A Centralized Portal to Free Biomedical Literature: Europe PubMed Central

I was recently alerted to the Europe PubMed Central portal by a post on the Science Intelligence and InfoPros blog, where Herve Basset describes the site as “not only a new Medline“:

Unlike PubMed Central, Europe PMC provides a single point of access to not only full-text articles but additionally the abstracts available through PubMed. The Europe PMC interface also offers novel features and functionality, including links to other relevant content, integrated text and data mining tools and grant reporting services through Europe PMC plus.

Europe PubMed Central is a portal created by the the European Bioinformatics Institute, The University of Manchester (Mimas and NaCTeM), and the British Library (in cooperation with the with the National Center for Biotechnology Information at the U.S. National Library of Medicine), which allows users to search a variety of open access biomedical literature. The portal lists coverage of the following publications:

  • PubMed abstracts (about 22 million)
  • Europe PMC full text articles (about 2.2 million, of which over 400,000 are Open Access)
  • Patent abstracts (over 4 million European, US, and International)
  • National Health Service (NHS) clinical guidelines
  • Agricola records (500,000)
  • Supplemented with Chinese Biological Abstracts and the Citeseer database.

Read on for an overview of how to search Europe PubMed Central to locate open-access biomedical literature, patent abstracts, and even grant information!

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How to Stay Updated on Yearly Changes to MEDLINE

It’s that time of the year again.  No, not fall, Halloween, or the beginning of the Christmas shopping season (that started in July); it’s time for the annual MEDLINE®/PubMed® Year-End Processing (YEP) activities.  If you look at the Major Recent Updates section of the MEDLINE system report on Intellogist, you’ll notice that during September of 2011 and 2012, there are mentions of an annual update to the Medical Subject Headings (MeSH), the controlled vocabulary for MEDLINE. The yearly MeSH update is one part of the YEP activities that occur every fall.  The MEDLINE file is a central resource for biomedical prior art that can be freely accessed through the PubMed interface, so patent searchers should be aware of the updates made annually to the database and its controlled vocabulary, as well as how these changes may affect their prior art searches.

After the jump, learn all about the year-end processing activities for MEDLINE and how these changes may affect your searches on PubMed!
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The Intuitive Alternative to PubMed: Search MEDLINE on BibliMed

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The MEDLINE database is an excellent source of non-patent literature prior art for professional patent searchers, especially for fields like medical devices and pharmaceuticals.  PubMed may be one useful free way to access MEDLINE data,  but it is by no means the only option.  As Herve Basset (of the fantastic blog Science Intelligence and InfoPros) points out in a comment on a previous Intellogist blog post about 5 recent changes to PubMed:

I would rather advise to switch to PubMed alternatives: GoPubMed, PubGet, Biblimed…

I decided to take a look at one of the PubMed alternatives recommended by Herve, BibliMed.  BibliMed is a free search interface that accesses MEDLINE data and provides unique search and viewing features like a tag cloud of MeSH term suggestions to add to your search and a list of books relevant to your query.  BibliMed may not include the command line search option that makes PubMed attractive to expert searchers, but the intuitive and creative search features on BibliMed will be very useful for students and novice searchers who aren’t comfortable crafting complex queries and using MeSH terms.

After the jump, learn about the intuitive search and viewing features available through BibliMed!
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5 Recent Changes to the PubMed Interface

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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!
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The Latest Data Updates on PubChem

[tweetmeme source=”Intellogist” only_single=false] The National Institute of Health first released PubChem in 2004, and today PubChem is an important free chemical search platform for patent searchers and other chemical researchers.  According to the “About” section, PubChem allows users to search for “information on the biological activities of small molecules,” and the chemical structures link to other Entrez resources, like PubMed scientific literature. This winter, two new data sources were added to PubChem, and patent searchers looking for prior art in the pharmaceutical and biotechnology fields may find useful data from both resources.

Continue reading for an overview on PubChem and a look at the latest updates to PubChem data coverage!

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Semantic Searching within National Library of Medicine Databases: NLMPlus

[tweetmeme source=”Intellogist” only_single=false] What is the most effective way to search for biomedical information? You can search through a wide range of interfaces within the databases of the NCBI Network: PubMed offers an advanced search form with a variety of limiters and expert command line searching, PubChem offers a chemical structure search option, NCBI BLAST offers genetic sequence searching, and NCBI Entrez offers a federated search portal for all NCBI databases.  One type of search seems to be missing, though.  Where is the semantic search option?

Users now have the option to search biomedical data and services of the National Library of Medicine (NLM) through NLMPlus, a “semantic search engine and biomedical knowledge base application” created by WebLib LLC.  The application was a winner of the NLM Show Off Your Apps Challenge in November 2011, and the president of WebLib confirmed that the company “plans to maintain and enrich the product indefinitely,” according to a recent article from Information Today.

Continue reading to learn about the semantic search features of NLMPlus!
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NEEDLE – Search the National Nuclear Archive and More

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Does it seem like new search system technology is popping up all the time to you? Don’t worry, you’re not crazy! Here at the Intellogist® Blog we’ve looked at new search technology this year including Xyggy (also see this follow-up) and IBM’s Watson (which is set to play Jeopardy next year).

Today we’ll take a gander at NEEDLE, a search system developed by the Idaho National Laboratory (INL). NEEDLE is a unique system with helpful sources available to search for free, including a prominent nuclear power database.

Want to know how you can see this new technology in action, better your prior art searching, and get a glimpse at the future of patent search? Read on, my friends.

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