1. Chemical Information and Chemical Informatics Literacy at Indiana University
Gary Wiggins
School of Informatics
Indiana University
4/5/2019

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.
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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
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4. Special Programs at IU
MLS or MIS Programs with Specialization in Chemical Information (SLIS)
SLIS Graduates:
BS and MS Programs in Chemical Informatics (with PhD on the way)
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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.”
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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
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7. Sample Course Pages Indiana:
Pennsylvania:
Vanderbilt:
Cornell:
Purdue:
UC, Santa Barbara:
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8. Patents: What Every Chemist Should Know
A new patent is issued every three minutes.
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9. Graduate Courses Two three-credit graduate courses
C571 Chemical Information Technology
C572 Molecular Modeling & Computational Chemistry
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10. 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
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11. Also Polycom Participants
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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)
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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)
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14. Options for CA Searching
SciFinder Scholar (C471)
STN on the Web (C472)
STN Express with Discover!
STN Easy
CA Student Edition (OCLC)
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15. Minerva CrossFire License
Beilstein CrossFire plus Reactions
Gmelin
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16. Other Tools Cambridge Structural Database
Specialized Reaction Databases
EROS
SPRESI
Organic Syntheses (FREE!)
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17. Other “Free” Tools Used
ChemFinder
NIST Chemistry WebBook
ChemSketch and ISIS/Draw
Many Web sites, e.g. PubMed, ChemIDplus, EPA Chemical Registry System, etc.
EndNote, ProCite, Reference Manager (campus license)
Microsoft NetMeeting and Excel (campus license)
Daylight software (campus license)
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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
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19. 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
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20. 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
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21. 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
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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
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23. Chemical Information Literacy--
Is it affordable?
It MUST be!
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24. Sample Chemical Informatics Activities
SMILES
Database Creation
Scanning and Indexing of Groth’s Chemische Krystallographie
Database of Lawson Numbers
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25. SMILES input for Structure Searching
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26. SMILES for 1,2,3-Tribromobenzene
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27. Groth, P. (Paul), 1843-1927. Chemische Krystallographie
Leipzig: W. Engelmann, 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.
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28. Groth: Access Database
Portion of the table with chemical names, molecular formulas, SMILES, and links to images on the Web.
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29. Groth: Image from page 4: 6
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30. XMorph Rendering of a Crystal
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31. Groth: Image from page 4: 6
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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
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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:
Lawson Numbers:
System Number = Lawson Number divided by 8 (roughly)
Inherited the ambiguity of the page number placement
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34. Lawson Number Search for LN 289 in Usha’s Database
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35. Lawson Number Search
Find a compound with a cyclopentane ring with three free sites (over 440,000 substances) and with both LN and LN 289
Result: 10 substances on 4/15/2004
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36. Lawson Number Search Yields Very Diverse Results
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37. Thanks to Graduate Fellowship Sponsors:
Daylight Chemical Information Systems
MDL Information Systems
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