Communicating in Chemistry
Gary Wiggins
2007 Patterson-Crane Award Lecture
May 8, 2007
Columbus, Ohio
CONGRATULATIONS
CHEMICAL ABSTRACTS SERVICE
on the occasion of its 100th anniversary!
Impact of the Computer on
Communication in Chemistry
• “Rapid growth of the huge volume of chemical
knowledge stored away in the literature makes it
harder and harder to find specific information
quickly and easily.”
• “. . . more than 10,000 compounds have been
exhaustively searched in a little more than a
minute.”
• On May 4, 2007 CAS Registry had 31,621,384
organic and inorganic substances.
• Source: C&EN April 15, 1957, 98, 100.
Where was the First Demonstration
of Chemical Structure Searching?
• US National Bureau of Standards
• Source of this information:
Dr. David R. Lide, Jr., 1991 Patterson-Crane
Award Recipient, in a posting on CHMINF-L,
the Chemical Information Sources Discussion
List, 4/26/2007
Communicating Through an
Intermediary
• Intermediaries (aka, librarians, online searchers)
were responsible for the tremendous growth in
online searching in the period 1970-1990.
• Informal poll of CAS customers in 1990 revealed
that a single professional searcher was
supporting from 70 to 300 customers.
– Seals, James V., Jr. “The Past as Prologue,” delivered
at Infobase ’90 Special Symposium on the Future of
Electronic Information Services in Chemistry
Skipping the Intermediary with
SciFinder
• 1995: SciFinder released to the industrial market
• “SciFinder is better than having a set of CA in
my lab.”
– Williams, Jan. “SciFinder: Scientists online at their
desktops.” Online User 1996 (Jan/Feb), 31-35.
• Schwall, Kirk; Zielenbach, Kurt. "SciFinder: A
new generation of research tool." Chemical
Innovation 2000 (October), 30(10), 45-50.
Electronic Journals
• http://pubs.acs.org/journals/chtedd/index.html
• “The ACS Publications website has been
redesigned and restructured. The page
you are attempting to access may have
been moved or deleted.”
What?!!!
I was attempting to access the following article from
Chemical Innovation:
– Schwall, Kirk; Zielenbach, Kurt. "SciFinder: A new generation of
research tool." Chemical Innovation 2000 (October), 30(10), 4550.
However, it no longer seems to be available because the
link to the article from the title page of the journal leads
to a page that has this on it:
– “The ACS Publications website has been redesigned and
restructured. The page you are attempting to access may
have been moved or deleted.”
Is it really true that a publication of the ACS is no longer
available on the web?
--4/3/2007
Response on 4/13/2007:
Greetings,
Thank you for your message. After having
this investigated, the technicians have
informed me that Chemical Innovation is
no longer supported/available. I hope this
information is helpful.
Thank You,
Solution: Interlibrary Loan
• An article that you requested “SciFinder: a new
generation of research tool” has been received
and processed by the Interlibrary Loan Staff. You
can now receive this item by logging on to IUB
Document Delivery Services and choosing the
"View/Download Electronically Received
Articles" option from your main menu.
• Scanned article from IUPUI’s print copy came on
4/4/07, one day after requested
Missing E-Journal Content:
Not Just an ACS Problem
We recently discovered that online
volumes 74, 75, and 76 of Journal of the
American Oil Chemists' Society were
missing (not available online at the
Springer web site). Our inquiry to Springer
about this problem received the following
response:
– Source: Dr. Howard M. Dess, CHMINF-L, 4-62007
From Springer, With Regret
• Unfortunately, the volumes/issues/article you
mention is/are currently missing on
SpringerLink. From the production dept. we
learnt that the content is in the process of being
digitised. It is planned but not scheduled. We do
all our best to fill the gap as soon as possible.
• We kindly ask to accept our apologies for the
inconvenience caused.
• With kind regards,
• SpringerLink Support Team
Web 2.0
• Phrase coined by O'Reilly Media in 2004
• Refers to a perceived second-generation
of Web-based communities and hosted
services that facilitate collaboration and
sharing between users
– Social networking sites
– Wikis
– Folksonomies
– Source: Wikipedia, 5/6/07
Recent ACS Symposium
“Communicating Chemistry”
• CHED, March 27, 2007, ACS Chicago
– “Open notebook chemistry using blogs and
wikis,” J-C Bradley et al.
– “Open access peer reviewed portal for
communicating chemistry: Analytical Sciences
Digital Library,” H. A. Bullen
What’s a Blog?
• A blog (short for web log) is a website
where entries are made and displayed.
• Content:
– commentary or news on a particular subject
– some function as more personal online diaries
– The ability for readers to leave comments in
an interactive format is an important part of
most blogs.
– Souce: Wikipedia, 5/507
Useful Chemistry Blog
• Jean-Claude Bradley’s blog at Drexel invites you
to “Post specific problems in chemistry that need
to be solved.”
• Other components:
– UsefulChem Molecules, as of 4/2/07 had only 231
molecules and 241 on 5/6/07
– UsefulChem Wiki
– UsefulChem Experiments
– Quick access to Jean-Claude’s CHED presentation:
http://drexel-coas-talks-mp3-podcast.blogspot.com/
• http://usefulchem.blogspot.com/
UsefulChem
Another ACS Symposium on the “Evolving
Network of Scientific Communication”
• CINF, March 27, 2007, ACS Chicago
– “Implementation of scientific ‘blogging’ into
chemical laboratory research,” A. C.
Fahrenbach, A. H. Flood
– “Standard domain ontologies: The rate limiting
step for the “Next Big Change” in scientific
communication,” A. Renear
– “Enhancing the web experience with ACS
journals,” E. Jabri, S. Tegen
O2HU
RSS
• XML-based format that allows the syndication of
lists of hyperlinks, along with other information or
metadata that helps viewers decide whether
they want to follow the link
• A Web site will make a feed or channel
available, then computers can regularly fetch the
file to get the most recent items on the list.
– Source: RSS Tutorial for Content Publishers and
Webmasters http://www.mnot.net/rss/tutorial/
RSS Feeds: Book Reviews via ETH
• 25 scientific journals with book reviews are
tracked.
– http://www.clicaps.ethz.ch/fmi/xsl/bookreviews_rss_en.xsl
• “I use the RSS feed and it's really super! . . our
systems folks have built a Firefox LibX extension
for UChicago, so I can highlight the book title
and do a search in our catalog without rekeying.
The combination of these two functions saves
me a lot of time. . .”
– Source: Andrea Twiss-Brooks (U of Chicago)
CHMINF-L, 4/5/07
From “No Stone Left Unturned” to
“Good Enough”
• The Web has brought about a significant
change in the way information is sought.
• Librarian colleagues note a shift from a
desire for comprehensive searches to just
enough to get by with.
• “Good enough!”
SciFinder Scholar Search
• Search for cheminformatics found 173
(188) references
• Search for chemoinformatics found 176
(191) references
• Not the same references in the two
answer sets formed on 5/5/2007
• Nevertheless, the combination of the two
gives a comprehensive search.
Mitch’s ACS + Nature + APS +
Science+ RSC + Springer Search
• Uses Yahoo Pipes to search all ACS, Nature
Publishing Group, American Physical Society,
Science, and Royal Society of Chemistry RSS
feeds plus Springer chemical publications
• Results can be syndicated in RSS format and
plugged into an RSS reader
• Reader notifies you whenever a new publication
containing what you searched for was published
• http://pipes.yahoo.com/pipes/pipe.info?_id=XHB
pdITV2xGyLtzzy6ky6g
Yahoo Pipes
• a GUI-based interface for building
applications that aggregate Web feeds
and other services, creating Web-based
applications from various sources
• Lets users "pipe" information from different
sources and then set up rules for how that
content should be modified (e.g. filtering).
– Source: Wikipedia, 5/5/2007
Search on Mitch’s Site for
“Cheminformatics”
•
•
•
•
•
•
A Cheminformatic Toolkit for Mining Biomedical Knowledge
Abstract Purpose Cheminformatics can be broadly defined to encompass
any activity related to the application of information technology to the study
of properties, effects and uses of chemical agents. One of the most
important current challenges in cheminformatics is to allow researchers to…
Cheminformatics analysis and learning in a data pipelining
environment
Summary Workflow technology is being increasingly applied in discovery
information to organize and analyze data. SciTegic's Pipeline Pilot is a
chemically intelligent implementation of a workflow technology known as
data pipelining. It allows scientists to construct and execute workflows…
MotifMiner: Efficient discovery of common substructures in
biochemical molecules
Biochemical research often involves examining structural relationships in
molecules since scientists strongly believe in the causal relationship
between structure and function. Traditionally, researchers have identified
these patterns, or motifs, manually using domain expertise. However, with
the…
Search on Mitch’s Site for
“Chemoinformatics”
• Application of Chemoinformatics to the Structural Elucidation
of Natural Compounds
• This paper describes the characteristics of a free web-based
spectral database for the chemical research community, containing
13 C NMR spectra data from more than 4.000 natural compounds.
The number of entries is constantly growing. This database allows
for searches by chemical structure,…
• Statistical Distribution of Chemical Fingerprints
• Binary fingerprints are binary vectors used to represent chemical
molecules by recording the presence or absence of particular
substructures, such as labeled paths in the 2D graph of bonds.
Complete fingerprints are often reduced to a compressed format–of
typical dimension n = 512 or n = 1024–by…
ChemRefer
• Searches only chemical and pharmaceutical literature
that is full text and freely available on the web
• Search on “cheminformatics” found 7 articles on April 4
and 4 articles on May 5
• Search on “chemoinformatics” found 14 articles on April
4 and 7 articles on May 5
• Hyperlinks directly to all articles in journals such as:
–
–
–
–
Chem. Pharm. Bull.
Pure Appl. Chem.
Curr. Opin. Chem. Biol.
Org. Biomol. Chem.
• http://www.chemrefer.com/
Open Access and the Progress of
Science
Ontology
• A data model that represents a set of
concepts within a domain and the
relationships among those concepts
• Used to reason about the objects within
that domain
• A form of knowledge representation about
the world or some part of it
– Source: Wikipedia, 5/507
RSC’s Project Prospect
• Ontology Terms features drop-down boxes if the
article contains terms from the Gene Ontology,
Sequence Ontology, or Cell Ontology.
– Highlights in blue the terms from the ontologies
• Highlights in yellow terms that appear in the
IUPAC Gold Book
• Highlights in pink the compounds identified in
the paper.
Chem. Commun., 2007, 49 - 51,
DOI: 10.1039/b615122a
ACS’s Biotech Exchange et al.
• Network of tools to facilitate information
sharing and communication
• Registered members may send
messages, post questions, and maintain a
member profile.
• http://biotechexchange.org/
• ACS Chemical Biology
– Features Chemical Biology Wiki and ChemBio
WIKI Spot, an online journal club
Folksonomy
• A user-generated taxonomy for
categorizing and retrieving web content
such as Web pages, photographs and
Web links, using open-ended labels called
tags
– Source: Wikipedia, 5/507
NPG’s Connotea
• Free online reference management service
• Save links to articles, references, websites, etc.
with one click
• Puts your entire reference library online for
access at home, work, or while traveling
• Also a social bookmarking tool:
– categorize articles with “tags”
– share references
– view other people’s collections
• http://www.connotea.org
Connotea
Will Web 2.0 Changes Be
Embraced by Scientists?
• “Scientists are more interested in their
careers and grants than using tools
that promote better communication
and data sharing.”
– David Lipman, Director, NCBI as quoted in: Butler,
Declan. “Data sharing: the next generation.” Nature
446, 10-11 (1 March 2007)
– http://www.nature.com/nature/journal/v446/n7131/full/
446010b.html
Gary’s Weather Forecasting Stone
Future
• Tried and true behavior patterns will linger for a
long time.
• But, everything changes: Semantic Web as a
substrate for collective intelligence
– Web 2.0 empowers people to create innovative
communication tools.
• Scientists will increasingly embrace tools that
promote better communication and data sharing.
• If you build it, they will come—
• especially if THEY help build it.
Thank you!
Moving on to retirement
Bibliography
• “Electronic searching moves ahead.” C&EN April 15, 1957, 98, 100.
• Griffiths, W. “ChemRefer – An Introduction.” EBank/R4L/SPECTRa
Workshop
http://www.ukoln.ac.uk/events/ebank-r4l-spectra/presentations/wgriffiths.ppt#256,1,ChemRefer - An Introduction
• Bradley, Jean-Claude. “Open notebook chemistry using blogs and
wikis.” http://drexel-coas-talks-mp3-podcast.blogspot.com/
• Butler, Declan. “Data sharing: the next generation.” Nature 446, 1011 (1 March 2007)
• Kidd, Richard. “Semantic enrichment boosts information retrieval.”
Research Information April/May 2007, (29), 23-25.
http://www.researchinformation.info
• Leach, Martin; Tedeschi, Michael. “If THEY build it, THEY will come.”
Bio-IT World April 2007, 6(3), 30-31, 33.
• Petkewich, Rachel. “New education tools.” C&EN April 23, 2007,
85(17), 44-45.
Bibliography (cont’d)
• Ray, Louis C.; Kirsch, Russell A. “Finding chemical records by digital
computers.” Science 1957, 126(3278), 814-819.
• Schwall, Kirk; Zielenbach, Kurt. “SciFinder: A new generation of
research tool.” Chemical Innovation October 2000, 30(10), 45-50.
• Seals, James V., Jr. “The Past as Prologue,” delivered at Infobase
’90 Special Symposium on the Future of Electronic Information
Services in Chemistry
• Swan, Alma. "Open access and the progress of science.“ MayJune 2007, 95(3).
http://www.americanscientist.org/template/AssetDetail/assetid/55131
• Todd, Matthew H. “Open access and open source in chemistry.”
Chemistry Central Journal 19 February 2007, 1(3).
http://journal.chemistrycentral.com/content/pdf/1752-153X-1-3.pdf
• Williams, Jan. “SciFinder: Scientists online at their desktops.” Online
User 1996 (Jan/Feb), 31-35.