Libraries 2.0

In mid-2007, Amanda Nottke, a PhD student in Harvard Medical School's pathology department was helping her advisor write up a grant application. They wanted to study a Caenorhabditis elegans protein they thought could model a mammalian enzyme called LSD1, which regulates histone structure. Other potential C. elegans homologues had been identified, but Nottke suspected that their protein, which she declined to name, had the closest sequence similarity to the mammalian version.

Nottke first went to BLAST - the database of nucleic acid sequences maintained by the National Center for Biotechnology Information (NCBI). But she couldn't find a mammalian gene that matched the entire C. elegans sequence; only pieces matched. Her advisor recommended they visit David Osterbur, a science librarian at the Countway Medical Library at Harvard Medical School. Osterbur helped Nottke perform her search in a sequence alignment database called ClustalW, a program designed for these kinds of searches. Sure enough, the percentage similarity between the two sequences was about 60%, a homology that was strong enough to pursue. "We just went in and met with him and [within the hour] left with the answer we needed," says Nottke. "It was super helpful."

Not the bifocal-sporting, cardigan-clad Dewey decimal experts of 25 years ago, science librarians in today's universities are a well-versed treasure trove of knowledge, even in life sciences. "People think they know how to search for things, when they really don't know how to use some search tools efficiently," says Osterbur.

"We're in this Google age and people just want to type something in and get results with limited effort," says Marcus Banks, manager of education and information services at the University of California, San Francisco, library. "That frustrates librarians because in some cases it's not that much more effort to get a much better result." Most librarians today have a graduate degree in information or library sciences. And librarians like Osterbur, who has a genetics PhD, often possess degrees in their specialty, such as biology.

Science librarians of today can scope out particular resources for you, give your lab a tutorial session on special database searching, or hunt down ancient and obscure citations. Here are better ways to get and manage information from popular databases, plus top tips from science librarians on how to make the most of your university and the Internet resources.

1. Get a MyNCBI account. Fast and free, having a MyNCBI account lets you save searches in PubMed Central. On the PubMed home page simply click on "My NCBI" on the left side of the page and register. Once you're registered you can search, save searches, and get email alerts whenever new citations fall under your search parameters.

2. Search with MeSH. All the papers in PubMed are indexed by a librarian who reads the paper and notes all the search terms that apply to that paper, cataloguing them as Medical Subject Headings (MeSH). Click on the MeSH database link on PubMed's home page, where a quick tutorial will take you step by step through using the search. MeSH can be more useful than performing a general search because it allows you to capture the synonyms associated with your topic across multiple fields. Once you've set up a MeSH search that pulls the papers you are looking for, save the search and get weekly alerts for any new citations.

1. Who's citing you? Some science librarians are surprised to find out that researchers aren't using the citation tracker in ISI's Web of Science (created by The Scientist's president and founder, Eugene Garfield). Looking at who has cited a paper since its publication gets you to the forefront of research, as opposed to looking backwards at a paper's cited references. You can see who's citing your papers (potential future collaborators) or see which research groups in your field are getting the most citations (and coming out with the hottest findings). After you've done a search in the Web of Science and retrieved a paper of interest, click on it to view its abstract and citation. Directly under the "Author" and "Source" you'll see "Times Cited" followed by a number. Click on the number to see a list of all the papers that have cited the paper you selected.

2. Get your ToC on. Stay on top of new publications by having your favorite journals' table of contents E-mailed to you, thanks to Current Contents Connect. Inside the Web of Science, register your E-mail address and add your favorite journals under the "My Journal List" link at the top right of the screen to get E-mailed or RSS ToCs immediately when they are published.

One of the biggest challenges for researchers is not finding information on a particular subject, but managing it. To that end the two major resources available are EndNote and Refworks. They each have their pros and cons, but can help keep citations for bibliographies in line, automatically download and organize PDFs of papers you've searched for, and get citations into the correct format for reference sections when you're writing papers. If you can't pick either one you can share data between programs. In general, EndNote is a bit more complicated, but has more perks such as spell check and citation search saving. To help you choose which is right for you, here's a break down of each:

1. Power of Three. Researchers can get hooked on PubMed, but there can be as little as 60% overlap between PubMed and other databases. Josephine Tan, education and information consultant in clinical sciences at the UC SF, recommends always doing a literature search in three places such as PubMed, Google Scholar, and Web of Science. Choose databases based on what you're looking for: if you want papers on basic science involving animals include BIO SIS and CA B Abstracts in your search; if cognitive science is your bent, don't forget ERIC as one of your three databases.

In another example of threes, break your research topic down into three subject areas and search each one separately to see what you come up with. If you're looking for papers on blindness associated with brain neoplasm search each term separately: blindness, brain neoplasm, and just neoplasm.

2. Get Rid of Duplicates. Don't get overwhelmed by thousands of search results if you're searching a broad topic: Use a database like Ovid to search multiple databases at once (like Medline and BIOSIS) and then click on "remove duplicates" to cull duplicate paper citations.

3. Get a Sneak Peak. Not all databases cover conference proceedings. In order to see some research before it's published check out Scopus, which covers 500 conference proceedings and is as current as 2008. Also check out BIO SIS, which is updated monthly with conference notes. Scopus also offers abstracts of articles in press from publishers including Elsevier, Nature, Springer, and BioMed Central.

4. Keep it in Writing. Instead of calling your librarian for help or visiting the library, start by sending an Email request, advises UCSF's Banks. Librarians are dogged creatures who won't rest until a citation or article is found, often forwarding the E-mail to fellow librarians who may have search ideas or know of specialized resources.

5. Ask for it! Most people don't realize that libraries have spending budgets and can get backfiles -older records- to all online journals, says Lori Bronars, life science librarian at Yale University. Researchers can also request that their libraries buy certain books or periodicals.

6. Get Tagging. To take collaboration into the virtual world, you can tag especially helpful resources and share them with other researchers using a tag site like Del.icio.us.com. Tag particular articles, databases, and Web sites and find like-interested researchers who may have tagged the same things. Some universities have set up their own internal tagging systems, such as PennTags at the University of Pennsylvania.

7. Make a Date. Invite your science librarian to a weekly lab meeting or journal club. "This is a great way for us to get a sense of what is going on, really get a feel for the research," says Tan. This also helps librarians spot materials that might be useful to you. Tan has been attending journal club meetings of the medical education department at UCSF for three years. Now, when a new researcher describes their project, Tan knows just the right databases to help them find papers.

8. Follow up. After your librarian has got a feel for your research, give him a set of buzz words related to your area of study, recommends Barbara Cavanaugh, head of the veterinary school library at the University of Pennsylvania. For example, if you're working on transgenic animals, tell the librarian to look out for books and journals that cover subjects like germ cells. Librarians can scout new journal subscriptions or book purchases based on these words.

9. Archive 2.0 Ask your librarian to create a blog that he/she updates regularly with search tips for databases. This way, there will be a place online where you can search for reminders of how to do certain searches, and check for newly updated tips. Tan's blog specializes on research in medical education, scouting out special tips just for that group, or posting notes from tutorial sessions she's led in their department. Her blog is a targeted information Web site for that specific group of researchers, so you can suggest your librarian create a page for your needs.

10. Set a Time Cap If you've spent an hour without finding anything useful or related to your subject, says Tan, it's time to get in touch with a librarian.

Update: This article was updated on 12/02/08 to reflect that both RefWorks and EndNote format reference lists according to the journal publication requirement.