A Wiki-Based Chemical Information Instructional

Resource

Gary WigginsIndiana University

School of Informaticswiggins@indiana.edu

May 21, 2007

Abstract In 1991, McGraw-Hill published the book Chemical Information Sources, an at-the-

time innovative textbook that included a disk with a database containing citations to 2500 reference materials and the software to search it. The database was later converted to a Web-searchable format, the Chemical Reference Sources Database, and the lecture notes for the undergraduate Chemical Information Sources class were placed on the Web. In 2006, all instructional modules associated with the course were converted to the Wiki format, thus allowing others to contribute to the material. Wikis are also used for some courses in the IU School of Informatics graduate cheminformatics degree and certificate programs, e.g., “Chemical Information Technology” and “Programming for Science Informatics.” The Chemical Information Sources Wiki has 20 modules covering everything from how to find a method of synthesizing a compound to how to find a job. The tool is integrated with a related Wiki source, SIRCh, Selected Internet Resources for Chemistry, and other Web resources. In addition, links are provided to relevant sections of the Clearinghouse for Chemical Information Instructional Materials where additional materials that are designed to instruct people in the use of chemical reference tools can be found. Experiences in creating and maintaining the Wiki resource in a shared-author, open-access environment will be presented.

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 (2002)

http://xlink.rsc.org/?DOI=b207793k

ACS CPT Statements 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.” (2003)

• “Students should be able to use the peer-reviewed scientific literature effectively and evaluate technical articles critically. They should learn how to retrieve specific information from the chemical literature, including the use of Chemical Abstracts and other compilations, with online, interactive database-searching tools.” (2007 draft)

2003 CPT Recommendations on How to Gain Proficiency

• Proficiency in chemical information retrieval should be acquired through formal instruction.– Through a course dedicated to the subject of

chemical information retrieval, – Through integration into other chemistry

courses, – Through coordination and monitoring of each

student's satisfactory achievement, preferably by one faculty member or librarian.

2007 Draft CPT Recommendations on How to Gain Proficiency

• Approved programs must provide instruction on the effective retrieval and use of the chemical literature. – A specific course is an excellent means of imparting

information-retrieval skills, though such a course usually would not qualify as an in-depth course.

• 37% used this option in 2005.

– Integrating the use of these skills into several individual courses is also an effective approach.

• 73% used this option in 2005.

– Both library and online exercises should be a part of such instruction.

Little Red Book

A good idea

with the wrong info

technology.

What’s a Wiki?

• A website that allows visitors to add, remove, and edit content

• A collaborative technology for organizing information on Web sites

• Wikis allow for linking among any number of pages.

• The ease of interaction and operation makes a wiki an effective tool for mass collaborative authoring.

• Source: Wikipedia, 5/17/2007

Graduate Cheminformatics Courses Taught with a Wiki

• I571 Chemical Information Technology– http://cheminfo.informatics.indiana.edu/djwild/

I571_2006_wiki/index.php/Main_Page

• I573 Programming for Science Informatics– http://cheminfo.informatics.indiana.edu/djwild/

I573_2007_wiki/index.php/Main_Page

Chemical Information Sources Wiki

• http://cheminfo.informatics.indiana.edu/cicc/cis/index.php/Main_Page

• Purposes: – To provide a free guide to the many sources of

reference materials available to those with questions related to chemistry

– To provide a convenient text to supplement instruction in chemical information retrieval

• Historical Roots: the C471 Chemical Information Sources course taught from 1976-2003 in the IU Chemistry Department

Overall Organization of the CIS Wiki

• How and Where to Start

• How and Where to Search: General

• How and Where to Search: Specialized Sources

• Communication in Chemistry

• Miscellaneous

How and Where to Start

1. The Publication Process: Primary, Secondary, and Tertiary Sources

2. Guides to Chemical Information Sources and Databases

3. General Information on Computer Searching

4. Current Awareness, Reviews, and Document Delivery

5. Background Reading: Dictionaries, Encyclopedias, and Other Books

Books

Screen Shot 1

How and Where to Search: General

6. Searching by Author or Organization Name and by Known Citations

7. Searching by Subject

8. Chemical Name and Formula Searching

9. Structure Searching

Example 2

How and Where to Search: Specialized Sources

10. Searching for the Synthesis or Reactions of Specific Compounds or Classes of Compounds

11. Chemical Safety and Toxicology Information

12. Analytical Chemistry

13. Physical Property Information

14. Chemical Patent Searching

Beilstein 1

Communication in Chemistry

15. Chemistry Newsgroups, Discussion Lists, and Blogs

16. Molecular Visualization Tools and Sites

17. Science Writing Aids

ChemDraw Example

Miscellaneous

18. Chemical History, Biography, Directories, and Industry Sources

19. Teaching and Study of Chemistry

20. Careers in Chemistry

Teaching

Usage of the CIS Wiki

• Visitors since January 1, 2007 (as of 5/17/07)– Range from 1235 (Background Reading) to

10,700 (Chemical Name and Formula Searching)

– Average number of visits per page: 3263

Other CIS Wiki Features

• SIRCh: Selected Internet Resources for Chemistry– http://cheminfo.informatics.indiana.edu/cicc/cis/

index.php/SIRCh:_Selected_Internet_Resources_for_Chemistry

• CRSD: Chemical Reference Sources Database– http://www.oscar.chem.indiana.edu/cfdocs/

libchem/crsd/crsdintro.html

SIRCh

CRSD Search

Parting words . . .

If you're not part of the solution, you're part of the precipitate!

Moving on to retirement

Bibliography• ACS Committee on Professional Training. Chemical Information Retrieval.

http://www.chemistry.org/portal/Chemistry?PID=acsdisplay.html&DOC=education\cpt\ts_cheminfo.html

• ACS Committee on Professional Training. Undergraduate Professional Education in Chemistry: Guidelines and Evaluation Procedures. Draft, 2/27/2007. http://acswebcontent.acs.org/education/cpt/acs_draftguidelines.pdf

• Culp, F. Bartow. "Ten or so things that every chemistry librarian absolutely, positively has to have to keep from being an absolute plonk." Sci-Tech News, February 2004, 58(1), 9. also published as: SLA Chemistry Division E-Newsletter Winter 2004, 18(3), 19-20). http://www.sla.org/division/dche/Newsletters/Feb_2004.pdf

• Garritano, Jeremy R.; Culp, F. Bartow.   ”Chemical information instruction, 1984-2004: who is leading the charge?”    Abstracts of Papers, 229th ACS National Meeting, San Diego, CA, United States, March 13-17, 2005  (2005),  CINF-107. Also found at: http://units.sla.org/division/dche/2005/garritano.pdf  

• Gasaway, Laura. “The open archives movement.” Information Outlook October 2004, 8(10), 36, 39-40.

Bibliography• Glen, Robert; Aldridge, Susan. “Developing tools and standards in

molecular informatics.” Chemical Communications 2002, (23), 2745-2747. DOI: 10.1039/b207793k http://xlink.rsc.org/?DOI=b207793k

• Huber, C.; Porter, K. “Cheap tricks.” http://www.indiana.edu/~cheminfo/workshop/cheap.html

• McLeland, Le-Nhung. What every chemist should know about patents. http://www.chemistry.org/portal/resources/?id=1b41692a6cf811d6f8dd6ed9fe800100

• Murray-Rust, Peter; Rzepa, Henry S.; Tyrrell, Simon M.; Zhang, Yong. “Representation and use of chemistry in the global electronic age.” Organic & Biomolecular Chemistry 2004, 2(22), 3192-3203 (correction: 2005, 3(10), 2037).

• Somerville, Arleen N..   ”Chemical Information Instruction in Academe: Recent and Current Trends.”  Journal of Chemical Information and Computer Sciences  1998, 38(6), 1024-1030.

Bibliography• Wagner, A. Ben. "Finding physical properties of chemicals: A

practical guide for scientists, engineers, and librarians.” Science & Technology Libraries 2001, 21(3/4), 27-45. (published Fall 2003) Text for personal and professional use available at: http://ublib.buffalo.edu/libraries/asl/staff/documents/wagner_phys_prop_stl_art.pdf

• Wiggins, Gary. “Overview of databases/data sources.” in Gasteiger, Johannes, ed. Handbook of Chemoinformatics: From Data to Knowledge in 4 Volumes. Wiley-VCH: 2003, v. 2, pp. 496-506. http://www.indiana.edu/~cheminfo/C571/wiggins_chapter_2003.pdf

• Wiggins, Gary. “Teaching chemical literature, databases, and chemical informatics.” CPT; Committee on Professional Training [newsletter] Spring 2004, 4(1), 1-2. http://acswebcontent.acs.org/PDF/cpt/nl_cpt_spring2004.pdf