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The NCBI Entrez service, a gateway to multiple life sciences collections hosted by the National Center for Biotechnology Information (NCBI), links to a number of free databases that are invaluable free resources for various types of non-patent literature. We’ve briefly looked at PubChem as a useful source of chemistry-related prior art, and users can search for genetic data through NCBI BLAST and Online Mendelian Inheritance in Man ® (OMIM). One of the most popular resources available through Entrez, the PubMed search platform, is probably familiar to any patent searcher who’s hunted for biomedical non-patent literature. PubMed is a massive free online database of medical information provided by the National Library of Medicine (NLM) and the National Institutes of Health (NIH), and the platform interface has undergone multiple changes over the last few months that will make searching, evaluating, and saving results an easier task for anyone who needs to use PubMed.
Read on as we look at the five most recent changes to the PubMed interface, including a new filter sidebar, support of versioned citations, and more!
The Basics About PubMed
The PubMed system includes citations and abstracts for biomedical literature from MEDLINE and additional life science journals. The PubMed/MEDLINE database can be searched using standard search terms (e.g., keyword, author) or the NLM Medical Subject Heading (MeSH) Terms. MeSH is the controlled vocabulary used for indexing articles and provides a consistent way to retrieve information that may use different terminology for the same concepts.
Users can keyword search PubMed through a simple search form, use an advanced search option to build a complex query using field qualifiers and Boolean operators, or enter a complex query directly into the simple search form (i.e. use the simple search form as a command line interface).
Free optional registration is available through My NCBI. Additional features available to registered users include automatic e-mailing of search updates, ability to save records, and filters for search results.
Here is a quick round-up of the most recent changes to the PubMed interface since February 2012. These updates were originally listed under the “PubMed New and Noteworthy” RSS Feed, which links to detailed articles about each update on the the NLM Technical Bulletin. See earlier updates under the Major Recent Updates section of the PubMed community report.
February 2012 – Versioned Citations
PubMed now supports versioned citations. According to the NLM Technical Bulletin article (see link in title above), “revisions, scientific updates, and updates of reviews are examples of content that could be versioned.” The version information will be displayed on the Summary and Abstract sections of the record. Versions will be identified with the original PubMed ID followed by a unique version number (in the format PMID.version). In the versioned citation, “the article’s original publication date is retained, and the version publication date is enclosed in square brackets.”
The PubMed Abstract display has been updated with a “Save items” portlet to provide an easy way to add citations to a My NCBI collection. The “Save items” option will appear as a drop-down menu to the right of the full record, and the user will need to sign in to their “My NCBI” account to save the record to “Favorites” or another collection.
April 2012 – “Citation Manager” Selection
The PubMed “Send to” menu has been updated to include a “Citation manager” selection. Select the “Citation manager” option in under the “Choose Destination” drop-down menu to “download a text file (with an nbib extension) in the tagged MEDLINE format.” According to the NLM Technical Bulletin article (linked above), the user can then import this file into the citation manager software of their choice.
May 2012 – Filter Sidebar
The Filter Sidebar has replaced the Limits page in PubMed. Users can view the filter options in a sidebar to the left of the search results, where they can narrow the result list based on various criteria (text availability, publication dates, species, article types, etc). Select “Choose additional filters” to open a menu and select additional filter categories to display in the sidebar. Select the “more” options under specific filter categories to view more filter options which can be utilized. The NLM Technical Bulletin article (linked above) mentions that “the PubMed default Review and Free full text filters have been moved to the filters sidebar.”
May 2012 – New Ranking Algorithm for Author Searches
The PubMed abstract display was modified to display results using a ranking algorithm when users click the author search link. According to the NLM Technical Bulletin article (linked above):
Because an author may share the same name with other authors, the objective is to display more relevant results by disambiguating common author names. When users click the author name link on the abstract display, an author search is executed in PubMed. If an author name is computationally similar to an author name for additional PubMed citations, the results will display those citations first, in ranked order, followed by the non-similar citations. The results sort notation will display as ‘Sorted by Computed Author.’
Professional patent searchers who need to scour the earth for all available prior art during a comprehensive search will appreciate the updated search interface on PubMed that streamlines the search and viewing process. The filters sidebar replaces a cumbersome “limits” page that took a few extra clicks to access and apply to the search results. Now, users can instantly refine their search directly from the results list. The “sorted by computed author” search and the versioned citations both help users more quickly rank and identify the most relavent results or versions of a result. The “Save items” portlet and “Citation manager” option allow the user to quickly compile and export the most relevant results into a concise list that can be manipulated through any type of citation manager software. These subtle changes to the PubMed interface may not seem like enormous improvements, but they can save a prior art searcher time when every second counts.
Have you noticed any time-saving updates to PubMed or other NCBI search platforms that weren’t mentioned in this post? Let us know about them in the comments!
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This post was contributed by Joelle Mornini. The Intellogist blog is provided for free by Intellogist’s parent company Landon IP, a major provider of patent searches, trademark searches, technical translations, and information retrieval services.