Showing posts with label PubMed. Show all posts
Showing posts with label PubMed. Show all posts

Monday, May 9, 2011

GoPubMed: the knowledge-based PubMed search

GoPubMed is a search engine that provides PubMed results "sorted into meaningful categories," as well as the ability to narrow those results in ways that are meaningful to the searcher, providing relevant citations without the need to comb through an overwhelming results list.

GoPubMed uses the Gene Ontology (GO) and the National Library of Medicine's Medical Subject Headings (MeSH) as knowledge structures to determine how to sort these results, and claims that the result categories will "in many cases ... already represent the answer to your question," which is certainly a different way of discovering information in PubMed's enormous - again, sometimes overwhelming - database.

The example GoPubMed provides on the FAQ page is a search for the protein Rab5, which turns up a list of top related terms as well as categories this term appears in in the Knowledge Base, both of which might lead to a more expansive perspective on the original search question.  As promised, navigating through the drop-down menus below each category does provide a wealth of information, which might both answer the question that prompted the initial search as well as provide new terms with which to build a more in-depth search. The ability to narrow from here - to include specific resulting terms in a narrower search, or to exclude ones that are way off - leads to a custom-built results set.

As you might expect, search results can also be narrowed by location, publication or publication date; unfortunately, they can't yet be narrowed by what a particular institution has access to, so if you're searching GoPubMed from MGH for articles rather than the answer to a basic question, the best option would be to find citations via this search engine and then click over to our website and search them from our link to PubMed, which can be limited to resources we provide access to.  


If you were previously a MeshPubMed user, this service has now been integrated into GoPubMed.

Friday, October 30, 2009

PubMed Redesign

PubMed has a new look. The National Library of Medicine (NLM) has redesigned its interface with the goal of making it easier to use while continuing to promote scientific discovery. For more information on what's different, please read the latest NLM Technical Bulletin.

We've also added new functionality that you will benefit from when you access PubMed from the library web site. When you perform a search, you will now be able to see a link to filtered results for MGH Treadwell Library in the upper right corner of the results screen. Clicking on this link will show you the results of your search that can be obtained—online and in print—from Treadwell Library. When viewing individual results, you'll still see the Treadwell Library Online and Treadwell Library Print Collection icons (shown below) that tell you in what format these can be obtained.

Treadwell Library OnlineTreadwell Library Print Collection


To take advantage of this feature, be sure to access PubMed from the link on the library's home page or databases page.

Please let us know if you have questions or comments.

Tuesday, June 16, 2009

Biomedical Text Mining Tools

If you are looking for new ways to search & mine PubMed and other databases from NCBI, try this website: http://arrowsmith.psych.uic.edu/arrowsmith_uic/index.html .

I like ADAM for trying to figure out the myriad of ways researchers refer to the Factor V Leiden mutation (FVL, for example) or IL2 or any number of gene expression notations, drugs, and other entities that can be written in a shortened form.

I tried the "Anne O'Tate" tool for data mining a search on melanoma and tumor growth factors that gave me over 3,000 citations. There was a facet called "Topics" that pulled out 5,000 discrete topics along with a count of articles mentioning these new terms. I can use these to refine or expand my search. There is a facet for "Authors" that can tell you who's who in a certain area of research as well.

Keep in mind that these tools are experimental, but could be real time-savers, or better yet, great sources of epiphanies about your own research. Give them a try!