Skip to content | Skip to search box

Books & Bytes

Volume 8, Number 4    April 1996

Books & Bytes is produced by the HSLIC Library Staff for Health Sciences Center personnel. Copyright University of Washington.

Table of Contents

  1. New Look for HealthLinks
  2. Nursing & Allied Health Database Enhancements
  3. Electronic Book Renewals
  4. Molecular Sequence Database Searching on the Web
  5. Library Resources for Basic Sciences Researchers
  6. PAIS Offers Public Policy Information
  7. Reference on the Net
  8. Health Reference Center Gold Update
  9. Recent Gifts
  10. Internet Navigation Tools
  11. Serial Title Changes: January - March 1996
Contributors to this issue: Martha Means, Lisa Oberg, Paula Palmer, Steve Rauch, Sarah Safranek, Janet Schnall, Mary Van Court, Carolyn Weaver, and Stuart Yarfitz

New Look for HealthLinks

A new version of HealthLinks, the UW Health Sciences Web site, has just been introduced. Point your Web browser to http://healthlinks.washington.edu to check out the new look.

The new home page is more compact, yet offers more access points than earlier image maps. Text under the HealthLinks banner offers links to the Health Sciences Schools, the Medical Centers, the Library's programs and services, and some pertinent University-wide services. Most secondary pages use a banner and blue arrows to provide a sense of continuity throughout the entire site.

The buttons that comprise the Topic Directory provide links to worldwide resource pages supporting the multifaceted missions of the Health Sciences Center. These pages are being actively developed and share a common look and feel. We will be working with the departments and schools over the next few months to fill these areas. We have added links to the University's home page, and to an Internet Search page to assist in locating still more resources on the Web.

Perhaps the most substantive change is the addition of a searching capability. Searching generally defaults to the area one is browsing (e.g., clinical care), but you have the choice of selecting another area or all HealthLinks pages. We have added a specialized search for HealthBeat articles under the Your Health section /your_health/hbeat (now http://uwphysicians.org/hbeat/), where searching is done solely within the article archive of some 1,000 files. While the search feature is intended primarily to help users find resources among the 1,100+ files on HealthLinks, it also helps us administer the Web site.

Behind the scenes, HealthLinks is now being served by the Netscape Communicator Server software. A development site where pages are edited and new resources are created permits spell-checking and validation of links for the documents on HealthLinks. When ready for public view, a list of the files is fed to a computer script that moves them to the public site.

The new look of HealthLinks required many hours of work by staff members of the IAIMS Program and the Health Sciences Library. We hope that this new look and structure will accommodate your needs as well as future developments and growth. Work has already begun on adding a database component to HealthLinks, as well as other enhancements, so stay tuned for updates. Comments are welcomed at iaims@u.washington.edu.

[Return to Table of Contents]

Nursing & Allied Health Database Enhancements

The 1996 reload of the Nursing & Allied Health database has recently been completed and offers the following enhancements.

Nursing & Allied Health is an excellent resource for researchers. Its particular strengths are

The inclusion of Research Instrument records is a special asset. Each record has a description of the instrument, including its purpose, variables measured, question format, administration and scoring information, and how to obtain the instrument for use. Many records include the full text of the instrument itself.

For an introduction to the research aspects of Nursing & Allied Health, including hands-on computer time, register for the class, "Using Electronic Nursing Databases" on May 14. To incorporate a Nursing & Allied Health demonstration into a classroom session, contact Janet Schnall (543-7474), Librarian Liaison to the School of Nursing, or send an email message to hsl at u.washington.edu.

[Return to Table of Contents]

Electronic Book Renewals

Two electronic renewal options now make it easier than ever to renew borrowed library materials. All renewal methods require you to provide two numbers: your library card number (located on the back of your UW identification card), and the barcode number of the item(s). The item barcode number, a 14-digit number starting with 39352, is found on the inside or outside back cover of the item.

Materials may be renewed via email by sending a message to renew@lib.washington.edu. Type your library card number and the item barcode numbers of all items to be renewed in the body of the message. A return message by email will confirm new due dates.

An online renewal form is available at http://www.lib.washington.edu/services/borrow/renew.html. The form can also be reached through HealthLinks via the path The Library -> Services -> Request Forms-> Document Request Services -> Renew a Book. After this form is submitted, a return email message will confirm new due dates.

Materials may also be renewed by calling the Circulation Desk at any of the UW Libraries or submitting a written list of your items by mail or in person. Items may generally be renewed twice if no one else has requested them. After the second renewal, items must be brought to a library. They may be immediately checked out again if no one has requested them.

If you have any questions about renewal procedures, please contact HSLIC Circulation at 543-3390 or send an email message to hsl at u.washington.edu.

[Return to Table of Contents]

Molecular Sequence Database Searching on the Web

With the growth of the Internet and the Web there has been a tremendous increase in online molecular sequence analysis resources available to researchers. These resources include approximately 100 different databases containing molecular biology information; powerful database search engines; software archives; servers running sequence analysis tools; integrated interfaces; and online documentation.

As the Human Genome project and other model organism mapping and sequencing programs progress, the size and complexity of these resources are growing rapidly. Ready access to this information is becoming essential for many areas of biomedical research and clinical practice. This article provides some basic information about a few of the World Wide Web resources for molecular sequence analysis. Additional sites will be discussed in future issues of Books & Bytes.

GenBank, the primary public repository for DNA sequence information in the US, is maintained by the National Center for Biotechnology Information (NCBI), part of the National Library of Medicine. Similar databases are maintained in Europe (EMBL) and Japan (DDBJ), and updates are exchanged daily among them. GenBank has grown from 680,000 base pairs in 600 entries in December 1982 to approximately 463,800,000 bases in 686,000 sequence records in February 1996. There are six GenBank releases per year, with daily database updates. An overview of GenBank can be found at http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html.

A GenBank record consists of two basic components: the DNA sequence itself, and descriptive information. The descriptive information includes a unique locus name and accession number, a definition, keywords, a phylogenetic description of the organism, bibliographic references, and gene features. These features include the locations of coding regions, intron/exon boundaries, translations of coding sequences, promoters, map position, and protein domains. Sequences are submitted individually by authors as they publish journal articles, as well as by the various genome project consortia. NCBI provides two tools for sequence submission: Sequin (http://www3.ncbi.nlm.nih.gov/Sequin/index.html), a stand-alone program available on disc or by FTP, and BankIt (http://www3.ncbi.nlm.nih.gov/BankIt/index.html), a Web form. The descriptive annotation is the responsibility of the submitter, and differences in phrasing and keywords sometimes present problems in searching.

Protein Sequence Databases

The major primary protein sequence databases are Protein Information Resource, PIR, (http://pir.georgetown.edu/) and SwissProt. PIR contains experimentally derived protein sequences as well as the translations of coding regions from GenBank. SwissProt, distributed as part of the EMBL databases, contains all PIR annotated sequence data, as well as additional sequences entered by the curators or translated from EMBL DNA entries.

In addition to the primary sequence databases, a number of protein motif databases have been developed. PROSITE (http://ca.expasy.org/prosite/) is a database of biologically significant sites, patterns, and profiles that can be used to help identify to which known family of protein (if any) a new sequence belongs. The BLOCKS (http://www.blocks.fhcrc.org) database was developed at the Fred Hutchinson Cancer Research Institute in Seattle. The database consists of multiply aligned segments or blocks corresponding to the most highly conserved regions of proteins, and can be used to sensitively identify related segments in unknown sequences.

The Protein Data Bank (PDB) (http://www.rcsb.org), maintained by the Brookhaven National Laboratory, is an archival computer database of experimentally determined three-dimensional structures of biological macromolecules. The database contains atomic coordinates, bibliographic citations, primary sequence and secondary structure information, as well as crystallographic structure factors and 2D-NMR experimental data. As of March 11, 1996, it included 3996 protein, 297 nucleic acid, and 12 carbohydrate structures. In addition to atomic coordinate data, the PDB Web site provides links to SWISS-3DIMAGE, a database of annotated 3D images.

A molecular visualization program such as RasMol is required to view the images in SWISS-3DIMAGE, or to construct and manipulate three-dimensional images from the atomic coordinate data. RasMol is freely available in Macintosh, Windows/PC, and UNIX/X-terminal versions from http://www.umass.edu/microbio/rasmol/getras.htm. Molecules R US (http://molbio.info.nih.gov/cgi-bin/pdb) is a Web forms interface which facilitates access (browsing, searching and retrieval) to the molecular structure data in PDB. Output can be returned in various forms including text, as an interactive structure for RasMol or other viewer, or in different forms such as line drawing or space filling models generated on the server.

The Genome Database (GDB) (http://gdbwww.gdb.org/), hosted by Johns Hopkins University School of Medicine, is an international collaboration in support of the Human Genome Project. GDB stores, curates, and provides electronic access to genomic mapping data submitted by international researchers involved in identifying and sequencing the estimated 100,000 human genes. GDB is a relational database which includes genetic and physical mapping data, polymorphism and mutation data, probes, cell lines, and bibliographic references. The GDB Web interface enables the user to construct complex queries relating to the different data objects and returns output with hypertext links between related items.

Access to GDB requires a forms capable Web browser such as Netscape, as well the helper application Mapview for graphical display of maps. Mapview can be downloaded from http://gdbwww.gdb.org/gdb/mapviewHelp.html. Version 6.0 of GDB, released in January 1996, also allows the user to perform customized map queries based on order and distance. In addition to the public data, GDB also contains private data not yet released to public view. This includes submissions by multiple edit groups such as those working on specific chromosomes.

Starting points for the BioWeb

Molecular Sequence Analysis Support Services

Several programs are available in the Health Sciences Libraries to assist researchers in finding and using molecular sequence databases and other research tools. Contact Stuart Yarfitz, Biological Research Information Consultant, at 616-4626 or by email to meminie@u.washington.edu.

Information Management Education classes include an introductory class on Web resources hsl at u.washington.edu. for biological research, "Netsurfing for Biologists," and the more advanced "Molecular Biology Database Searching". Both of these classes include hands-on training using Netscape Navigator. See p. 3 for the current schedule.

A series of Web pages designed as pathfinders to various types of biological information resources is under development. These resources will be posted on the bioinformatics home page at /basic_sciences/molbio/. In HealthLinks follow the path The Library -> Toolkits -> Molecular Biologist.

[Return to Table of Contents]

Library Resources for Basic Sciences Researchers

Basic Sciences researchers will find many collection resources and library services which are designed to help them be more productive and efficient. A sampling of what is available follows.

Laboratory Methods Manuals

Methods in Molecular Genetics Series. Kenneth W. Adolph, editor. Academic Press, San Diego. The following titles in this series can be found in the HSLIC collection:

Gene and Chromosome Analysis: Health Sciences Book Stacks QH442 G432 1993 pts. A, B, C.

Molecular Microbiology Techniques: Health Sciences Book Stacks: QH441 M7183 1994 pt. A.

Molecular Virology Techniques: Health Sciences Book Stacks: QW 160 M7178 1994 pt. A.

Other Methods Resources

Basic Methods in Molecular Biology, by Leonard G.Davis, W. Michael Kuehl & James F. Battey. Norwalk, Conn: Appleton & Lange, 1994. Health Sciences Book Stacks QH 506 D262b

Current Protocols in Immunology. Edited by John E. Coligan ... [et al.]. New York : Greene Pub. Associates and Wiley-Interscience, 1992-. Health Sciences Reference Books QW 525 C976 1992.

Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.]. New York : Greene Pub. Associates and Wiley-Interscience. 1992-. Health Sciences Reference Books: QH506 C87 1992.

Current Awareness Tools

Journal literature is the backbone of scientific communication, and keeping up can be a daunting task. The Library subscribes to three sections of Current Contents on CD-ROM (Clinical Medicine, Life Sciences and Agriculture, Biology & Environmental Sciences), to help users keep abreast of recent developments in their field. These databases are available for self-searching at HSLIC; or a weekly search can be conducted on your behalf. For more information contact your library liaison or go to Email Alert Services (/help/alerts.html) for details.

Citation Management Software

Managing your reprint collection can be a challenging task. A bibliographic citation management software package can make this process more streamlined and efficient, particularly when creating bibliographies for manuscripts. Two packages, available both in Macintosh and Windows versions, are supported by HSLIC: EndNote Plus, by Niles & Associates, and Reference Manager, by Research Information Systems. Both work well with MEDLINE, other UWIN/Willow databases, Current Contents on CD-ROM, and with many other database formats. Library staff can help users import references into these programs and make informed choices when purchasing software. For more information, call the Information Desk at any Health Sciences library or send an email message to hsl at u.washington.edu.

User suggestions for additional basic sciences materials to be added to the collection (print or electronic) are welcomed. A Purchase Recommendation form is available at /hsl/forms/purchase.html.

[Return to Table of Contents]

PAIS Offers Public Policy Information

Looking for information on public and social policy issues? Search the Public Affairs Information Service (PAIS) database on UWIN/WILLOW for information on food safety, welfare reform, international travel, health insurance, criminal justice, population control, communicable disease control, poverty and other social conditions, and similar topics.

PAIS, with more than 400,000 citations, emphasizes factual and statistical information, providing access to the public policy literature of business, economics, law, international relations, government, political science, social work and other social sciences. PAIS offers a good entry point into the realm of government information, with discussions on the making and evaluation of public policy from professional publications, as well as reports on public affairs from the serious general press.

Use PAIS, along with National Newspaper Index, to access information which has not yet had time to appear in peer-reviewed publications, in addition to journals, books and thousands of government documents. Up to a third of the references are to foreign journals and books, providing strong international coverage. Look for PAIS in the Social Sciences databases group on UWIN/WILLOW.


    Author:     Petersen, Carol Dawn 
    Title:      Female-headed families on AFDC: 
                who leaves welfare quickly and who
                doesn't.
    Pub. Info:  Je 1995.
    Notes:      Includes bibliographical references.
    Abstract:   Examines factors affecting length of 
                stay on Aid to Families with 
                Dependent Children (AFDC) and 
                assesses implications of this for 
                welfare reform; US. 
    Subject:    Family allowances - United States.
    Subject:    United States - Social policy.
    Subject:    Public welfare - United States.
    Subject:    Single parent family - United States.
    Subject:    Transfer payments - United States.
    Source:     Journal of Economic Issues 29:619-
                28 Je 1995 
    SSN:        0021-3624 
    Language:  eng
Sample PAIS entry

[Return to Table of Contents]

Reference on the Net

Commencing with this issue, "Reference on the Net" will become a regular column in Books & Bytes to highlight some of the most useful health sciences resources.

MedAccess is available locally via HealthLinks -> Library -> Reference -> Reference Resources from Elsewhere or by pointing your Web browser directly to http://www.medaccess.com. MedAccess offers useful health and wellness information to the consumer in simple and understandable forms. You can use the searchable Locator database to find out about physicians, hospitals (types, size, accreditation, services offered), preferred provider organizations (PPOs), health maintenance organizations (HMOs), and nursing homes; consult full-text newsletters, health guides, healthcare alerts and workbooks; obtain information about health care benefits that enables employees to make informed decisions; find instructions on how to access vital records; and locate a directory of government agencies concerned with health and healthcare issues, including descriptions of each agency, addresses and telephone numbers.

The Physician's UPIN (Unique Physician Identifier Number) database is available via HealthLinks -> Library -> Databases or by pointing your Web browser to http://www.CPG.mcw.edu/www/upin.html. The database contains the unique number identifying physicians (both solo and group practice) who provide services under Medicare and a directory of the numbers. The information is intended to assist the health care community in meeting claims coding and filing requirements. The database contains a file identification record, state identification records, and physician practice setting records. Physician records are in alphabetical order by state and by physician name within state. Information is not included at this time for residents, interns, and those practicing solely within health care maintenance organizations or other prepaid capitation systems.

Reuters Health Information Services is available via HealthLinks under Internet Search or via The Library -> Journals -> Headline News -> Medical or Health-Related News Resources; or point your Web browser directly to http://www.reutershealth.com. Reuters offers health care-related headline news in the form of abstracts with citations to journal articles. Subject coverage includes clinical medicine, epidemiology, economics, ethics, legal issues, managed care, pharmaceutical industry, professional development, regulatory issues, and science. Use the Reuters search engine to find information in their archives. A link to World News provides access to international news of a more general nature. Reuters also offers a fee-based subscription service, GeoMedica. This interactive education, information, and communications service is designed specifically for the office-based primary care physician.

[Return to Table of Contents]

Health Reference Center Gold Update

As announced in the last issue of Books & Bytes, ethernet and modem access to Health Reference Center Gold (HRCG), a leading consumer health information database, is now available to UW faculty, staff or students with an account on the UW computing network. Users must be using Windows 95, Windows NT, or Windows for Workgroups (ethernet connection only) using the Microsoft TCP/IP stack.

To request an HRCG password and configuration instructions for accessing the HSLIC server, send an email message to hsl at u.washington.edu. Enter 'HRC Access' as the Subject. In the body of the message include your name, UW email address, mailing address, UW department, and UW status (faculty, staff, or student).

UW departments with an existing Windows NT network that is restricted to UW users may be eligible to establish a 'trust relationship' with HSLIC that will permit easy networked access to HRCG for all Windows machines on your network. If your department is interested in this option, please send an email message to cweaver@u.washington.edu with the name, phone number, and email address of your systems administrator.

We regret that because of networking difficulties, Macintosh access to HRCG is not possible at this time. We hope to be able to offer this product to Macintosh users in the future.

[Return to Table of Contents]

Recent Gifts

Acknowledgment and appreciation are extended to the following individuals, organizations and departments who have recently made contributions to the HSLIC collections:

Dr. Ramin Ahsaci;
Prof. Charles E. Alpers;
Prof. Jon R. Conte;
Prof. Ruth F. Craven;
Dr. Anatole S. Dekaban;
Mr. Martin Falsberg;
Dr. John P. Geyman;
Prof. J. David Godwin;
Prof. Tom Greer;
Dr. Vivien Hanson;
Dean Sue T. Hegyvary;
Ms. Jennifer Hess;
Prof. Anne Loustau;
Prof. George M. Martin;
Ms. Anna Mastroianni;
Ms. Patricia Oelwein;
Prof. Oliver H. Osborne;
Dr. Roy C. Page;
Dr. Virginia P. Sybert;
Virginia Mason Hospital;
and the following UWMC departments:
Anesthesiology;
Health Services;
N.W. Primate Center.

[Return to Table of Contents]

Internet Navigation Tools

To cope with the bewildering array of information sources available on the Web, two types of navigation tools are available: classification schemes and search engines. The Navigating the Web page on HealthLinks (/search) offers a compact list and detailed description of these tools.

The classification schemes organize resources by subject, geography, alphabet, or other logical arrangements. These easy-to-use tools encourage browsing and often offer search capabilities as well. Good examples are Yahoo! (http://www.yahoo.com/search.html) and MedWeb (http://www.medweb.emory.edu), which organize the health sciences sites on the Web by topic.

Web search engines are computer programs (a.k.a. robots, spiders, wanderers, or worms) which automatically roam the Internet, collect sites, index them, and create searchable databases. Each robot searches the Internet in a different way and indexes and stores the information differently. Examples of search engines are AltaVista (http://www.altavista.com/) which indexes the full text of over 22 million Web pages and has simple and complex searching; Excite netsearch (http://www.excite.com), which performs concept and keyword searching of a database with more than 11.5 million Web pages; and WebCrawler (http://www.webcrawler.com), which is useful for quick searches.

There are also "meta-search engines" that search the search engines. For example, the UW-based MetaCrawler (http://www.metacrawler.com) queries eight search engines and organizes and displays the results in a uniform format. (Go2Net, now InfoSpace, took over exculsive operation of MetaCrawler in 1997 -- see http://www.cs.washington.edu/research/projects/WebWare1/www/metacrawler/index.html).

Some sites are just collections of search engines. For example, All-in-One Search (http://www.searchallinone.com) is a collection of forms-based search engines. [url updated mar2005] Find it on the Web (http://www.kcls.org/kcls/searchengines.html) is an annotated listing of search engines. c|net search.com (http://www.search.com) lists more than 250 Internet search engines by category. Within HealthLinks, click on the Internet Search button on the main screen for quick access to a variety of search tools. Some of the factors to consider in selecting which one to use are the size and currency of the database; the speed of searching and ease of use; unique features; and the clarity of user instructions. Check out the following Web sites for more information about search tools:

[Return to Table of Contents]

Serial Title Changes
January - March 1996

Newly added titles: Title changes: [Table of Contents]