Depth-First: Tag chempedia

SciFinder Web, Greasemonkey, and REST: Embracing Divergence in Chemical Information Systems

Rich Apodaca — Wed, 19 Nov 2008 17:41:00 +0000

Recently, Alain Borel posted a message to the CHMINF-L list describing his successful attempt to get links to external datasources to show up in SciFinder Web:

I'm dreaming of a world where chemical data is hyperlinked as thoroughly as text data is today (or even more)... here's my small contribution to this goal.

...

Basically, Greasemonkey allows you to rewrite the HTML content of a web page before it is rendered in the browser window. Thanks to this, I've been able to write a script that adds links to external databases through registry numbers. Currently, ChemSpider, Chempedia and Chemexper [links added] are supported - I also have a private version that links to our Intranet chemical stocks application. The pleasant side for those who worry about intellectual property is that neither side of the link needs to know what's on the other side, and even the plugin doesn't know what's inside the database records.

Greasemonkey is the client-side script plugin engine that enables users to change the appearance and content of any site. Although originally designed as a Firefox extension, as least some Greasemonkey scripts can be run in Safari and Chrome. A recent paper describes some of the potential for this form of scripting in the life sciences.

Alain's script, which can be freely downloaded, uses CAS numbers to link SciFinder records to the external databases. Although I don't have access to SciFinder Web, Alain's description makes it sound like each entry for a specific substance in SciFinder Web is given an additional set of links out to external datasources.

What's REST Got To Do With It?

One of Alain's external datasources is Chempedia. A unique feature of Chempedia is the way it exposes a an electronic paper trail for CAS numbers. Rather than just reporting a CAS registry number, it fully discloses which organization is asserting that a particular CAS number belongs with a structure.

For example, see this entry on [525-66-6].

Chempedia was designed from the start to apply the principles of REST. The big idea behind REST is that every resource on the Web, such as a CAS number, can be manipulated by exactly four methods: GET; PUT; POST; and DELETE.

The highly-desirable side-effect of designing Web sites around the concept of resources being acted on by exactly four methods is that sites applying this philosophy become orders of magnitude easier to mash up.

Alain's Greasemonkey script is an example of a client-side mashup. But how did he do it?

CAS Numbers are First-Class Citizens

Each CAS number on Chempedia is a resource that can be accessed by a URL taking the form:

http://chempedia.com/registry_numbers/REGISTRY_NUMBER

where REGISTRY_NUMBER is the CAS number of interest. For example, acetaminophen has the registry number [103-90-2] and it can be accessed with this URL:

http://chempedia.com/registry_numbers/103-90-2

If you request a CAS number that doesn't exist, you should receive a 404 error, although a bug in Chempedia is currently preventing that from happening.

To link SciFinder Web to Chempedia, Alain's user script simply looks for which CAS number the SciFinder page is talking about and constructs the RESTful URL. It doesn't get much simpler than that.

Conclusions

Chemistry is a large, established field. Not surprisingly, specialization is an essential part of being a chemist. It's therefore to be expected that chemical databases will diverge into a variety of specialized forms. One size will almost certainly not fit all.

We can deny this simple fact and build ever more complex and unusable chemical information systems. Or we can accept it and custom-build our services for the job at hand.

RESTful server architectures and mashups offer a powerful way to accomplish this goal.

Image Credit: betenoir

Building Chempedia: Learning About Contributors

Rich Apodaca — Wed, 02 Jul 2008 11:50:00 +0000

Chempedia is a free online chemical encyclopedia similar in concept to the Merck Index, but radically different in implementation. One key difference: the Merck Index is compiled by a small number of paid professionals while Chempedia is compiled by thousands of unpaid volunteers. Although this distinction raises a host of intriguing questions, one of the most basic revolves around what can be said about these volunteers in the aggregate. This article, the first in a series, explores this issue with some statistics compiled from Chempedia.

Learning About Contributors

Chempedia works in part by aggregating content from Wikipedia dealing with single molecular entities, or "Compound Monographs." This content is created by the now famous process of individuals taking upon themselves the responsibility of fixing what's broken in Wikipedia. (Some take it upon themselves to break what's working, but that's another topic.)

Chempedia associates each of its Compound Monographs with the last Wikipedia user to edit it. The current interface to these relationships is available on the Chempedia contributors page.

The interface to this page is currently limited. The analyses reported here were made for the most part by querying the Chempedia database directly.

Each contributor is linked to a contributor summary page containing links to that user's Wikipedia homepage and talk page, as well as a complete listing of all active contributions. For example, you can view the contributor page for one of Chempedia's most active contributors, Arcadian.

The data model is also limited. Because Chempedia only records the last Contributor to edit a Monograph, when another Contributor edits a Monograph, the link between the previous Contributor is lost. As a result, many Contributors have no associated Monographs.

How Many Monographs?

Chempedia currently hosts 6,308 Compound Monographs.

How Many Contributors?

Chempedia currently lists 2,516 Contributors. Of these, 1,046, or 42% are associated with one or more Monographs, meaning that they were the last to edit. The remainder are associated with no Monographs for which they were the last to edit.

Here is a list of the top 20 Contributors and the number of Monographs they were the last to edit:

anonymous	1022
DOI bot	904
Edgar181	378
Fvasconcellos	170
Meodipt	151
Arcadian	144
Chem-awb	133
Chowbok	122
Rifleman 82	114
SmackBot	105
Thijs!bot	99
ChemNerd	85
Puppy8800	80
DumZiBoT	78
Axiosaurus	63
Chempedia	63
Carlo Banez	55
Benjah-bmm27	52
OKBot	51
Cacycle	50

These Contributors represent 1.9% of all active Contributors and collectively are responsible for being the last to edit 62% of all Monographs. Although not performed here, a histogram plotting number of contributions would be expected to follow a power law.

'Anonymous' is an aggregation of all users who edited a Monograph without a Wikipedia account. 16% of all Monographs were last edited by an anonymous user. Leaving out the aggregated 'anonymous' users indicates that roughly half of all Monographs were last edited by the top 19 Contributors.

What is a Contributor?

Although it's difficult to say a lot about individual Contributors, most appear to have some training in science, although that training may not have involved chemistry or biology. Still others (for example, SJP) appear to have been drawn to contribute to a Monograph based on their nonscientific experience with the title compound or in an effort to fight vandalism or otherwise improve the nonscientific content of the Monograph. The ability of services like Wikipedia (and by extension Chempedia) to provide a platform for those without formal training in a particular area to make useful contributions is without question one of its most useful (and controversial) features.

Some Contributors are not even human, but rather robots designed to improve the quality of Wikipedia articles in general. For example, SmackBot performs an array of tedious quality control jobs such as fixing bad checksum ISBNs (CAS Numbers, anyone?) and capitalization errors.

Conclusions

Wikipedia's collaboration model has made the creation of a free and continuously-updated chemical encyclopedia feasible. Applying chemistry-specific user interfaces and data models exposes this hidden treasure. Although it's tempting to think of this process as mainly being the work of a handful of trained scientists, the numbers suggest a much broader base of contributors. Future articles will explore this idea.

The Other Vector Graphics Markup Language

Rich Apodaca — Fri, 06 Jun 2008 14:39:00 +0000

Scalable Vector Graphics (SVG) is a technology that enables the creation and publication of high quality images that can be scaled to any resolution. SVG is ideally suited for the Web, and all major browsers now support it - except Internet Explorer (IE). This poses a problem: vector graphics are by far superior to raster images for many applications, but the lack of native IE support makes SVG a non-starter for most developers. This article discusses a little known IE capability that might provide a solution.

Oh Brother, Where Art Thou?

Way back in 1998 a group of companies including Microsoft submitted a proposal for a vector graphics language called Vector Markup Language (VML) to the W3C. This set in motion a series of events that culminated in the development of what we know today as SVG. But while use of SVG quickly expanded, VML remained almost exclusively limited to Microsoft products.

Soon after, IE 5 introduced the ability to decode and display VML - a capability that exists today in IE 7.

SVG and VML are two vector graphics languages, each designed to do essentially the same thing. For basic shape rendering, their similarities outweigh their differences.

About VML

To understand why VML never caught on, you need look no further than the documentation - or the lack thereof. The original VML submission is a decade old and has not been updated.

For the most part, VML documentation is scattered and incomplete. Nevertheless, there are some useful resources. Here, in no particular order are some of them:

Microsoft Documentation Authoritative, but lacking in examples.
VML, SVG, and Canvas Discusses some of the differences between VML and SVG.
Cum mortuis in lingua mortua Good history of VML.
Examples of the Vector Markup Lanugauge There are far too few of this kind of site.
VectorConverer A PHP library that uses XSLT to interconvert SVG and VML. Unfortunately, the stylesheet didn't work in my hands under Xalan or Ruby/xslt - and I know almost nothing about PHP.
Julie Nabong's Masters Thesis Julie wrote and documented an SVG/VML XSLT for interconverting the two languages.

JSDrawing: Interconverting Vector Languages on the Fly

One VML resource deserves special note - JSDrawing. This library seems to be capable of generating Flash, VML, or SVG from a common vector graphics language precursor. I'm not sure how practical this approach would be, but it does provide some food for thought.

Why It Matters

Chemistry is in a good position to take advantage of vector graphics. Chemical structures, being closely based on graph theoretical constructs, would seem to be a perfect match for vector languages like SVG and VML, especially on the Web. So far it hasn't happened, primarily for the reasons outlined above.

Currently, if you want to display 2D chemical structures in Web pages you're faced with some tradeoffs:

Raster Images. This is by far the most common practice. This option unfortunately makes it very difficult to redesign the layout of a site or support multiple views of the same structure, especially with databases of one million plus compounds becoming commonplace. Even if images are never regenerated, they need to be stored and retrieved, adding to cost and complexity. Images could be dynamically generated, but at the expense of substantial memory and CPU requirements.
Applets. This is the approach currently taken by Chempedia, the free chemical encyclopedia, and gives complete flexibility in page layout and structure appearance. Changing the dimensions of a structure is as simple as changing the size of a div. Unfortunately, some browsers handle multiple applets better than others. Firefox on OS X is very slow at refreshing applets while scrolling, and IE requires a Javascript trick to remove the 'click to active' message that causes some flashing when in progress.
Vector Graphics Through Plugins There are at least two SVG plugins for IE (one by Adobe and the other from Examotion). Will all of your users be able to find and install them? Unless the answer to both questions is 'yes', this option is probably best left as a last resort. Another option is to render SVG on IE through the Flash or Silverlight plugins. But as far as I can tell, neither approach is ready for prime-time.
Native Vector Graphics Available on all major browsers including Internet Explorer 5/6/7, Firefox 1/2, and Opera 8/9. Combines the flexibility, lossless depiction, inlineability and low data storage/retrieval overhead of applets with the speed of images. Interactivity and other special effects can be achieved through DOM manipulation. All of this depends, of course, on the vector graphics format being compatible with the rendering engine.

In some circumstances, serving VML to IE clients and SVG to everyone else would be a viable option - if it were possible to generate VML.

Conclusions

Vector graphics have a lot to offer chemistry, especially when used with Web applications. The combination of VML and SVG offers a proven technology platform that's ready today, but only if you can generate VML.

A Simple and Portable Ruby Interface to InChI - Part 2: Silencing Console Output

Rich Apodaca — Fri, 30 May 2008 10:04:00 +0000

The previous article in this series described a simple and portable method for interfacing Ruby to the cInChI-1 binary. One disadvantage was noisy console output. This article offers a minor modification to disable it.

The Code

module InChI
  def inchi_for molfile
    output = %x[echo "#{molfile}" | cInChI-1 -STDIO 2>/dev/null]

    output.eql?("") ? "" : output.split(/\n/)[1]
  end
end

Here, we're taking advantage of the ability to redirect certain output streams to /dev/null.

Testing the Code

Saving the above in a file called inchi.rb, we can test it from IRB. To make things interesting, let's pull a molfile from Chempedia:

$ irb
irb(main):001:0> require 'open-uri'
=> true
irb(main):002:0> require 'inchi'
=> true
irb(main):003:0> include InChI
=> Object
irb(main):004:0> open 'http://chempedia.com/compounds/83490.mol' do |f|
irb(main):005:1*   puts inchi_for(f.read)
irb(main):006:1> end
InChI=1/C15H15NO3S/c17-14(16-18)11-20(19)15(12-7-3-1-4-8-12)13-9-5-2-6-10-13/h1-10,15,18H,11H2,(H,16,17)
=> nil

We should be able to run this code unmodified on any UNIX-like system in which the cInChI-1 binary is on the path. And of course we could take this one step further by allowing command line options to be passed in as parameters to the inchi_for method.

Simplicity has its advantages.

Simple CAS Number Lookup (and More) with Chempedia

Rich Apodaca — Mon, 26 May 2008 13:06:00 +0000

Despite many ingenious and energetic attempts, CAS Registry Numbers® remain chemistry's only universal method for referencing chemical structures and substances. They're so woven into the fabric of chemistry and trade that the US Patent and Trademark Office discusses them in the same context as Domain Names, Drivers License Numbers, ZIP Codes, and UPC Barcodes. But for all of the system's advantages, it suffers from a significant limitation: without access to the CAS Registry database, it can be difficult if not impossible to link a chemical structure with a CAS Number. This article discusses a unique approach to this problem.

Finding CAS Numbers on Chempedia

Let's say you've found the CAS Number [58-08-2] and needed to look up the chemical structure it refers to. How would you do it?

We can use Chempedia to find the answer. Entering "58-08-2" into the text query box takes us to the corresponding Registry Number Summary.

Under the heading "Compound Monographs", this page tells us that one Compound Monograph referencing the CAS Number [58-08-2] exists. We can easily see that both the name and chemical structure are consistent with Caffeine.

However, the section under the heading "Compounds" gives us something unique. Rather than simply telling us that the structure of Caffeine is linked to CAS Number [58-08-2], Chempedia tells us how it arrived at this conclusion. As you can see, there are over a dozen references matching CAS Number [58-08-2] with a single chemical structure.

More than that, Chempedia give us links to the organizations making these assertions and the actual Web pages recording them.

Rather than just giving the answer, Chempedia says how it found the answer.

Authority, Confidence, and the Electronic Paper Trail

By definition, the only authority on CAS Registry Numbers is Chemical Abstracts Service itself. But for many, many organizations, full-time access to the CAS Registry database is hopelessly out of reach, and access of the form required to incorporate the CAS Registry system into third-party products is a non-starter.

In other words, there is a widespread need to work with CAS Numbers independently of the CAS Registry System, but any such attempt is inherently non-authoritative. How can we work within this constraint?

What's lacking is the concept of confidence.

To illustrate, let's try to find the structure associated with the CAS Number [480-41-1]. In contrast to our earlier search, this one takes us to a summary page with three different structures! (see below)

Each of these three structures share the same connectivity, but different stereochemistry. The first structure (presumably) represents a racemate, the second represents the (S) enantiomer, and the third represents the (R) enantiomer.

At this point, we need to decide whether we've really found the structure for the CAS Number [480-41-1]. And we could use Chempedia's electronic paper trail to guide our thinking. Both the racemate and (S) enantiomer have five references linking structure and CAS number, whereas the (R) enantiomer only lists one.

We can also see that the racemate and and pure (S) enantiomer each are associated with yet another CAS Registry Number, [67604-48-2]. Examination of this record shows that two structures are cited, the same two structures we were originally considering.

Clearly, there's some confusion regarding the exact identity of the structure represented by CAS Number [480-41-1]. Nevertheless, we can guess that the Registry Numbers [67604-48-2] and [480-41-1] refer to the racemate and (S) enantiomer of the flavinoid Naringenin, although we don't know which is which.

For some applications this answer would be sufficient. For others, however, it wouldn't. The key point is that Chempedia has enabled us to arrive at this conclusion by exposing the electronic paper trail of third-party CAS Registry Number assignments.

Chempedia offers a way to debug CAS Registry Numbers.

Chempedia currently contains just over 380,000 unique CAS Numbers. To browse through the entire set, ten at a time, you can begin with this page. Notice how RESTful URLs are used throughout.

Web 2.0 and All That

Those who have spent time using or developing "Web 2.0" applications may recognize a potentially powerful analogy between CAS Registry Numbers and the concept of tagging. A tag is an alphanumeric string associated with some resource of interest, for example, a photo, a scientific paper, a URL, or a blog post.

Although originally designed to uniquely identify a chemical substance or structure, when used in the wild, CAS Registry Numbers sometimes more closely resemble the fuzzy semantics of tagging.

Chemical information system that use CAS Numbers processed by third parties need to take this reality into account or run the risk of misleading users. Chempedia offers one method for doing so.

Conclusions

Chempedia currently contains just over 380,000 CAS registry numbers. Although this is a minuscule fraction of the total CAS Registry, Chempedia's collection comprises some of the most widely used and most important substances known. More importantly, Chempedia now offers a tool for understanding the often complex associations between chemical structure and CAS Registry numbers that exist in real-world chemical information sources.

In this sense, Chempedia could be a useful tool for small organizations to double check their CAS Number assignments and for individuals to quickly look up the chemical structure of a given CAS number and understand ambiguities.

Chempedia also lays bare both the confusion and consensus around CAS Registry Numbers used in the real world. If CAS Numbers in the wild are more like tags than unique identifiers, what can we do with this insight? Future articles will describe some possibilities.

Small Molecule 3D Coordinates From PubChem

Rich Apodaca — Fri, 23 May 2008 10:53:00 +0000

The PubChem team has quietly introduced a new feature - 3D coordinates for many of the small molecules in its compound collection. To my knowledge, these coordinates are only currently available via FTP. From the README:

The data contained here consists of a theoretical 3D description of PubChem Compound records computed using the MMFF94s force field without coulombic terms, including MMFF charges. Each provided theoretical 3D conformer is not a stationary point on the hyper-potential surface (i.e., is not at a minimum energy). Rather, the theoretical 3D description is a low energy conformer selected from a conformer model (a theoretical description of the conformational flexibility of a chemical structure consisting of multiple 3D representations or poses sampled using an RMSD {root mean squared distance} threshold) describing energetically-accessible and (potentially) biologically relevant coformations of a chemical structure.

Not every PubChem Compound record will have a theoretical 3D description. Structures considered too large (containing more than 50 non-hydrogen atoms) or too flexible (containing more than 15 rotatable bonds) are excluded. Furthermore, chemical structures containing elements other than H, C, N, O, F, P, S, Cl, Br, and I are also excluded.

Generation of theoretical 3D descriptions of small molecules is computationally intensive. As such, some PubChem Compound records may be added at a later time.

(A few open source packages for generating 3D conformers are also available.)

Recently, Geoff Hutchison wrote in to suggest that a potentially useful new feature of Chempedia could be the ability to directly obtain 3D coordinates for a molecule of interest.

One very economical way to do that would be to use PubChem's 3D dataset. It would also be trivial to display these coordinates as a resizable Jmol applet, in analogy to Chempedia's recently-added 2D molecule resizing feature.

Of course, there are many other potential uses for the PubChem conformer dataset, especially when applied to Web applications.

Building Chempedia: Social Networking Applied to Chemistry

Rich Apodaca — Wed, 21 May 2008 10:40:00 +0000

Chempedia is a free online chemical encyclopedia; it's also a work in progress, the contents of which are being written by numerous volunteers worldwide. A previous article described initial work toward connecting the people behind Chempedia's content with the compound monographs they're writing. This article will describe new features that take this idea much further.

Contributors

Chempedia now uses the concept of a "Contributor" as part of its data model. Each Compound Monograph has one associated Contributor, the Wikipedia user who last edited it. In other words, a one-to-many relationship exists between a Contributor and a Monograph.

Of course, this model is simplistic; Compound Monographs are edited by multiple users over time, and so the relationship should be many-to-many. Nevertheless, for now a one-to-many relationship works well enough.

Learning About Contributors

You can view a complete list of contributors to Chempedia. As you can see, over 1,000 Wikipedia users are currently listed. The number in parentheses appearing after each contributor's username is the number of Monographs for which Wikipedia lists them as the last editor.

Chempedia contains just over 6,400 Compound Monographs; the fact that 1,000 Wikipedia users contributed to making that happen is remarkable. That such a large number of users contribute relative to the number Monographs may be surprising given the rule of thumb that only 2-10% of users are responsible for the majority of the work on community-driven projects. While the majority of work may well be done by a relatively small group of Contributors, these numbers demonstrate a widespread interest in creating and maintaining information about chemical compounds.

Chempedia lets you learn more about what an individual Contributor has done. Clicking on a Contributor name takes us to a Contributor summary page showing all of the Monographs on which they are listed as Contributor, as well as their Wikipedia home and talk pages. The latter can be used to take part in discussions.

A particularly active contributor (one of several) goes by the name of Edgar181. As of this writing, s/he is listed as the Contributor on 458 Compound monographs, and the last one s/he edited was Methylparaben.

And 1,000 Contributors represents only a lower limit due the the large number of anonymous contributions, which on Chempedia are lumped together. As you can see, over 1,100 Compound Monographs were last edited by a Wikipedia user who didn't log in.

Thank Goodness for Robots

Quite a few Contributors have the letters 'Bot' in their names. A 'Bot is a script designed to do work on Wikipedia that would be tedious and/or error prone if done by humans.

One of my favorites is ClueBot. From the ClueBot Wikipedia user page, this script's purpose in life is to revert Wikipedia vandalism, a job it does with breathtaking efficiency and accuracy.

For example, one of ClueBot's last pieces of work was to revert an edit made to Lysergic Acid Diethylamide in which a user tried to include some enthusiastic, but subjective, comments about Albert Hofmann's discovery.

In less than one minute, ClueBot had not only identified the comment as vandalism (despite the fact that no 'offensive' language was used), but had removed it as well. Amazing.

Connecting Contributors to Monographs

Chempedia is quickly forming a densely connected network of people and molecules. What can we do with this?

A new edit status line has been added to Monographs summaries (above). With it, you can easily see the number of edits that have occurred, when the last one happened, and who did it. Links will take you directly to the Wikipedia edit history page and to the Chempedia Contributor page for the last editor.

For example, the entry for Modafinil currently lists Paul gene as the last contributor. Bringing up his Chempedia contributor page, we can see that he's listed as the last Contributor on three other Monographs, all of which are organic compounds of pharmacological interest. Curious about whether this might be one of Paul gene's interests, we click on the User Page link at the top right of the contributor page and find out that this Wikipedia user received a Ph.D., works in academia, and has an interest in pharmacology, immunology, chemistry, kinase inhibitors, and antidepressants.

Newly-Edited Monographs

It might be of interest to know when Compound Monographs are edited. This can be done from the Browse link at the top-left main menu. On this page Monographs are sorted in descending order according to the last edit timestamp. The most recently-edited monographs appear on the first page, which is currently updated once every 30 minutes or so.

Hot Monographs

We may also be interested in which Compound Monographs are receiving the most edit activity. We can do that by choosing the Active link at the top-right submenu. As of this writing, Heroin is the most actively edited Monograph, with 10 edits since May 19^th. Clicking on the link in the edit status line, we can see what all the activity is about.

Conclusions

None of the technology described here is especially new or innovative; social networking has been part of information systems for several years now and relational databases are designed to make discoveries possible by linking disparate pieces of information. What is new is Chempedia's application of social networking, facilitated by relational databases, to chemistry. I'm unaware of any other chemical information system that takes the possibilities of social networking as far as Chempedia has taken them.

There's quite a bit more that could be done to link people and molecules on Chempedia, but for now, it's time to move onto some related areas. It turns out that the use of CAS numbers, when used outside of the CAS database system itself, raises all kinds of difficult and interesting questions around trust and authority in which social networking ideas can be applied. But that's a story for another time.

Building Chempedia: Resizable Structures With ChemWriter

Rich Apodaca — Mon, 19 May 2008 09:42:00 +0000

One of the difficulties in viewing 2D chemical structures is that molecules vary in size. In particular, larger molecules become difficult to read when confined to a small section of a screen. This article shows how this problem has been addressed in Chempedia using the 2D rendering capabilities of the ChemWriter package.

As an example, consider Chempedia's entry for Aluminon. Although the summary box at the right shows the structure for Aluminon, it may not be completely readable due to the large size of the molecule.

To solve this problem, Chempedia has implemented a "zoom" link for all monographs containing a chemical structure. Clicking on the zoom link for Aluminon gives a magnified, scaled, stretchable, and resizable view of the molecule.

To implement this feature, Chempedia uses the ChemWriter PainterApplet. Simply setting the width and height attributes of the <object> tag to "100%" gives an applet that resizes itself as the surrounding window is resized.

Implementing a resizable 2D structure image window using AJAX and dynamic images is possible, but would be much more difficult to implement. It could also potentially produce a much higher, and unpredictable demand on server memory, CPU cycles, and bandwidth.

ChemWriter makes it possible for the server to delegate resizable image processing to the client, resulting in a much more responsive feature with minimal effect on the server.

Building Chempedia: The Human Element

Rich Apodaca — Thu, 15 May 2008 14:50:00 +0000

The study of chemistry is an inherently social activity. From the papers we use and cite, to the conferences we attend, to the informal discussions we engage in daily, being a chemist means interacting with your fellow chemists. Yet strangely, most chemical information systems either totally ignore this central fact, or provide only the most meager of tools to harness it to its full potential. This article discusses how Chempedia currently integrates the social with the scientific, and what may be in store for the future.

Chempedia as a Tool for Scientific Collaboration

Like all chemical reference works, Chempedia is written by people with their own interests, skills, and ambitions. Unlike almost every other chemical reference work, Chempedia (through Wikipedia, on which it's based) offers intriguing possibilities to directly collaborate and learn from its contributors - or even become one of them.

How can Chempedia better facilitate scientific collaboration?

A Simple But Possibly Useful Feature

Yesterday, a new feature was added to Chempedia that makes it easier to understand the recent history of a Compound Monograph. The new feature shows the date that a Compound Monograph was last edited, and the Wikiepdia user who edited it:

Clicking on the link takes you to the Wikipedia users page, in this case the one for Meodipt. (Wikipedia users frequently use handles rather than their given names.) From Meodipt's page, we can see that s/he received degrees in chemistry and pharmacology and is currently studying law. Meodipt's interests include pharmacology, chemistry, law, and science. We can also see that Meodipt is maintaining a good-sized list of CAS numbers for drugs, grouped by indication.

We might be curious about what Meodipt found worth changing, and how s/he changed it. We could do so by first clicking the Chempedia edit link. In the Wikipedia box (framed by the red dotted lines), we would then click on the 'history' tab. Clicking on the 'last' link for the top entry shows us exactly what Meodipt changed on Pravadoline's compound monograph (also visible through this link).

Looking Ahead

Linking a real person to changes in a Compound Monograph could be enormously useful, if done properly. After all, bringing people with highly focussed interests together is the essence of scientific collaboration. The Chempedia/Wikipedia combination provides one way to do that.

As Chis Anderson puts it, "social networking should be a feature, not a destination." Scientists were social networking long before the Internet, the computer, and the telephone were invented; indeed scientists who fail to connect with their fellow scientists have a difficult time of prospering. When seen from this perspective, it's surprising that good 'social networking' features would not be viewed as a top priority in chemical information systems.

The Chempedia author credit system in its current form is rather simplistic and may not actually promote scientific collaboration at all. But it's not hard to imagine ways to make it far more effective. Future articles will discuss some of the possibilities.

The Daily Molecule: The Wonders of Chemistry - One Molecule at a Time

Rich Apodaca — Wed, 14 May 2008 11:58:00 +0000

Chemistry is a big field judged by any standard, including the proliferation of American Chemical Society (ACS) divisions. Each subdiscipline in chemistry is in turn so big, that once a chemist becomes 'differentiated' it's easy to lose touch even with neighboring subdisciplines. It doesn't have to be that way. This article introduces a new service, The Daily Molecule designed to make it just a little bit easier (and hopefully fun) to stay in the chemical loop.

What Is It?

The idea is simple: every weekday, a new molecule will be featured on The Daily Molecule with a short write-up and some leading references. Although molecules in the news will get first priority, any molecule is fair game.

The material for The Daily Molecule will be drawn from Chempedia, which in turn gets some of its content from Wikipedia. In other words, the entries on the Daily Molecule will be largeley written by my fellow chemists.

The process of creating a Daily Molecule entry is not time-consuming, but much of what is being done manually now could be automated in the future. The technology platform lends itself well to many forms of chemistry-specific modification (see below).

I hesitate to use the term 'blog' to describe The Daily Molecule, but the description may be helpful to an extent.

The Daily Molecule is unlike a blog in that most content will be generated by others, selected by some criteria, reformatted for consistency, and published. In that sense, The Daily Molecule is a something like a mini scientific journal, but it turns the process of acquiring content on its head.

If chemistry ever evolves beyond the current model of publication, which seems inevitable at this point, the journals of the future may resemble The Daily Molecule in one or more ways.

Technology

The software running The Daily Molecule is a modified version of SimpleLog, a Web application based on Ruby on Rails. Unlike most blogging engines, SimpleLog focuses on implementing only the most basic publication features, and doing them to perfection. If you know a little Ruby and can work with Rails, you can do a lot with SimpleLog.

One of the first items of business will be to implement reCAPTCHA support and activate comments on articles.

Some ideas for chemically-enabling The Daily Molecule include a graphical abstract sidebar and (sub)structure search. Currently, the 2D chemical structure images posted to The Daily Molecule have complete connection tables embedded as metadata, a feature with some interesting possibilities.

The Molecule of the Day/Week/Month

The basic idea behind The Daily Molecule is not new. Many other services have sprung up over the last ten years that operate, at least on the surface, similarly. Some examples:

Molecule of the Day
ACS Molecule of the Week
Drugs and Poisons
Saturday Night Synthesis
The Molecule of the Month (may be the oldest continuously-operated MOTM site in existence)
3dchem.com Molecule of the Month
Protein Spotlight
PDB Molecule of the Month
Prous Molecule of the Month

Quite a few others don't appear on this list.

The different idea behind the The Daily Molecule is that chemical content already exists in on the Web in machine-readable format with licenses that permit its re-use; all that's needed is a way to aggregate, format, and package that information in a form suitable for once-daily scanning and cheminformatics manipulation.

Conclusions

Like no other medium, the Web blurs artificial distinctions: between work and play; between private and public; between on-topic and off-topic; between fame and obscurity; between mine and yours; between big and small; and between profit and non-profit. Chemistry may be late to the party, but is not immune to its call.