Chemical Information and Chemical Informatics Literacy at Indiana University

1. Chemical Information and Chemical Informatics Literacy at Indiana University Gary Wiggins School of Informatics Indiana University wiggins@indiana.edu

2. Abstract The Department of Chemistry at Indiana University offers four one-hour chemical information or chemical informatics courses on the undergraduate level and two three-hour courses on the graduate level. Most of the courses have been taught via teleconferencing across two campuses during the past two years, with some lectures delivered from England in one graduate course. A mix of free and commercial software and databases is used in the courses. Methodology, software, and cost figures will be presented.

3. Huge Size of the Chemical Lit • ~ 50 million chemical substances • ~ 6 million reagents • ~ 7 million published reactions • ~16,000 protein crystal structures • ~250,000 small molecule x-ray structures --Robert Glen and Susan Aldridge http://xlink.rsc.org/?DOI=b207793k

4. Special Programs at IU • MLS or MIS Programs with Specialization in Chemical Information (SLIS) • SLIS Graduates: http://www.indiana.edu/~cheminfo/informatics/mls_mis_grads1.html • BS and MS Programs in Chemical Informatics (with PhD on the way) http://www.informatics.indiana.edu/academics/degrees.asp

5. ACS CPT Guidelines Statement on Chemical Information Retrieval • “A student who intends to become a practicing chemist, or who will use chemistry in allied fields of science and medicine, should know how to use the chemical literature effectively and efficiently.” • http://www.chemistry.org/portal/Chemistry?PID=acsdisplay.html&DOC=education\cpt\ts_cheminfo.html

6. Undergraduate Courses • Four one-credit undergrad courses • C371 Chemical Informatics • C372 Molecular Modeling • C471 Chemical Information Sources and Services • C472 Computer Sources for Chemical Information

7. Sample Course Pages • Indiana: http://www.indiana.edu/~cheminfo/instructional_materials.html • Pennsylvania: http://www.sas.upenn.edu/chem/library/infoclass/index.html • Vanderbilt: http://www.library.vanderbilt.edu/science/Chem250/Chem250.htm • Cornell: http://www.library.cornell.edu/psl/chem602/ • Purdue: http://www.lib.purdue.edu/chem513/ • UC, Santa Barbara: http://www.library.ucsb.edu/classes/chem184/

8. Patents: What Every Chemist Should Know • A new patent is issued every three minutes. • http://www.chemistry.org/portal/Chemistry?PID=acsdisplay.html&DOC=government%5Ccapitolconnection%5Ccc_Feb2003.html#patents

9. Graduate Courses • Two three-credit graduate courses • C571 Chemical Information Technology • C572 Molecular Modeling & Computational Chemistry

10. Course Enrollments

11. Also Polycom Participants

12. Instructors • My role in the programs: Director, Chemical Informatics Program; Interim Director, Bioinformatics Program (School of Informatics) • IUB faculty: Mu-Hyun Baik • IUPUI: Sam Milosevich, Doug Perry and Mahesh Merchant (Laboratory Informatics) • Visiting faculty, Adjuncts: David Wild; Kevin Gilbert, John Barnard, Bill Milne; Kelsey Forsythe, John McKelvey (IUPUI); • Guest lecturers: Guenter Grethe, Marc Nicklaus • Bioinformatics: Sun Kim, Mehmet Dalkilic, Predrag Radivojac; Jeffrey Huang (IUPUI)

13. Methodology • Much material on the Web • Lots of hands-on experience with both printed and electronic tools • Emphasis on re-use of data retrieved without re-keying • Emphasis on understanding the content and coverage of the tools and selecting the right tool(s)

14. Options for CA Searching • SciFinder Scholar (C471) • STN on the Web (C472) • STN Express with Discover! • STN Easy • CA Student Edition (OCLC)

15. Minerva CrossFire License • Beilstein CrossFire plus Reactions • Gmelin

16. Other Tools • Cambridge Structural Database • Specialized Reaction Databases • EROS • SPRESI • Organic Syntheses (FREE!)

17. Other “Free” Tools Used • ChemFinder • NIST Chemistry WebBook • ChemSketch and ISIS/Draw • Many Web sites, e.g. PubMed, ChemIDplus, esp@cenet, EPA Chemical Registry System, etc. • EndNote, ProCite, Reference Manager (campus license) • Microsoft NetMeeting and Excel (campus license) • Daylight software (campus license)

18. CAS Academic Program • Access after 5:00 PM and on weekends • Learning files for CA and Registry databases • Deep discounts on usage: 80% for PhD-granting institution; 90% for non-PhD • Limited Databases: CA, CAOLD, Registry, CIN and Learning Files (including LCA, LREGISTRY, LCASREACT, and LMARPAT) • Requires CA Subscription in some format

19. C472 STN Search Costs(Academic Program)

20. Costs of Other Tools(FY 2002/2003)

21. Costs of Other Tools(FY 2003/2004)

22. Wish List • MDL DiscoveryGate Program: $54,000(?) [includes Beilstein and Gmelin, but not Science of Synthesis] • Scitegic’s Pipeline Pilot • Spotfire DecisionSite • Spectral Databases, e.g., BioRad’s KnowItAll Academic Edition: $?????? • Other Tools: • OpenEye Software OEChem 1.2 (free) • Chem TKLite

23. Chemical Information Literacy-- • Is it affordable? • It MUST be!

24. Sample Chemical Informatics Activities • SMILES • Database Creation • Scanning and Indexing of Groth’s Chemische Krystallographie • Database of Lawson Numbers

25. SMILES input for Structure Searching

26. SMILES for 1,2,3-Tribromobenzene

27. Groth, P. (Paul), 1843-1927.Chemische Krystallographie • Leipzig: W. Engelmann, 1906-19. 5 v. • T. 1. Elemente: Anorganische Verbindungen ohne Salzcharakter. Einfache und complexe Halogenide, Cyanide und Azide der Metalle, nebst den zugehörigen Alkylverbindungen. • T. 2. Die anorganischen Oxo- und Sulfosalze. • T. 3. Aliphatische und hydroaromatische Kohlenstoffverbindungen. • T. 4. Aromatische Kohlenstoffverbindungen mit einem Benzolringe. • T. 5. Aromatische Kohlenstoffverbindungen mit mehreren Benzolringen heterocyclische Verbindungen.

28. Groth: Access Database • Portion of the table with chemical names, molecular formulas, SMILES, and links to images on the Web.

29. Groth: Image from page 4: 6 • http://www.indiana.edu/~cheminfo/Groth/groth400006.pdf

30. XMorph Rendering of a Crystal

31. Groth: Image from page 4: 6 • http://www.indiana.edu/~cheminfo/Groth/groth400006.pdf

32. Future Developments • Metadata coding and XML for selected CHEMINFO Web pages • Links to XMorph renderings from the Groth database • Structure searching of the Groth database with JME Molecular Editor input of SMILES • Put DB on the Web with Cold Fusion

33. Lawson Number • Originally used in the program SANDRA • Algorithmic expression of the System-Numbers in the printed work Beilstein Handbook of Organic Chemistry • System Numbers: 1-4720 • Lawson Numbers: 8-32759 • System Number = Lawson Number divided by 8 (roughly) • Inherited the ambiguity of the page number placement

34. Lawson Number Search for LN 289 in Usha’s Database

35. Lawson Number Search • Find a compound with a cyclopentane ring with three free sites (over 440,000 substances) and with both LN 31459 and LN 289 • Result: 10 substances on 4/15/2004

36. Lawson Number Search Yields Very Diverse Results

37. Thanks to Graduate Fellowship Sponsors: • Daylight Chemical Information Systems • MDL Information Systems