T H E   N I H    C A T A L Y S T N O V E M B E R -  D E C E M B E R    1 9 9 8 



by Susan Chacko, PhD,
Computing Facilities Branch, CIT

How can any scientist possibly keep up with the scientific literature in her own mini-speciality, let alone the broader perspective of the field and hot new topics in other areas? Well, if she's at NIH, it's pretty much a piece of cake.

First, like scientists anywhere, an NIH scientist needs only her favorite web browser to access Medline, a research staple for many years—in its earlier incarnation as Grateful Med and now as PubMed. Produced by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine, Medline indexes abstracts and citations from about 3,900 biomedical journals in the United States and 70 foreign countries and is updated weekly. Searching PubMed is straightforward, and search terms can include author names, journal titles, MESH (Medical Subject Headings—a dictionary of biomedical terms) words, and phrases. In addition, PubMed offers an entry point to the nucleotide and protein databases in NCBI's Entrez. PubMed is free and open to the world.

Beyond PubMed, however, NIH-based scientists are lucky enough to also have access to the Web of Science, a proprietary literature database offered by the NIH Library and the NIH Center for Information Technology. Ever used the Science Citation Index to track a research topic, starting from a seminal paper in the field? Or do you occasionally look to see how often your own papers have been cited? Well, the Web of Science is an on-line version of the Science Citation Index Expanded. It includes 5,300 major journals, almost twice as much as the print or CD-ROM version.

The Web of Science is licensed to the Bethesda NIH campus, and some (but not all) other NIH locations. It can be accessed only from NIH computers. (This includes dial-in access through Parachute.) If you have questions about whether you are eligible to access it, call the NIH Library.

Once you reach the Web of Science web page, it's best to do a "Full Search." You can search by subject term, author name, journal title, or author affiliation. In addition, the Web of Science can search for articles that cite a particular paper or author. Unlike Medline, there are no indexing terms; the system searches only for words in the title, citation, author names and affiliations, abstract, and the key words supplied by the authors.

These are wonderfully useful services, but short of spending an hour a week running your searches, how can you keep track of new articles? That's where Porpoise comes in. Porpoise (Publish or Perish with POISE), developed by Peter FitzGerald at CIT, will automatically search each week's updates to the Web of Science for your own favorite search terms, and will send you a weekly e-mail message with the results in one of several available formats.

To use Porpoise, you will need a valid NIH e-mail alias, the 4- or 5-letter code that uniquely identifies you in the NIH Directory Service. There is an e-mail address associated with your NIH e-mail alias, and your Porpoise search results will be mailed to that address. Go to the Porpoise web page, choose "Create a New Search Profile," enter a profile, and look at your results. You can modify your profile endlessly (with "Edit Search Profile") until it is tailored precisely to give you citations from a particular, well-defined field of interest. Then sit back and read your weekly e-mail update in comfort! (A useful tip: If your favorite journal tends to wander around the lab before it reaches your desk weeks later, enter its name as "Source" in Porpoise. The table of contents of that journal will be e-mailed to you in the weekly updates.)

What if your weekly update informs you of a fascinating paper in the field, but you don't have the time to walk over to the library to photocopy it? The NIH Library has purchased the complete text of over 300 major scientific journals, including Science and Cell. You can read the paper on-line, or download the paper of interest and print it. Don't have the time or patience for this? Go to the Porpoise web page and choose "Process a Search Profile NOW." Search for the article, select it, go to "Marked List," and select "Order from NIH Library." A copy of the article will be sent to you by campus mail in two to three days. You can also order documents through the Web of Science and through PubMed's Loansome Doc feature.

It's even possible to save the citations from a search into a reference-managing program like Reference Manager or EndNote Plus. For Web of Science or Porpoise output, you'll need to download the ISI/RIS Web Capture Utility and an appropriate filter. See the Porpoise Help page for details.

And soon to come: WHALES (Web Homology ALErt Service), a sequence-alerting service from the Helix Systems at CIT. If you want to know when new sequences relating to fibroblast growth factors are deposited in Genbank, or when new sequences with high homology to your favorite membrane protein sequence appear in the Swissprot database, WHALES is for you.

For a text search, it's much like Porpoise: You can set up a profile with a text search for some word or phrase, and choose to search Genbank, Genpept, Swissprot, or the Protein Data Bank. Once a week, WHALES will search through the new sequences in your chosen database(s) and e-mail you with the result. For homology searches, you put your own sequence into the profile, and WHALES will run a weekly Blast, gapped Blast, or Fasta search (at your choice) against the new sequences and send you e-mail with the alignment result. Watch the Whales web page for announcements.

Fishing Lines

All the services offered have online help—look for a Help button or link on their web page. The NIH Library has handouts on searching PubMed and the Web of Science and on requesting documents electronically. The library also holds seminars and tutorials on using these tools efficiently. You need a library barcode sticker on your NIH ID to order documents electronically.

Medline:   <http://www.ncbi.nlm.nih.gov/PubMed/>

Web of Science & Porpoise:   <http://publishorperish.nih.gov>

WHALES:   <http://molbio.info.nih.gov/whales/>

NIH Directory Service:   <http://directory.nih.gov>

NIH Library:   <http://nihlibrary.nih.gov>   (helpline 496-1080)

Parachute:   <http://parachute.nih.gov/parachute.html>

ISI/RIS Web Capture Utility:   <http://www.risinc.com/webcap/isicap.html>

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