Depth-First: Tag socialnetworking

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.

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: 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.

Name That Graph Revealed: Oligarchy 2.0

Rich Apodaca — Wed, 05 Sep 2007 08:28:00 +0000

Web 2.0 may be all about participation, but the numbers reported by The McKinsey Quarterly suggest a self-selecting oligarchy rather than a democracy. Success may well depend more on engaging the top 2-10% of users rather than appealing to all of them. Food for though when forming your next community, be it electronic or otherwise.

image credit: The McKinsey Quarterly

The Scientific Debate: Digg Meets Science?

Rich Apodaca — Tue, 16 Jan 2007 15:00:00 +0000

Recently I stumbled upon a new service called The Scientific Debate by way of a comment on Derek Low's blog In the Pipeline. It's actually a very clever idea: think Digg for biology papers. Business seems to be slow right now, but the site is less than one month old.

Would something like this work in Chemistry? Sites like Postgenomic Chemistry and Chemical Blogspace already provide an intriguing window into what scientists themselves think of their literature. The blogs (and their numerous comments) demonstrate the willingness of large numbers of scientists to do this kind of work for free - not unlike CAS's long-gone all-volunteer abstracter department. Given that submitting a paper to a Digg-like site and offering a few sentences is much faster than writing a blog, maybe the idea would catch on if done right.