Chemical Information and Chemical Informatics Literacy at Indiana University Gary Wiggins School of Informatics Indiana University wiggins@indiana.edu 4/5/2019

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. 4/5/2019

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 4/5/2019

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 4/5/2019

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 4/5/2019

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 4/5/2019

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/ 4/5/2019

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 4/5/2019

Graduate Courses Two three-credit graduate courses C571 Chemical Information Technology C572 Molecular Modeling & Computational Chemistry 4/5/2019

Course Enrollments Course 1997 1998 1999 2000 2001 2002 C371 NA 10 5 111 97 84 65 56 55 C571 1 12 C372 C472 7 15 21 C572 4/5/2019

Also Polycom Participants 4/5/2019

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) 4/5/2019

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) 4/5/2019

Options for CA Searching SciFinder Scholar (C471) STN on the Web (C472) STN Express with Discover! STN Easy CA Student Edition (OCLC) 4/5/2019

Minerva CrossFire License Beilstein CrossFire plus Reactions Gmelin 4/5/2019

Other Tools Cambridge Structural Database Specialized Reaction Databases EROS SPRESI Organic Syntheses (FREE!) 4/5/2019

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) 4/5/2019

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 4/5/2019

C472 STN Search Costs (Academic Program) Year # of Students Costs 1999 15 $59.16 2000 21 $111.83 2001 7 $43.56 2002 10 $439.23 4/5/2019

Costs of Other Tools (FY 2002/2003) Title Cost SciFinder Scholar Ph.D. Package 2 $74,100 SciFinder Scholar Sixth Seat $15,800 Minerva CrossFire (Beilstein/Gmelin) $38,493 Cambridge Structural Database $2,000 DGRWeb [$750] EROS; Encyc. Reag. Org. Synth. $2,205 Inorganic Cryst. Structure DB [$1,400] Analytical Abstracts $2,024 4/5/2019

Costs of Other Tools (FY 2003/2004) Title Cost ACS Journal Archives $4,500 ACS Web Editions $42,398 Royal Society of Chemistry Plan A & G $20,417 Tetrahedron Family Subscription (Elsevier) $27,263 Pcmodel [Free to IU only] Spartan ’02 Essential Edition (50 seats) $5,500 SPRESI $1,000 CRC Handbook of Chemistry & Physics $1,295 Access Perry’s (Lange’s, Perry’s, + 1 other) $2,500 TOTAL (ALL) $241,645 4/5/2019

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 4/5/2019

Chemical Information Literacy-- Is it affordable? It MUST be! 4/5/2019

Sample Chemical Informatics Activities SMILES Database Creation Scanning and Indexing of Groth’s Chemische Krystallographie Database of Lawson Numbers 4/5/2019

SMILES input for Structure Searching 4/5/2019

SMILES for 1,2,3-Tribromobenzene 4/5/2019

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. 4/5/2019

Groth: Access Database Portion of the table with chemical names, molecular formulas, SMILES, and links to images on the Web. 4/5/2019

Groth: Image from page 4: 6 http://www.indiana.edu/~cheminfo/Groth/groth400006.pdf 4/5/2019

XMorph Rendering of a Crystal 4/5/2019

Groth: Image from page 4: 6 http://www.indiana.edu/~cheminfo/Groth/groth400006.pdf 4/5/2019

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 4/5/2019

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 4/5/2019

Lawson Number Search for LN 289 in Usha’s Database 4/5/2019

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 4/5/2019

Lawson Number Search Yields Very Diverse Results 4/5/2019

Thanks to Graduate Fellowship Sponsors: Daylight Chemical Information Systems MDL Information Systems 4/5/2019