PubMed - free medline from the National Library of Medicine

PubMed Toppings: Adding Sprinkles to PubMed

by.... Donna Berryman, Outreach Coordinator
National Network of Libraries of Medicine (NN/LM®)
New England Region.

Generally, this column is devoted to exploring some facet of PubMed itself. This time around, there's a bit of a different slant: delicious PubMed toppings. Other groups/organizations have built services that, in their opinion, enhance PubMed or provide services that PubMed itself does not. Some of these may be extremely useful to librarians, so PubMed Particulars is taking a walk up to the counter and ordering dessert.

Alerting Services

As of this writing, PubMed is unable to automatically notify you when citations of interest are added to the database. Yes, search strategies can be stored in the Cubby and then, with a click, it is possible to see what's been added to PubMed since the last time the search was run. However, PubMed's Cubby waits for you to come to it. It can't push information to you. NLM is working on developing that capability, but it's not available yet. In the meantime, here are brief introductions to two free alerting services that are worth looking into: PubCrawler and BioMail.

PubCrawler
http://pubcrawler.gen.tcd.ie/

PubCrawler wins the award for the best slogan: "It goes to the library. You go to the pub." It was developed by Karsten Hokamp and Ken Wolfe from the Department of Genetics at Trinity College, Dublin, Ireland.
PubCrawler will perform scheduled searches of PubMed (it will also search NCBI's Nucleotide Database) and, via email, notify the user when the search has been completed along with new citations that meet the search criteria.
Registration is required and then users may set up their queries using the PubCrawler Configurator (see the website). If you loved Internet Grateful Med, you'll probably like the Configurator as its format is reminiscent of IGM. There are boxes in which to enter terms and then drop-down menus for selecting the search tag to be associated with that term. The developers recommend that search strategies be tried out in PubMed before being saved in PubCrawler and they also refer users to PubMed's Help in order to learn to build effective search strategies. Queries may be modified at any time. As for notification: users may choose whether to receive the full results via email or simply receive an email with a link to a web page that contains the results. And PubMed's Related Articles feature is available for the results.
Results are archived for a specified period of time on a designated web page, so it is possible to go back and look at results that were obtained on a given date.
It's totally free! And it's easy to use. PubCrawler has excellent help and a good FAQ.

BioMail
http://biomail.org/

BioMail was written and developed by Dmitry Mozzherin, Alfonso Ali Herrera, and Holly Miller, and the BioMail Team from the State University of New York at Stony Brook with funding help from the National Library of Medicine.
This is another totally free service that is very easy to use. BioMail will search PubMed or NCBI's Nucleotide database.
Once again, registration is required. Then, users can enter a search strategy and set the schedule for searching. Here, too, it is recommended that people test their searches out in PubMed first. BioMail allows the use of PubMed's field tags and serch qualifiers. Results are sent via email either as an HTML attachment, as an HTML formatted email, or in a text email, according to the user's specifications.
There are some really nice things about BioMail. One is that users could literally copy a search strategy from their PubMed Cubby and paste it right into the search box in BioMail. Another is that the results come with several options:
* collecting (storing) selected citations in a "Reference Treasury" - somewhat similar to PubMed's Clipboard without the expiration date;
* button for displaying results in the MEDLINE format - required for importing citations into bibliographic software; and,
results come with one-button access to the BioMail configuration page for changing individual settings.
Once again, BioMail is totally free and easy to use with an excellent FAQ and helps along the way.