the chemical information instructor
edited by ARLEEN SOMERVILLE Carison Library
Univesity of Rochester Rochester. NY 14627
Undergraduate Online Chemistry Literature Searching An Open-Ended, Course Segment Approach Ron C. Cooke California State University-Chico, Chico, CA 95929-0210; [
[email protected]]
In the information age chemists no longer need to study scores of bound volumes to gather information. Information is literally a t our fingertips a s we effortlessly connect our small computers to larger computers with gigantic memory banks. We type our requests for information and the remote computers oblige by sending citations, abstracts, physical and chemical data, patents, and even fulltext articles. There is no doubt, a s chemistry teachers, we should enlighten our students about the world of online database searching and telecommunications. Questions do arise: How can this be done economically and with a modest amount of equipment? How can security be maintained? Who will teach this technology? Should the training be a n independent course? California State University-Chico (CSUC) has a writing proficiency requirement in every course in every major. Writing, in science education, should include the training needed to communicate creative work be it original or review. An important prelude to communication is a review of relevant literature in books, journals, articles, and patents. The chemistry department a t CSUC established a n online searchine nroeram a s a course s e m e n t rather than a dedicated course. his eliminated theproblems assomated uirh croatine il new course and also allowed Ihxildity in determiningthe segment content. The content w a s t a i lored to its associated course. The purpose of this article is to present the methods we used hoping that they may be useful to others in establishing similar programs. Database Vendor We chose Dialog a s the database vendor. The Dialog Classroom Instruction Program (CIP) bas very low rates ($18-21 per connect hour), bas over 300 databases, and is available 24 hours a day, 7 days per week. The databases provided in the CIP are complete; not "learning files" with a limited content. The CIP is available by commercial telecommunications networks or via the internet. Cost and Connections Dialog has two pricing options for the CIP. If a n internet connection (e.g., Telnet connection to DIALOG.COM) is used, the cost is $18 per hour. This can be utilized a s a normal account that is billed monthly or a s an alternative, a self-expiring password account can be purchased. For example, suppose each student will need two hours online. Yon can purchase a number of two hour accounts (with individual user numbers and passwords) for $36 each. At the
end of the time period, the accounts expire. This method adds a n extra measure of security and lends itself to having students pay the cost as "lab fees." The internet connection can be accessed up to 9600 baud. If a commercial telecommunications service such a s SPRINTNET or BT is used, the cost is $ 2 1 per hour and is billed monthly The connection rate is 300-9600 baud depending on locality. Equipment
Any computer or terminal that is capable of connecting to Dialog is adequate. The connection can be via modem or network. We found that a mobile "workstation" consisting of computer, modem (or network connector), and printer was ideal. I t was very useful to be able to move to the classroom or lab to use where it was needed. If low speed connections (up to 2400 baud) are made, many dot matrix printers can keep up with the flow of data. In this way, the student doing the online search can finish the search and walk away immediately with his or her search results. If faster connections are made (or if software does not support "echo" of incoming data to the printer), the incoming data can be collected a s a file and printed later. Procedure
Examples of chemical searching classes have been published in this J o u r a l . Abrash ( I ) described a literature course that had a n online component that utilized a "learning file", that is, a low cost file in which the information is static and not current. Jenkins (21 established a n undergraduate online searching course that also utilized learning files. These are examples of courses that involve students in searching for specific citations and information that is found in either of two database files: one is bibliographic and the other is nonbibliographic. We chose a n alternative strategy. The online searching became part of a n existing course. The weekly search was in addition to the normal laboratory exercise. We employed a wide range of current, complete database files and weekly searching exercises were open-ended in that much of the time there was no "correct answer" or specific information to be found. The command language of the database vendor was learned in this open-ended fashion. Later, we included some challenging exercises that did require specific information to be found. A culminating exercise gave each student a problem to investigate. This problem was delivered to the student by electronic mail. The stndents investigated the problem and sent the information back to the author of the inquiry by Email. Volume 71
Number 10 October 1994
867
Weekly Procedure The mobile workstation is brought to the laboratory portion of the course. Students have been given the daily search lesson in advance and have already signed up for a 15-minute block of time during the normal three-hour laboratory They do the normal laboratory exercise that is reauired for the oarticular course exceot for the 15 minutes (or less) of online searching required per student. The software is programmed to allow automatic log on and log offto Dialog. Students quickly finish their search and then resume their normal activitv. An instructor is alwavs available but, with automated iog o d o g off and open-ended searching, is only needed occasionally. Security
Database time is exoensive and is orotected bv " oass. word. It is inconvenient to restrict log on to instructors. It is more natural to have each student log on and log off from an online session. We protect our system by programming the oassword into macro kevs within the telecommunications software. Each student has a protocol for logging on and off that includes the use of these macro kevs. In this way the password is never seen on the screen. This is a simple approach to security and anvone familiar with the sof&are'fan enter a command to see the makeup of the macro keys. We keep this possibility to a minimum by maintaining the software with the encoded password on a floppy disk rather than the hard drive. The floppy is removed after each search session and kept in a secure place. The password can be changed if there is any breach in security. An alternative approach to security is Dialog's self-expiring password discussed earlier. Instructor for the Course
The instructor for the course needs to be familiar with computers, printers, modems, and network connections. Competency in online searching can be accomplished by attending Dialog workshops or the instructor can be selftaught. Dialog has training booklets and searching curriculum specifically designed for searching chemical databases (3). The topics in these manuals range from simple command language for a keyword search to complex substructure searching. Sample Lessons
The following lessons are possibilities that could be used with practically any chemistry course. The search techniaues and command laneuaze remain the same. onlv the nature of the information sought changes. In some df the lessons. seauential order is important: for example. a basic keyword se'arch should come Lefore arefined search with proximity operators. In other cases, order is not important. Note that in the following lessons a ? is the system prompt. A command follows the prompt and is shown in capital letters (for clarity-any case will work). To illustrate, here is a very simple search:
- -
? SELECT cation
S1 20468 ?TYPE SlrT111-10
cation
I n t h i s search t h e term "cation" is SELECTED (searched). The response to that search is 20468 records that contain the term cation. These are stored in memory and called set 161).The next command is to TYPE (display on the computer screen) the titles (TI) of the first 10 records of set 1. 868
Journal of Chemical Education
Lesson 1 Questions are tailored for the particular course or even the particular student. We like to start with vame, openended questions that leads to large, often irreievani retrieval. This gives the students a feeling for the enormity of scientific information and the need to compose search strategy in a way that leads to relevant information. An example might be "investigate the toxicity of benzene." At this point the student has been introduced to Boolean logic and the AND, OR, and NOT operators. The search looks like this in the database CA Search: ? SELECT benzene S1 198092 benzene ? SELECT toxicity 52 126727 toxicity ? SELECT S1 AND 52 53 1766
52 AND S3
The student then TYPES out a few of the 1766 records ("hits") and finds that most have nothing to do with the desired topic. They find that ?SELECT benzene also retrieves bromobenzene and benzenesulfonic acid. They find records that include the words benzene and toxicity but have nothing to do with benzene toxicity. They quickly realize that to increase their search precision, they must refine their search strategy. This refinement becomes the topic for the second lesson. Lesson 2 The refinement of the basic search can take different shapes. Students learn about proximity operators. These ope;ators link terms in more r e s t r i c t i ~ e ~ wthan a ~ s "AND." They learn that the "S"operator is a good choice because it demands that the search terms be in the same subfield of information. They learn that search terms can be limited to a single term by adding a /FF suffix. For example SELECT benzene retrieves 198092 hits while SELECT benzene/FF yields 57164. Searching can be limited to certain languages (ENG for English) and certain years (e.g. 19921994). Searches can be further refined bv limiting the search terms to the title (TI). The following example Lows how all these refinements can change the original search. ? SELECT benzene S1 198092 benzene ? SELECT toxicity 52 126727 toxicity ? SELECT SIIFF 53 57164 SlIFF ?SELECT S3(S)S2 S4 497 S3(S)S2 ?SELECT S31ENG AND S21ENG S5 399 S3lENG AND S2lENG ?SELECT s 5 m S6 299 ~5rn ? SELECT S6/1992:1994 S7 10 5611992: 1994
Lesson 3
To further refine searches, we pose questions to our students: How do I know if I have an author's name spelled correctly? Can I search for all the records associated with a certain author? How do I know if I have an accepted chemical name? Is there another, and perhaps better, term I could use in my search? Students answer these questions by using the EXPAND command. This command is common to most databases and gives an alphabetical listing of the terms contained within the index that is expanded. If the index contains an online thesaurus. alternate forms of the search term can be discovered. We kually assign both a term and an author for the student to EXPAND. Here is a n example.
?EXPAND enthalpy
Ref
Items
El E2 E3 E4 E5
2 1 15742 0 1
RT
5 1
Index-ten enthalpometric enthalpres 'enthalpy enthalpy-entropycurve enthalpy,apparent molar
In this exam~lethe term enthalov is found to have 5 related terms (R?). These can be &&tigated by using the command EXPAND E3 which gives terms such as "heat of reaction", which has related terms that can be further exoanded to find "heat of formation". which also has related terms. Students find this expanding process very useful to find good search words or phrases. Lesson 4
ture is translated to a ROSDAL string and searched. Atomic, molecular, and generic modifications of a given structure can also be searched. Given the following strue ture, a typical assignment would be to find the name of the compound and find information about analogs that are halogenated para to the -OH on the ring.
First, the molecule is numbered. Any numbering system can be used; an arbitrary example is shown above. All atoms except hydrogen are numbered. Next, the connectivity is described using - (hyphen) for a single bond, = (equal sign) for a double bond, and # (pound sign) for a triple bond. In this case, the search would be for the string
Ib say that chemical nomenclature is complicated is an understatement. Chemicals are given trivial names, IUPAC names, CAnames, Beilstein names, trade names, and 1=2-3=4-5=6-1.6-70.1-8=9N-lON=ll-120-8 synonyms. We encourage students to use both registry numbers and names to eive more comolete coverage - in where commas separate pieces of the description. This their online searching. In this exercise, students are given search returns one hit with the name 2-(1,3,4)oxadiazol-2a chemical name and a auestion. They first find reeistrv yl-phenol (remember the numbering sequence in the number(s1 and synonymis) in the n o ~ b i b l i ~ g r a ~ h i c b a t a - search string is arbitrary and may not correspond to the base CHEMSEARCH. The synonyms and registry numaccepted numbering system). bers are then "MAPPED" (stored in memory). When a bibFor the halogenation possibilities, a new position (13) is liomaphic database is opened, this stored information is created para to the -OH and the search string is usid i s part of the searih strategy. Students are encour1=2-3=4-5=6-1,6-70,1-8=9N-10N=ll-120-8,3-l3X aged to trr multiple databases. As an example, a search for i
