1	The Evolution and Coming Revolution of Scientific Information Resources – The Decline of the Middlemen Stephen R. Heller Consultant Silver Spring, MD 20902 steve@hellers.com
2	The slides from this and related presentations can be found at: http://www.hellers.com/steve/pub-talks/
3	Content/Information Where do you get it and what do you get? How is it disseminated? How can you and how do you use it? Technology is changing all of this!
4	10 Critical Factors Affecting Chemical Information collection, processing, and dissemination in the 21st Century 1. Internet - WWW 2. Internet - WWW 3. Internet - WWW 4. Internet - WWW 5. Internet - WWW 6. Internet - WWW 7. Internet - WWW 8. Internet - WWW 9. Internet - WWW 10. Internet - WWW
5	Prediction is very difficult, especially about the future. - Niels Bohr Give them a number and give them a date, but never both - Edgar Fiedler If you have to forecast, forecast often - Anonymous
6	Wherever there is power, there is resistance. Michel Foucault The History of Sexuality, Volume 1: An Introduction, New York, Vintage Books, 1978, page 95
7	Evolution From the 1960’s to 2007 there has been an evolution of scientific information from paper to electronic form, coupled with a revolution in computer and network communication capabilities (i.e., the Internet) which is transforming the way information is collected, processed, disseminated, and used.
8	Evolution Web 1.0 - We have evolved from everything on paper, which needed to be centrally organized and distributed from a central source to … Web 2.0 - Currently uncontrolled chaos and a revolution with data and information being dumped into systems around the world.
9	Scribes in the 15th century were not happy with Johann Gutenberg. Publishers in the 21st century are not happy with Tim Berners-Lee/Internet If horses could vote we would never have cars.
10	1960’s Printed Abstracts from CAS, UK Few databases/compilations All on paper – Simple text; few diagrams A handful of computers worldwide Chemical Information was supported by a thriving chemical industry
11	1960’s The chemist would read the CAS sections appropriate to their research needs. Then he/she would go to the library to read the full journal article of interest. Often this meant a request for an interlibrary loan to obtain the article.
12	2007 Everything is electronic Databases are common in chemistry and biology Everyone has a PC and Internet access Data and databases are commonplace and large Databases have gone from primarily text to value-added indexing, coding, structures, and linking (e.g. PubChem) The chemical industry has been overtaken by biology/biochemistry/biomedicine causing problems for the ACS/CAS Bioinformatics data is the antithesis of the chemical data franchise Current Awareness has evolved into Continuous Awareness
13	2007 The chemist logs onto CAS/SciFinder®, ISI Web of Science®, Integrity®, ScienceDirect®, Scirus.com®, Chemindustry.com®, PubChem, or Chemweb.com® to search for something of interest. Then he/she clicks in the hyperlink, using LitLink or ChemPort and, assuming you have a paid for access to the journal article, the article appears immediately on your computer screen for you to read or print out and take to the bathroom to read. Now document delivery is easy and fast. More importantly, one learns from the experiences of others - being able to do computer searches of the literature helps a lot and allows one to read more articles of interest.
14	Organizations that fail to recognize and confront technological and market changes often tend to lose their positions, if not their organizations. History is replete with such examples. In the 18th century the power looms replaced the handloom weavers, In the early 20th century the horse and buggy industry giving way to automobiles. In the late 20th century the airplane replaced the train and boat for long distance traveling. Now, at the start of the 21st century the technology of the Internet is threatening the way in which the 3+ century old scientific publishing industry and libraries which subscribe to scholarly publications have done business for many decades.
15	Evolution becomes a revolution when there are a sufficient number of mutations to take over and replace the old forms of life. When the “tipping or change point” comes is impossible to predict, but it WILL come.
16	It takes very little to make a significant change. For example, moisture at +1 C is rain. At –1 C, it is snow. And 1 cm. of rain = 10- 20 cm. of snow.
17	When it comes to change, some organizations are so dense, light bends around them. But others, see change coming and do or try to adapt.
18	In the 1950’s to the early 1990’s scientists had considerable support staff to type, edit, file, communicate, and so on. But now, with computers and the Internet everyone in this room can: Edit text better a secretary Calculate more accurately than the bookkeeper File better than the office clerk Communicate cheaper and faster than the mail room Draw better the art department
19	“The blockbuster model does not work as a business anymore,” There are lots of reasons for this. For one, as Pfizer discovered with the failure of torcetrapib, when you live by the blockbuster, you die by the blockbuster —companies simply need to become less reliant on a small handful of big moneymakers that will inevitably go away. ... “If you go the blockbuster route any setback is going to be catastrophic.” For another, the larger society has become much less tolerant of Big Pharma’s tactics. There is a backlash against the kind of direct-to-consumer advertising that has propelled many drugs into blockbuster status. The game-playing by many companies to extend the life of their patents is under attack by the US Congress and the FTC. The FDA is giving tougher scrutiny to drug applications — especially for drugs that are only marginally different from those already on the market. “In some ways, Big Pharma is a victim of its own success. There was a tremendous period when they were coming up with drugs for chronic diseases that affected lots of people. There is now a lot of very good generic product on the market. And while there have been significant innovations, there hasn’t been a big wave like the last one.” It had a great deal of success doing things one way. And however much its people may say they want to change and thrive, Mr. Kindler is about to discover the same thing executives in the newspaper and auto industries already know. It’s hard to teach an old dog new tricks. The Dangers of Swinging for the Fences - Jor Nocera, NY York Times, Published: January 27, 2007
20	AOL – Started charging $19.95 per month for Internet access. It evolved and grew to be the largest online service. But the Internet also evolved and grew and the AOL monthly fee model began to develop problems. The number of users went from 35+ million to under 20 million, while usage of the free service Google went from zero (0) to tens of millions. In August 2006 AOL announced: "We’re in the process of offering all of our content and many of our services for free -- with or without an AOL Internet connection.”
21	"New scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it." Max Planck, "Scientific Autobiography and Other Papers", Williams & Norgate, London (1950), pages 33-34.
22	The circulation of daily U.S. newspapers is 55.2 million, down from 62.3 million in 1990. The percentages of adults who say they read a paper "yesterday" are ominous: 65 and older -- 60 percent. 50-64 -- 52 percent. 30-49 -- 39 percent. 18-29 -- 23 percent. A structural change in the way get information 4/25/2005 “Unread and Unsubscribing” - George F. Will – US syndicated columnist
23	Most Popular Web Sites Yahoo!- free Google - free MySpace – free social network MSN - free EBay Amazon Craiglist – free classified ads CNN news - free Wikipedia - free # 19 – NY Times - free # 27 – BBC - free # 66 – FaceBook – free university/college social network # 290 – NLM/NIH - free # 7,756 - ACS # 41,695 – CAS # 180,328 – ISI/Web of Science
24	Members/Users MySpace – 100 million users/profiles; 2,210,000 users/day Ebay – 100 million users -- 5,044,00 users/day FaceBook – 8 million users/profiles of university students NLM/NIH – PubMed/PubChem – 500,000 users/day CAS – 1000 organizations - ? users/day Yahoo! - 16,031,000 users/day Google – 15,130,000 users/day Wikipedia – 4,260,000 users/day ComScore.com – June 2006 analysis
25	Science Publishing and the Web TheWeb 2.0, social networking, wikis, mashups, and so on are poised to radically change the ability of scientists to share data and develop ideas both within and between organizations. “Scientists are eager to apply the awesome power of the Internet revolution to scientific communication, but have been stymied by the conservative nature of scientific publishing,” says PLoS co-founder Michael Eisen http://www.bio-itworld.com/issues/2006/july-aug/first-base/
26	Web 2.0 changes 1. Diminished stature for many existing institutions 2. Hierarchies are coming undone 3. Gatekeepers are being bypassed 4. Many intermediaries are no longer necessary Andrew Shapiro The Control Revolution, Public Affairs, New York, 1999 (ISBN: 1-891620-19-3)
27	Growth of Open Access Steve Heller’s Google News Alert Service (A non-scientific study ) Started May 2004 – 6 news articles January 2007 – 42 news articles
28	Open Access Information Peter Suber list (started in 2001): http://www.arl.org/sparc/soa/index.html Steven Harnad List (started in 1998): http://amsci-forum.amsci.org/archives/American-Scientist-Open-Access-Forum.html
29	The availability of for-free services such as those offered in the patent field by the EPO and now Google (plus others) is a real threat to financial viability of many traditional, high-cost information providers. A small core of faithful users -- who feel they need advanced features -- may stay with Thomson, CAS, Questel, Dialog, etc. But this small core may well be too small to support high-cost services. Harry Collier, private communication, January 2007 …And this small core of users are aging and retiring with the new generation which has been brought up on Google, FaceBook, MySpace, and similar technology and services.
30	Steve- “I had lunch with a senior manager at Springer. He told me that 95% of their search referrals come from Google and PubMed! I found this number quite impressive. I wonder why Elsevier spends millions developing their search interface?” February 2007
31	Microsoft – February 2007 Hires a “Industry Technology Strategist for the Pharma Industry”
32	'Wikinomics: How Mass Collaboration Changes Everything' Talk of the Nation (radio program), January 2, 2007 · YouTubers, wiki-users and MySpacers are at the vanguard of a movement that's changing the way we do business. Guest: Don Tapscott, co-author of Wikinomics: How Mass Collaboration Changes Everything http://www.npr.org/templates/story/story.php?storyID=6711038
33	Open Access in Chemistry Beilstein Journal of Organic Chemistry – less than 50 articles since August 2005 ChemistryCentral.com – just starting IJC – Over 100 articles in 7 years (1998-2004) Closed due to lack of papers.
34	IJC & BJOC submissions IJC BJOC 1998 - 38 1999 - 25 2000 - 14 2001 - 12 2002 - 8 2003 - 6 2004 – 4 2005 - 18 2006 - 26 2007 - 3 (up to 2/07) Totals – 107 47
35	Journals are a method of destroying information and data on a gigantic scale. Johnny Gasteiger
36	RSC – Project Prospect From 2/2007 electronic RSC journals will have metadata added to each article – CML, InChI, and OBO – Open Biomedical Ontologies. This way one can search using chemical structure and these index terms. Sooner, rather than later, secondary publishers (e.g., CAS) will find their role is no longer needed.
37	InChI A project whose time has come. Without the Internet InChI would be just another in a series of technically excellent, soon forgotten, projects for representing chemical structures. The Internet, an international scientific body (IUPAC), and international cooperation (US, UK, Czech Republic) has led to the speedy development, implementation, and use of InChI. While InChI is a public domain, open source system for creating a unique computer-readable identifier (“name”) it is NOT a registry system. InChI’s are created only by those who choose to adopt and use the algorithm. Registry systems which index the literature are complimentary to any InChI databases that anyone creates.
38	InChI Digital ‘Naming’ of Chemicals: Chemical structure is the true ‘identifier’ But, structure representations are not unique or convenient for computers. So, convert structure to a unique ‘name’ by fixed algorithms The IUPAC International Chemical Identifier (InChI)
39	Two Major Problems 1. Chemicals – Fast isomerization (tautomerization) – Ill-defined connectivity 2. Chemists – Differing conventions Depends on discipline, education and convenience Imprecision/uncertainty
40	InChI Layers Formula Connectivity Stereochemistry/Chirality Isotope Charge Fixed/Mobile Hydrogens And so on
41	How does InChI differ from SMILES? Like InChI, the SMILES language allows a canonical serialization of molecular structure. However, SMILES is proprietary and unlike InChI is not an open project. This has led to the use of different generation algorithms, and thus, different SMILES versions of the same compound have been found. In fact, we have found seven different unique SMILES for caffeine on Web sites: 1.[c]1([n+]([CH3])[c]([c]2([c]([n+]1[CH3])[n][cH][n+]2[CH3]))[O-])[O-] 2.CN1C(=O)N(C)C(=O)C(N(C)C=N2)=C12 3.Cn1cnc2n(C)c(=O)n(C)c(=O)c12 4.Cn1cnc2c1c(=O)n(C)c(=O)n2C 5.N1(C)C(=O)N(C)C2=C(C1=O)N(C)C=N2 6.O=C1C2=C(N=CN2C)N(C(=O)N1C)C 7.CN1C=NC2=C1C(=O)N(C)C(=O)N2C
42	5 Useful InChI URL’s IUPAC InChI URL: http://www.iupac.org/inchi The InChI-L Listserver WebBoard URL: http://webboard.rsc.org:8080/~INCHI-L InChI FAQ’s: Created by Nick Day, Cambridge University, UK: http://wwmm.ch.cam.ac.uk/inchifaq/ IUPAC Prague Group InChI URL: www.inchi.info http://video.google.com/videoplay?docid=-6653695245776470969&q=heller+chemical
43	InChI take-up by software developers and database providers Software: 1. Structure Drawing a. ACD Labs: ChemSketch http://www.acdlabs.com b. CambridgeSoft: ChemDraw http://www.camsoft.com c. ChemAxon: Marvin http://www.chemaxon.com d. BK-Chem: http://bkchem.zirael.org/inchi_en.html 2. Structure Search a. IBM (internal project) 3. Analysis software a. SciTegic: http://www.scitegic.com 4. Structure file interconversion a. OpenBabel: http://openbabel.sourceforge.net/RELEASE.shtml 5. Other software a. World Wide Molecular Matrix: http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere
44	Databases: (ordered by when adopted) 1. NIST WebBook http://webbook.nist.gov 2. NIH PubChem http://pubchem.ncbi.nlm.nih.gov 3. NCI DTP http://cactus.nci.nih.gov/ncidb2/ 4. EPA - DSSTox http://www.epa.gov/nheerl/dsstox/ 5. UC-SF ZINC project http://blaster.docking.org/zinc/ 6. KEGG http://www.genome.ad.jp/kegg/ 7. ISI Web of Science http://portal.isiknowledge.com/ 8. Carcinogenic Potency http://potency.berkeley.edu/structure.html 9. ChEBI http://www.ebi.ac.uk/chebi 10. Wiley Mass Spectra http:www.wiley.com/WileyDCA/Section/id- 131370.html 11. Prous Science Integrity http://integrity.prous.com/integrity/servlet/xmlxsl/ 12. FDA GeneTox and Chronic/subchronic Databases http://www.leadscope.com/fdadb_cat.php 13. Compendium of Pesticide Common Names http://www.alanwood.net/pesticides
45	Technical/Economic /Political Features of InChI 1. It works as well as any other system. 2. It is free-open source software. (Web 2.0) 3. Any organization can use for internal and/or external structure files at no cost. (Web 2.0) 4. It is sponsored by IUPAC and primarily implemented by the US scientific standards agency – NIST. 5. It allows one to have an alternative to the CAS Registry and to InChI’s can be freely searched for via Google/Yahoo/Microsoft. (Web 2.0) 6. It allows all those chemical information providers who compete with CAS to have a free alternative. (Web 2.0)
46	The Future Between researchers putting their results on the web, journal metadata projects such as the RSC has started, and Google/Yahoo/Microsoft developing ways to search text and chemical structures all non-copyright, non-proprietary information will be readily available. Who knows, Google or Microsoft might even buy all of Elsevier’s back-file content one day.
47	The Future 1. People will continue to pay for real added value. 2. People will pay for software and analysis tools that are worth the money. 3. Open Access journals will continue to evolve and will become the mainstream of scientific publishing. 4. Open Source, such as IUPAC/InChI will become the predominant structure representation form. 5. E-Notebooks/LIMS will grow and evolve into organization-wide linked information systems.
48	Acknowledgements Steve Bachrach, Mila Becker, Jost Bohlen, Pieter Bolman, Evan Bolton, Bob Bovenschulte, Steve Bryant, Harry Collier, Alice Cooper, Rene Deplanque, Guenter Grethe, Stevan Hanard, Sami Kassab, David Lipman, Gary Mallard, Randy Marcinko, Alan McNaught, Bill Milne, Carmen Nitsche, Josep Prous, Chris Reed, Rich Roberts, Peter Murray-Rust, Henry Rzepa, Steve Stein, Peter Shepherd, Bill Town, Andrea Twiss-Brooks, Wendy Warr, Ann Wolpert