REVIEWS Drug Discovery Today

Volume 13, Numbers 11/12

June 2008
f
c
m
a
R
e
v
i
e
w
s

I
N
F
O
R
M
A
T
I
C
Sings have offered this socializing aspect, historically, the publica-educating others, proliferating data or opinions, or connecting
with others for collaboration or advice. Although scientific meet-
tion process has been the primary manner by which
chronological order and generally provide commentary or news
on a particular subject (see http://www.en.wikipedia.org/wiki/
Blog). A typical blog combines text, images and links to other
blogs, web pages, and other media related to its topic (see Fig. 1 forscience or science in general, commonly with the intention ofavailability of tools to host wikis and blogs has provided the necessary building blocks for scientists with
only a rudimentary understanding of computer software science to communicate to the masses. This
newfound freedom has the ability to speed up research and sharing of results, develop extensive
collaborations, conduct science in public, and in near-real time. The technologies supporting chemistry,
while immature, are fast developing to support chemical structures and reactions, analytical data
support and integration to related data sources via supporting software technologies. Communication in
chemistry is already witnessing a new revolution.
The wikisphere and the blogosphere
Many scientists have an urge to communicate either their own
their own research groups but also, more generally, with the
public in general.
A blog or weblog is a website where entries are written in aInternet-based tools
and collaboration in
Antony J. Williams
ChemZoo Inc., 904 Tamaras Circle, Wake Forest, NC 27587, United States
Web-based technologies, coupled with a drive for i
resulted in the proliferation of scientific opinion, dcommunication to an extended audience has been facilitated.
This process can result in education, proliferation and collabora-
tion, but puts many hurdles in the path of social and collaborative
science, not least being the time associated with publishing data,
the limited communication channels for facile feedback associated
with a standard form of publishing, as well as the potential costs to
the readers and authors of accessing the information.
A shift is already underway in terms of willingness and an
interest in using web-based software tools to speed communica-
tion. Wikis and blogs are now common terms for the majority of
users of the worldwide web. Most, if not all, readers of this article
have at least browsed through Wikipedia to see what all the
attention is about and probably have browsed a few blog sites,
though not necessarily for the sake of science. Both wikis and
blogs are fast becoming chosen platforms for the exchange of
information between many scientists, not only as tools within
E-mail address: antony.williams@chemspider.com.
502 www.drugdiscoverytoday.com 1359-6446/06/$ - sor communication
hemistry
proved communication between scientists, have
ta and knowledge at an ever-increasing rate. Thean example of a chemistry blog written by a synthetic chemist).
The ability for readers to leave comments and interact with the
author is an important component of blogs (though such capabil-
ities do exist in the wiki environment in terms of discussion
groups) and is really the most interesting value proposition of
the medium itself. The original blog posting remains untouched
by the commenter, and is, therefore, less prone to abuse than the
wiki environment, but readers are free to add their comments,
generally in a mediated manner, where the blog host retains
control over the postings. The number of chemistry-related blogs
continues to grow dramatically and there have been efforts to
provide a unified view into some of these (see http://www.scien-
ceblogs.com/ and http://www.cb.openmolecules.net/) as well
as provide an environment regarding ‘how to’ participate in
scientific blogging (see http://www.wiki.scienceblogging.com/
scienceblogging/). Of the chemistry blogs online, many are hosted
by students and, in general, there is sadly a lack of contributors by
teachers in this environment. There are blogs from members of the
ee front matter  2008 Elsevier Ltd. All rights reserved. doi:10.1016/j.drudis.2008.03.015

 
R
e
v
i
e
w
s

I
N
F
O
R
M
A
T
I
C
Spharmaceutical industry, from the cheminformatics world, from
the open source chemistry software world and other willing
Drug Discovery Today Volume 13, Numbers 11/12 June 2008
FIGURE 1
The TotallySynthetic.com blog. Paul Docherty discusses complex syntheses
and offers readers an opportunity to comment, analyze and provide
feedback. Many articles are labeled with InChIKeys to allow indexing by
search engines (http://www.totallysynthetic.com/blog/).participants in the ‘blogosphere’. Many organizations are, appro-
priately, concerned with their employees blogging and, especially
for nonacademic environments, there are likely to be company
guidelines and policies in place.
The blog environment certainly provides more of a social
networking environment than a wiki and can result in a more
immediate response to a question, such as a call to collaborate on
a funding proposal (see http://www.blog.openwetware.org/
scienceintheopen/2007/11/22/e-science-for-open-science-an-
epsrc-research-network-proposal/), an immediate path to com-
munication of important issues (see http://www.wwmm.ch.
cam.ac.uk/blogs/murrayrust/?p=887), and in career-damaging
dialogs across the community (see http://www.pipeline.corante.
com/archives/2006/06/05/hexacyclinol_or_not.php).
A wiki is a type of computer software that allows users easily to
create, edit and link web pages (see http://www.en.wikipedia.org/
wiki/Wiki). A wiki enables documents to be written collabora-
tively, in a simple markup language using a web browser, and is
essentially a database for creating, browsing and searching infor-
mation. A defining characteristic of wiki technology is the ease
with which pages can be created and updated. Certainly Wikipedia
is the most well known option today, though there are many
others already online and used within the confines of an organiza-
tion to manage content.
There are active groups supporting the development of chem-
istry on Wikipedia and there are now thousands of pages describ-
ing small organic molecules, inorganics, organometallics,
polymers and even large biomolecules. Focusing on small mole-
cules in general, each one has a drug box (see http://www.en.wikipedia.org/wiki/Template:Drugbox) or a chemical infobox (see
http://www.en.wikipedia.org/wiki/Wikipedia:Chemical_infobox).
A drug box provides identifier information (chemical name, registry
number and so on) and commonly the identifiers link out to a
related resource. Chemical data, pharmacokinetic data and thera-
peutic considerations can also be listed.
Readers are probably aware of the criticisms of Wikipedia in
terms of potential quality issues. This author has been highly
impressed with the overall quality of the chemical information
on the site and, when the author has found errors, has been able to
make appropriate edits to the immediate benefit of the commu-
nity. A curation project is presently underway to validate each of
the chemical structures and associated information and should be
complete by March of this year (see http://www.en.wikipedia.org/
wiki/Wikipedia_talk:WikiProject_Chemicals#Good_news_-_fact_
checking_of_chemboxes.2C_etc and http://www.chemconnec-
tor.com/chemunicating/dedicating-christmas-time-to-the-cause-
of-curating-wikipedia.html). This is the true value of a wiki envir-
onment; mass participation to aid in the generation and the
validation of the content.
Wikis have recently been used as the basis of Open Notebook
Science [1], a term coined by Drexel University associate professor
Jean-Claude Bradley (see http://www.reactivereports.com/51/
51_0.html). The UsefulChem Wiki includes a series of experimental
pages, for example as shown in Fig. 2 (see http://www.usefulchem.-
wikispaces.com/All+Reactions) commonly linked to related blog
pages (see http://www.usefulchem-experiments1.blogspot.com/
2006/05/exp-009.html) and also includes a thesis being written as
the research proceeds (see http://www.usefulchem.wikispaces.com/
Alicia+Holsey). Bradley has also utilized the wiki medium to chal-
lenge the publishingcommunity (see http://www.usefulchem.blog-
spot.com/2007/04/wiki-paper-experiment-started.html) by writing
a paper written on a public wiki and using links to experiment pages
on a laboratory notebook wiki as valid references. Commonly, such
public exposure of research before publication is frowned upon by
publishers, but, as Bradley has pointed out, preprints are already
hosted on institutional repositories, so a shift to wiki-based public
chemistry, or Open Notebook Science, should not be that different.
Differently from most researchers, he prefers to keep a portion of his
future plans right out in public view on his ‘To Do’ list (see http://
www.usefulchem.wikispaces.com/pending). He is not alone, as his
Open Notebook Science efforts and the movement appears to be
gaining momentum with the support of vocal advocates, such as
Neylon (see http://www.blog.openwetware.org/scienceintheopen/
2007/12/12/a-big-few-weeks-for-open-notebook-science/), Murray-
Rust (see http://www.wwmm.ch.cam.ac.uk/blogs/murrayrust/
?p=671) and many others.
Wikis are now also being used as a corporate platform for infor-
mation sharing also. The largest drug maker in the world, Pfizer (see
http://www.pubs.acs.org/email/cen/html/090207084512.html),
already has Pfizerpedia. Christopher Bouton, a scientist at the
company used the MediaWiki platform, on which Wikipedia runs,
as his platform. One year after its launch in 2006, Pfizerpedia was
receiving 12,000 hits per month by 13,000 individual users across
Pfizer worldwide. This pattern is sure to continue within drug and
chemical companies, because of the ease of installing, running and
REVIEWScollaborating on such a system. With certain extensions to the
technology (vide infra), the platform could easily become an elec-
www.drugdiscoverytoday.com 503