                                                                                                Conversion of BIOSIS Previews Database Files                                  to Reference Text Files and Reprint Request Forms                                                                                                                               JOHN A. BYERS                                     _______________________________________________________________________________  ABSTRACT -  BIOSIS.EXE is a compiled BASIC language program for use on IBM-     compatible personal computers. The program converts a DOS text file of current  B-I-T-S (BIOSIS Information Transfer System) references into a DOS file of      standard scientific citations. The latter file can be imported into a word      processor or scientific reference manager. The program also makes a random      access database of references consisting of a title, author, journal, author    address, and key words. This database can be searched for specific references   and these selected for conversion into a DOS text file of citations as above.   The random access database is also used to construct reprint request cards      from information on the author, title, journal and address as well as the       user's name and address. The reprint request cards can be printed on regular    paper or on "Request-a-Print" (Institute for Scientific Information) cards.     The program also can process DOS files obtained from key word bibliographic     searches of BIOSIS Previews (which differ in file format) to obtain scientific  citations for word processing or reference managers.                           -------------------------------------------------------------------------------                                                                                  INTRODUCTION                                                                                                                                                    Today's scientific literature is voluminous, fast changing, interdisciplinary,  and accrues at an ever expanding rate. Researchers and teachers of entomology   thus may have a difficult time keeping up-to-date with the pertinent            literature. Often avenues of study are explored that are new to the researcher  and thus one must compile databases of scientific references in addition to     any that have been previously maintained. Fortunately, there is the personal    computer that can be used to store, manipulate and retrieve references from a   database. Commercial services such as B-I-T-S (BIOSIS Information Transfer      System) can provide the latest references on computer disk for viewing by       personal computers. BIOSIS Previews also can often be used at one's university  library for retrospective searches on a particular topic.  The located          references from such a search of the many bioscience journals and               publications, from the present back to 1969, can be downloaded to disk for a    fee.                                                                               I have developed a compiled BASIC program, BIOSIS.EXE, which runs on IBM-    compatible computers from the DOS command line. The program can take DOS text   files of either current monthly B-I-T-S listings or of retrospective searches   of BIOSIS Previews and make a database. This database can then be searched for  key words and the located references marked for export to a word processor in   a format resembling a standard scientific citation. The marked references can   also be formatted and printed as reprint request cards. Other commercial        databases can be imported such as MEDLINE (National Library of Medicine)        and CA Search (American Chemical Society), but exported citations may not be    formatted entirely accurate.                                                                                                                                    MATERIALS AND METHODS                                                                                                                                             The program BIOSIS.BAS was developed with the QuickBASIC programming          language (version 4.5, Microsoft). The source code was compiled to              BIOSIS.EXE, a binary machine-coded executable file, by the Microsoft            compiler version 4.50 and overlay linker version 3.69. IBM-compatible           computers can execute the program in monochrome or color using any type of      monitor and DOS 2.1 or higher.                                                     An IBM-DOS text file from BIOSIS Previews (retrospective search) or B-I-T-S  (monthly update) is required for processing by the program. Files from          retrospective searches can be downloaded from a number of commercial computer   databases such as Data-Star, ESA-IRS, DIALOG and STN. References in a BIOSIS    Previews text file may contain the subject identification codes (field tags)    of AN (accession number), AU (author), TI (title), SO (source), IN (author      affiliation), KW (key words), BC (biosystematic codes) and ST (supertaxa).      Other codes may include (CD, LG, YR, CC and AB). Monthly updates of recently    published articles are formatted slightly differently by BIOSIS such that the   AN code is replaced with an ID (identification) field code and the CS           (corporate source, author address) may substitute for the IN code above. The    use by the program of different field codes in BIOSIS files as well as other    databases is explained subsequently.                                                                                                                            RESULTS AND DISCUSSION                                                                                                                                             The major facilities and operation of BIOSIS.EXE are diagrammed in Fig. 1.   The arrows between boxes indicate relationships between program parts but do    not necessarily denote program flow.                                                                                                                            ******************************************************************************  Fig. 1. Relationships of program parts of BIOSIS.EXE, a BIOSIS Previews file    conversion utility and reference management/reprint request card system for the IBM-compatible personal computer.                                                                                                                                   BIOS-1                   BIOSIS.EXE                        BIOSIS.CD#                            BIOSIS TextFile   >    Add BIOSIS      <>    File with        in IBM DOS          References                      Field Codes     Text File Form            to Database     Ŀ     for BIOS-1                                                   View/Edit/Mark                                        BIOSIS.ADD               References      <Ŀ                                  in Database                      BIOSIS.BIO      Address of User<Ŀ                         Search for                >  Random Access                             Text Strings            >   Database of        PRINTOUT              in Database      <>    References                         and Addresses     Text File        >    Make Reprint            >    of Reprint   <Ŀ      Request Cards    <                        Request Cards       of Marked Refs.                                            in Database                                                                                                 OUTPUT               Format Marked Refs.                  > OR ?               in Database to                                    Text File of  <   Standard Refs.   <                   References              in Text File                                                                                        Mark/UnMark Refs.                                                                           BIOSIS.TXT          BIOSIS.DBD       >  Change Databases                              Random Access    Store/Get Name            HELP: Read          >  File to Read      of Database   <        This Paper     <          This Paper                                                                                                           ******************************************************************************  BIOSIS.EXE is used by typing `biosis' at the DOS command line. The program      loads and checks to see if a name of a database is in the file BIOSIS.DBD. If   no name is present then the default name (BIOSIS.BIO) is placed in the file.    The menu has seven options to choose from (Fig. 1) besides a help section,      shelling to DOS, or exiting from the program.                                       The first option is to add BIOSIS files to the database. This is done by    entering the name of the BIOSIS Previews file (e.g. named BIOS-1 and            represented in Fig. 2A).                                                                                                                                        ******************************************************************************  Fig. 2. BIOSIS.EXE processes a BIOSIS text file (A) and converts it to a        database style (B) which can be formatted to the standard scientific style (C)  or Pro-Cite style (not shown).                                                                                                                                 (A)                                                                             AN 37011682 8907.                                                               AU BYERS-J-A.                                                                   TI CHEMICAL ECOLOGY OF BARK BEETLES.                                            SO EXPERIENTIA-BASEL 45 (3). 1989. 271-283.                                     IN DEP ECOL, ANIM ECOL, UNIV LUND, S-223 62 LUND, SWEDEN.                       LG EN.                                                                          YR 89.                                                                          KW REVIEW     DENDROCTONUS-BREVICOMIS     ELECTROPHYSIOLOGY    PHEROMONE           BIOSYNTHESIS   OLFACTION   PERCEPTION   ORIENTATION   CUE  ANEMOTAXIS           INTERSPECIFIC   COMPETITION   HOST   TREE  SELECTION  ATTACK  DENSITY           AGGREGATION BEHAVIOR SEMIOCHEMICAL ATTRACTANT NORTH AMERICA EUROPE.          BC 75304 Coleoptera.                                                            ST ANIMALS#, INVERTEBRATES#, ARTHROPODS#, INSECTS#.                                                                                                             (B)                                                                             CHEMICAL ECOLOGY OF BARK BEETLES.                                               AU BYERS-J-A.                                                                  JO EXPERIENTIA-BASEL 45 (3). 1989. 271-283.                                    AD DEP ECOL, ANIM ECOL, UNIV LUND, S-223 62 LUND, SWEDEN.                      KW REVIEW DENDROCTONUS-BREVICOMIS ELECTROPHYSIOLOGY PHEROMONE BIOSYNTHESIS OLFACTION PERCEPTION ORIENTATION CUE ANEMOTAXIS INTERSPECIFIC COMPETITION HOST TREE SELECTION ATTACK DENSITY AGGREGATION BEHAVIOR SEMIOCHEMICAL ATTRACTANT NORTH AMERICA EUROPE. 75304 Coleoptera.                                                                                                                                  (C)                                                                             Byers, J.A. 1989. Chemical ecology of bark beetles. Experientia-basel 45 (3).   271-283.==review dendroctonus-brevicomis electrophysiology pheromone            biosynthesis olfaction perception orientation cue anemotaxis interspecific      competition host tree selection attack density aggregation behavior             semiochemical attractant north america europe. 75304 coleoptera                  ******************************************************************************                                                                                  The user may look at the BIOS-1 file to see if the formatting is such that all  text is indented three spaces except for the codes. If the file has been        corrupted, a reformatting facility is selected.  Otherwise the user continues   and is presented with a list of files (ending in .CD#) containing data for the  various field codes. The user selects the appropriate file name, if present,    and the codes are loaded and presented on a menu for editing. The codes can be  used without editing or new codes added for the respective authors, title,      journal and so forth. These codes make it possible to accommodate any of        several types of BIOSIS formats as well as other database styles such as CA     Search and MEDLINE. After editing the field codes, the BIOS-1 file is used as   the source of references for placement in the BIOSIS.BIO file. This latter      file is a random access database in which references from additional BIOSIS     Previews files can be added by running option one again. Alternatively,         another name can be chosen in order to create additional databases or the       BIOSIS.BIO file can be erased to begin a new database with this name. Each      record of the database has the reference reorganized so that the title is       placed at the top of a 12-line by 80 character area, followed by an author      symbol and the authors (Fig. 2B). The journal or publication is third followed  by the author address and key words if present (Fig. 2B).                          The second option "View/Edit/Mark References in Database" allows one to      scroll through the database and view the references. Any references that are    desired to export as a citation in the file OUTPUT or as a reprint request      card in the file PRINTOUT are marked by pressing the Insert key. References     are unmarked with the Delete key. A global unmarking of all references can      also be done. Facilities for searching for a text string and viewing the        located reference are provided while viewing the database.                         The third option, "Search for Text Strings in Database", allows complex      logic searches of the database fields for up to two sets of 20 text strings     simultaneously. The searches employ Boolean logic in one of four ways. Up to    20 text strings can be searched for in either (1) an OR or (2) an AND way.      Also these can be combined into (3) AND/OR and (4) AND+OR searches with a       total of up to 40 text strings. For example, an AND+OR search might look for    ("pheromone" AND "Scolytidae") and ("stridulation" OR "acoustic" OR             "vibration" OR "sound") in each reference. Prior to searching for the text      strings, the user is asked whether he or she wants to save this search profile  for later recall. If the search profile is saved, then the next time a search   is made the user may select option five to load the search profile and begin    the search without the need for entering the text strings. During the search    of the database, the program displays any located references on screen and      waits for keyboard input to mark (or unmark) or continue without marking until  all references in the database are searched. A search record showing the        number of references found out of the total number in the database is           displayed at the end of the search.                                                The fourth option, "Make Reprint Request Cards of Marked References in       Database", asks for the user's name and address which is saved in the file      BIOSIS.ADD. Then the choice between whether the printing will be on paper       (output in Fig. 3) or modified for use on Request-a-Print cards (Institute for  Scientific Information) is made.                                                                                                                                ******************************************************************************  Fig. 3. A reprint request card (in the text file: PRINTOUT) formatted from the  BIOSIS reference in Fig. 2 by the program BIOSIS.EXE. The person requesting     reprints detaches the upper right address and glues it to the opposite side     for use in mailing. The lower right address is also detached for use as a       record of the request. Upon receipt of the card, the author detaches the        address in the middle section (now top right) and attaches this to an envelop   containing the requested materials.                                                                                                                               Dear Dr. Byers:                                                                                          Requestor's name         Dr. Byers                  Please send me a reprint  Dept. of Entomology      DEP ECOL                  of your article in:        125 Everett St.          ANIM ECOL                                            Lakewood, Colo. 80226    UNIV LUND                 EXPERIENTIA-BASEL 45       USA                      S-223 62 LUND             (3). 1989. 271-283                                  SWEDEN                                                                                                                             -------------------------------------------------  Entitled:                  use mailing label above  Card sent: 11-08-1991                                                         Dr. Byers                 CHEMICAL ECOLOGY OF        Requestor's name         CHEMICAL ECOLOGY OF       BARK BEETLES...            Dept. of Entomology      BARK BEETLES...                                      125 Everett St.          EXPERIENTIA-BASEL 45      Thank You,                 Lakewood, Colo. 80226    (3). 1989. 271-283                                   USA                                                                                                                              Requestor's name                                    keep for your records       ******************************************************************************                                                                                  The program then goes through the database and formats the marked references    into reprint request cards using the user's address and the form option. The    "cards" are saved in a file called PRINTOUT which is overwritten each time      this facility is used. This file can be printed directly on perforated          Request-a-Print cards or on perforated computer paper. At the DOS prompt        simply type: copy printout prn (and the file will be printed). For laser        printers the file PRINTOUT should be imported into a word processor as DOS      text and the "cards" arranged to fit on the pages. An IBM graphic printer       emulation yields pleasing printer output from a word processor.                    The fifth option, "Format Marked Refs. in Database to Standard Refs. in      Text File", is used to take the title, authors, author address, journal, and    key word strings and reformat them into a standard scientific citation style    (Fig 2C). These are saved in a DOS text file called OUTPUT which is             overwritten each time this option is chosen. This file can then be imported     into word processing programs (e.g. WordPerfect, WordPerfect Corp., Orem,       Utah) as well as into the scientific reference manager, CardCat (Byers 1991).      Considerable programming was necessary to convert the several BIOSIS         punctuation styles for authors into the standard citation form. The date        (1900's or 2000's) is extracted from the journal string. The title and journal  letters are uncapitalized and then the first letter of each word in the         journal is capitalized. This saves time in the word processor as most letters   need to be lowercase in a standard citation. An additional feature is that      marked references can also be exported in a format compatible with MacIntosh    computers for use with the Pro-Cite (Personal Bibliographic Software, Inc., Ann Arbor, Michigan) bibliographic manager software. In this case the MacIntosh     system utility for text file conversion is used to convert the OUTPUT file      (which now includes a Pro-Cite code, tab stops, and various slashes) from IBM   to MacIntosh format. This file is then imported into Pro-Cite in the short      journal form. Of course the use of Pro-Cite on IBM-compatible computers does    not require the conversion step.                                                   A sixth option includes either a global unmarking or global marking of all   references in the database. The "Change Databases" option allows for an         `unlimited' number of databases: 208 available ASCII characters for file names       = [SUM(i=1 to 8) Pi^208] [SUM(i=1 to 3) Pi^208 + 1] = 2.7 x 10^25               where P stands for permutations, i is subscript, 208 is superscript.       Each time the program is started it gets the current database which is          permanently stored in the file BIOSIS.DBD until changed by the user. The user   can receive help from within the program by reading the file BIOSIS.TXT which   includes the contents of this paper with figures. This file appears to be a     standard sequential DOS text file but is actually a random access file which    allows scrolling the text forward and backward on the screen.                      Deitz & Osegueda (1989) discuss the effectiveness of retrieving              entomological literature from several databases including AGRICOLA, AGRIS       International, BIOSIS Previews, CAB Abstracts, Dissertation Abstracts Online,   Life Sciences Collection (Cambridge Scientific Abstracts), SCISEARCH, and       Zoological Record Online. They show that pertinent literature for a             particular subject is likely to be found in any of these databases in varying   proportions and redundancy. While the cost effectiveness may vary depending on  the blend of databases used, it was apparent that BIOSIS Previews had the most  relevant references.                                                               I have searched CA Search and BIOSIS Previews for all references in the      Journal of Chemical Ecology and found that the former contained only about 86%  of the articles while BIOSIS had all of them. Several key word searches and     reference retrieval strategies have been proposed (Marshall 1979; Harvey 1979;  Chiang & Chiang 1984; Eyers & Taylor 1988; Resh 1988; Deitz & Osegueda 1989).   The results of these articles indicate that an exhaustive search of the         literature is more costly and difficult than one might anticipate due to the    scattering of references and the complexity of designing a key word search      profile. However, a search of the largest database (BIOSIS) with the            appropriate key word profile will retrieve the majority of the pertinent        references.                                                                        The advantage of building one or more personal databases from a commercial   database such as BIOSIS is that the references in the personal databases can    be searched for many different combinations of key words over the course of     one's career. This is usually less costly, and more convenient, than to search  the commercial databases multiple times.                                           BIOSIS (2100 Arch St., Philadelphia, PA 19103-1399, USA) reviewed the        manuscript and they would like me to present the `fair use and copyright'       issue concerning the use of their databases. They have the policy that          downloaded information "may be freely used without further payment to BIOSIS    when temporarily stored in lieu of hard copy or printout form which is the      normal medium delivered by a VENDOR." However, the temporary storage/use        ceases when USER alters the archival characteristic and incorporates BIOSIS     information into an "active" system of any type. At present a payment of 15     cents per reference per year is due BIOSIS when one has more than 500           references in an active system.                                                    The BIOSIS.EXE program system can be obtained from the author (send a        formatted disk and mailer). Donations of $5 or 35 Swedish Kronor for shipping   would be appreciated. The system can be used to condition BIOSIS Previews       files prior to importing them into the scientific reference manager CardCat     (Byers 1991).                                                                                                                                                   Acknowledgment                                                                  Funding for the project was obtained in part from the Swedish Agricultural and  Forest Research Council (SJFR). Olle Anderbrant, se Persson and Fredrik        Schlyter provided valuable criticism useful in the design and debugging of the  program and in review of the manuscript.                                                                                                                        REFERENCES CITED                                                                                                                                                Byers, J.A. 1991. Cardcat: A scientific reference manager for IBM-compatible       personal computers. Amer. Entomol. 37:240-242.                                                                                                               Chiang, K. S. & H. C. Chiang. 1984. Literature retrieval in entomology. J.         Entomol. Res. 8: 86-88.                                                                                                                                      Deitz, L.L. & L.M. Osegueda. 1989. Effectiveness of bibliographic data bases       for retrieving entomological literature: a lesson based on the Membracoidea     (Homoptera). Bull. Entomol. Soc. Am. 35: 33-39.                                                                                                              Eyers, J. E. & E. R. Taylor. 1988. Online searching of parasitology literature.    Parasitol. Today 4: 324-328.                                                                                                                                 Harvey, S. 1979. CAB/CAIN evaluation project: a comparative study on the           performance of two agricultural databases in a computerized current             awareness service. (British Library Research and Development Report 5483).      Centre for Agricultural Publishing and Documentation, Wageningen,               Netherlands.                                                                                                                                                 Marshall, K. E. 1979. Online retrieval of information: a comparison of             different systems used to produce a bibliography on Ephemeroptera and           pollution, 1969-78. Canada Fisheries and Marine Services Technical Report       878, Winnipeg, Manitoba.                                                                                                                                     Resh, V. H. 1988. Publication patterns in entomology: an example based on          aquatic insects. Bull. Entomol. Soc. Am. 34: 145-150.                       -------------------------------------------------------------------------------                                                                                  John A. Byers is a Ph.D. graduate of the University of California at Berkeley   in entomology. He currently is a Hgskolelektor (Associate Professor) in the    Department of Plant Protection, Swedish University of Agricultural Sciences,    S-230 53 Alnarp, Sweden. His interests include chemical ecology of bark beetles and behavioral simulation.                                                     