project is a new approach toward chemistry education where an Open Access textbook environment is constantly being written and re-written partly by students and partly by faculty members resulting in a free Chemistry textbook to supplement or supplant conventional paper-based books. Anyone can view, although a freely available account is required to edit the site modules. The UCD ChemWiki was created and is currently directed by Prof. Delmar Larsen in the Chemistry department at UC Davis.

ChemWiki actually consists of two related efforts: The Core (the textbook itself) and WikiTexts (course-related materials). This review will only cover The Core.

The ChemWiki Core is comprised of a collection of pages organized around a chemistry sub topic: Analytical; Inorganic; Physical; Computational; Organic; and Biological.

Within each subcategory can be found a number of pages relating to special topics. For example, under organic chemistry is a chirality module. Under the three headings Introduction, Optical Activity, Circular Dichroism, and References can be found basic information relating to the subject.

After signing up for a free account, anyone can edit the contents of the ChemWiki page. After making several changes, it's possible to find them all again using the "Contributions" item under the "Tools" menu. Each user's contributions can be monitored by subscribing to their public RSS feed. In this way multiple authors collaborating on the same document can continuously monitor changes to it.

Before writing off ChemWiki as something that can't possibly work in practice, consider how Wikipedia was viewed when initially launched. Creating a textbook in a technical subject such as chemistry and creating a general-purpose encyclopedia may not both be equally suited to the Wikipedia model - only time will tell. One thing is clear: the economic model on which the current system of textbook publication is based may not remain viable for much longer. ChemWiki offers an intriguing alternative.

Kudos

• Collaborative effort to address a significant educational problem.
• RSS updates at the level of user and page.
• In-page editing using with rich text editor - not Wiki markup.

Ideas for Improvement

• Clearly-stated guidelines for style including text and graphics.
• Implement a user reputation system.
• Focus on getting one topic page into a form suitable for classroom use, then offer it as a model for the rest of the book.