Communicating in Chemistry

Gary Wiggins2007 Patterson-Crane Award Lecture

May 8, 2007Columbus, 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), 45-50.

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, 4-6-

2007

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.

• 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=XHBpdITV2xGyLtzzy6ky6g

Mitch’s ACS + Nature + APS + Science+ RSC + Springer Search

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

Workshophttp://www.ukoln.ac.uk/events/ebank-r4l-spectra/presentations/w-

griffiths.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, 10-

11 (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.“ May-June 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.