Bibliography-Building Software Eases A 'Cruel' Task

"One of the biggest nasty chores in writing a scientific paper is putting together the bibliography," says Walter Alvarez, a professor of geology at the University of California, Berkeley. "It's just always been a big nuisance." To help scientists cope with this chore, software packages to manage and produce bibliographies began to appear in the early 1980s. Now more powerful, more user-friendly, and more numerous than ever before, these programs offer the capability not only to automatically generate bibliographies, but also to do so in the appropriate formats for dozens of leading scientific journals. Scientists are also using these programs as research tools, creating bibliographic databases, specific to their study areas, that are searchable by, for example, user-created key words. "The thrust of these programs is on building your own database," says Sue Stigleman, a former librarian at the Health Sciences Library of the University of North Carolina, Chapel Hill, and author of a recent review of bibliography-formatting software (DATABASE, 15:15-27, February 1992). "Different people do different things [with that database]. A lot of people do writing that requires bibliographies, like grant proposals and journal articles. Other people just have a bibliography that they can search." While more than 40 such software products are available, there are leaders in the field, according to Stigleman. These are EndNote Plus ($249) from Niles & Associates, Berkeley, Calif.; Pro-Cite ($395) from Personal Bibliographic Software Inc., Ann Arbor, Mich.; and Reference Manager ($299, with journal formats $59 additional) from Research Information Systems Inc., Carlsbad, Calif. Stigleman says that some other programs also have substantial followings, including PAPYRUS ($99) from Research Software Design, Portland, Ore. Michael Hahn, a plant biochemist at the University of Georgia in Athens, like Alvarez, sees the ability to generate bibliographies for publication as the most useful feature of the bibliographic database programs. "I once did a collaborative grant with two colleagues," Hahn says. "I literally spent 24 hours putting the bibliography together for that grant, and that's the very last time I ever did that." Now, Hahn uses Reference Manager to format bibliographies drawn from his 13,530-reference database. "When I get ready to send out a grant application," he says, "the very last thing I do, usually about an hour before the thing gets photocopied, is to generate the bibliography. And that takes about 15 minutes. I haven't typed a bibliography in five years now." Alvarez, who uses EndNote Plus to manage his 4,020-reference database, notes that scientific journals often have unique reference styles and require that references accompanying a paper submitted for publication adhere to that style. "Nearly every journal has its own format for references," he says. "So, if you submit papers to a variety of journals--and most of us do--then you've got to have a different format for each one." Because of this situation, Alvarez adds, the resubmission of papers to different journals can mean significant extra work for an author not using a bibliographic database program like his. "Sometimes, you'll send a paper to a particular journal, and they'll say, `Well, this is too specialized for us; you should send it to a different journal,' " he says. "Then, if you don't have something like EndNote, you have to retype the whole business. With EndNote, you just push the mouse around two or three times, and it prints it out in a different format." Generally, these programs ask that an author use in-text reference markers when writing a paper for which the program will later be required to generate a bibliography. These markers will usually include a unique number assigned to the reference in the database. Then, when asked to do so, the bibliographic database program will use the markers to compile a bibliography in the journal format selected by the user. The program will also replace the in-text markers with the appropriate in-text reference for the journal selected. "You put the number in the manuscript, in brackets," explains Robert Roach, a research physiologist at the Lovelace Medical Foundation, Albuquerque, N.Mex., who uses Pro-Cite to maintain the 3,000-plus records in the Bibliography of High-Altitude Medicine, which he publishes and distributes worldwide in a variety of computer formats. "Then you take your [document] file to Pro-Cite. It goes through and looks at each of those numbers, pulls those records out of your database, and puts them in a word processing file that you can just pull into your document. Then, when you write it to the [document] file, it asks you what format you want it in." EndNote Plus creates bibliographies in a similar way. "I simply insert temporary citations that are codes to EndNote into my word processing document," says Barry Henderson, a biochemist and National Institutes of Health postdoctoral research fellow at the Massachusetts Institute of Technology, who has about 1,000 records in his database. "Then, when I finish the document, I open EndNote and format the document. EndNote goes in and pulls out those temporary citations and replaces them with the appropriate in-text citation for the target journal. And then it also builds the corresponding bibliography." In order for a user to take advantage of the bibliography- generating features of these programs, the bibliographic database program must be compatible with the word processing program being used, according to Stigleman. Microsoft Word and WordPerfect are commonly supported, as are a number of others, but users should check for this compatibility before investing in new bibliographic software. In support of their second most popular use, as research tools, the bibliographic database programs offer many ways to search and sort a database. Most will search by author, title, journal, date, and key word. Key word searches include full-text scans of abstracts, in many cases. And there are other special features offered. PAPYRUS, for example, allows the user to do a search, complicated or otherwise, and then assign a key word to the set of references that results from that search. "You can do a search, or several different searches, and then assign a key word to that group," says Jeff Breiwick, a fisheries biologist at the National Marine Mammal Laboratory, Seattle. "Then, in the future, you can select all those references just by asking for the references using the key word." Breiwick maintains two data-bases, one for himself of more than 4,500 references and one for the International Whaling Commission of about the same size. Additional features may include the ability to check for duplicate records. EndNote and PAPYRUS also allow the user to add notes to the record, similar in purpose to the 3" X 5" note cards familiar to many researchers. MAJOR SUPPLIERS IN THE BIBLIOGRAPHIC DATABASE SOFTWARE MARKET BIOSIS 2100 Arch St. Philadelphia, Pa. 19103 (800) 523-4806 Fax: (215) 587-2016 BRS Information Technologies 8000 Westpark Dr. Mclean, Va. 22102 (800) 289-4277 Fax: (703) 893-4632 CD-Plus Inc. 333 Seventh Ave., Sixth Floor New York, N.Y. 10001 (800) 950-2035 Fax: (212) 563-3784 Chemical Abstracts Service/STN International 2540 Olentangy River Rd. Columbus, Ohio 43210 (614) 447-3600 Fax: (614) 447-3713 Compact Cambridge Division of Cambridge Scientific Abstracts 7200 Wisconsin Ave. Bethesda, Md. 20814 (800) 843-7751 Fax: (301) 961-6720 Dialog Information Services Inc. 3460 Hillview Ave. Palo Alto, Calif. 94304 (800) 334-2564 Fax: (415) 858-7069 Excerpta Medica/EMBASE Publishing Group Molenwerf 1 P.O. Box 1527 NL-1000 BM Amsterdam, Netherlands 020 5803911 Fax: 020 5803439 Institute for Scientific Information 3501 Market St. Philadelphia, Pa. 19104 (800) 336-4474 Fax: (215) 386-6362 Niles and Associates Inc. 2000 Hearst Ave. Suite 200 Berkeley, Calif. 94709 (510) 649-8176 Fax: (510) 649-8179 Personal Bibliographic Software Inc. 525 Avis Dr. Suite 10 Ann Arbor, Mich. 48108 (313) 996-1580 Fax: (313) 996-4672 Research Information Systems Inc. 2355 Camino Vida Roble Carlsbad, Calif. 92009 (800) 722-1277 Fax: (619) 438-5573 Research Software Design 2718 S.W. Kelly St., Suite 181 Portland, Ore. 97201 (503) 796-1368 Fax: (503) 241-4260 SilverPlatter Information Inc. 100 River Ridge Rd. Norwood, Mass. 02072 (800) 343-0064 Fax: (512) 472-8527 U.S. National Library of Medicine 8600 Rockville Pike Bethesda, Md. 20894 (800) 638-8480 These programs are capable of building bibliographic databases of differing, but substantial, maximum record numbers. EndNote supports databases of up to 32,000 rec-ords, Reference Manager up to 65,000, Pro-Cite up to 100,000, and PAPYRUS up to 2 million. Because few individual users are likely to approach these numbers, these limits should not represent a constraint in most cases. For institutional users, the maximums may become relevant. The bibliographic references used to build a database are often gathered through a broad and various network of personal contacts, colleagues whose contributions are then simply typed into the database, say researchers. High-altitude physiologist Roach, for example, estimates that 50 percent of his bibliographic database entries come from personal contacts. But, increasingly, scientists are turning to an expanding selection of online, CD-ROM, and diskette databases as sources for their bibliographic references. With most of these programs, a scientist interested in importing data from these sources will need to purchase an additional piece of software to help translate the downloaded data into a form acceptable to the database. For that purpose, EndNote Plus markets EndLink ($99), Pro-Cite sells Biblio-Links ($295), and Reference Manager offers Capture ($99). PAPYRUS, on the other hand, includes format translation programming as part of its main package. There are hundreds of databases available in online, CD-ROM, and diskette formats from different vendors. However, for the biomedical researcher, certain of these databases and sources are more prominent than others, say librarians and other information specialists. According to Nancy Roderer, director of the Cushing/Whitney Medical Library at Yale University in New Haven, Conn., important databases include Medline from the National Library of Medicine, Bethesda, Md.; EMBASE from the Excerpta Medica/EMBASE Publishing Group, Amsterdam, Netherlands; BIOSIS from Phila- delphia-based BIOSIS; and Sci-Search and Current Contents from the Institute for Scientific Information (ISI), also of Philadelphia. Biochemist Henderson uses the Scientific & Technical Network International, or STN, from Chemical Abstracts Service, Columbus, Ohio. "Most academic campuses these days also provide some array of database access," Roderer adds. She suggests that researchers with ties to academic institutions should turn first to their institutions for access to databases. She points out, however, that local versions of national databases may be offered in slightly different formats, which can complicate data importation. Roderer asks: "If I'm downloading records from my own local version of a database, will the [bibliographic database] software work?" Perhaps not, she suggests. Vendors offering online access to the major databases and hundreds of additional specialized databases include BRS Colleague from BRS Information Technologies, McLean, Va., and Dialog from Dialog Information Services, Palo Alto, Calif., Roderer says. Many databases, such as Med-line, are available as CD-ROM and diskette products, with updates sent to subscribers at regular intervals. CD-ROM products that provide access to multiple databases include Compact Cambridge from Cambridge Scientific Abstracts, Bethesda, Md.; SilverPlatter from SilverPlatter Information Inc., Norwood, Mass.; and CD-Plus from CD-Plus Inc., New York, according to Charles Greenberg, media services librarian at the Columbia University Health Sciences Library in New York. Another well-known database that is available to researchers as a CD-ROM product is Science Citation Index from ISI. Diskette database sources include Current Contents on Diskette from ISI and Reference Update from Research Information Systems Inc. Scientists importing data from either online or CD-ROM sources should prepare themselves for some level of difficulty in the process, according to Stigleman. She suggests that a researcher who expects to import references regularly from the same database should run a test with the bibliographic database program he or she would like to use, to see what works and what doesn't. "But someone who imports from a variety of different databases is likely to have problems," she says, "regardless of which program they choose." The underlying problem, she says, is that database vendors use differing formats--even reformat-ting familiar databases like Medline, for example--so that each version of a database presents, potentially, a unique translation problem for the bibliographic database programs. "The real solution would be some kind of standardized downloading format," says Stigleman. "But none of the vendors want to do that, of course, because it's not in their best interests to encourage wholesale downloading and reuse of their material." According to Stigleman, none of the leading programs provides a true, active online or CD-ROM link. Instead, they offer methods to filter or translate data that has been captured to disk during a search session, so that it can then be imported into a program's data-base. She adds: "It's kind of a snake pit. The whole issue of downloading and importing is just not very clean." Users of these bibliographic software packages find that they have powerful new research capabilities in the databases they create, and they are generally delighted at being relieved of the burden of creating bibliographies for papers. But, even so, most have an additional feature or two they'd like to see in their program. Columbia's Greenberg would like to see network versions of these programs, for use on university networks. He says he has talked with the software manufacturers about the possibility, but does not expect to see such a product soon. "Typically, they make most of their money selling a lot of individual copies," he says, "so there's some reticence or reluctance to talk about whether a network version of this software should be produced. But it would be ideal for our situation." A limited network version of Pro-Cite was released on December 16. Multiple users may read or copy a database, but may not edit that database. "I'd like to see them systematically provide filters for downloading from existing databases, like Geo-Ref," says EndNote Plus-user Alvarez. "I'd like conversion programs that would let me do that." PAPYRUS does give instructions for attempting to import references from GeoRef, a Silver-Platter database, but notes that GeoRef is among the most difficult sources to work with, largely because it is not internally consistent in its formatting. Many researchers would like to see more input and output formats. Some would like to see full Windows versions of these programs-- currently, some are able to paste citations through the Windows clipboard into the word processor. And quite a few wish for standard database formats that would ease the task of downloading references or of sharing databases between users of different programs. Among existing and hoped-for features, however, it is the ability to generate bibliographies in almost any journal format and to reformat that bibliography as necessary that remains the central feature of these programs, the one most appreciated by researchers. "That ability basically takes a cruelty out of the life of practicing scholars," says geologist Walter Alvarez.

Bibliography-Building Software Eases A 'Cruel' Task

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