Science Intelligence and InfoPros

Little things about Scientitic Watch and Information Professionnals

Posts Tagged ‘PubMed

For the fun: PubMed and the End of the World!!!

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To read this nice post by the KraftyLibrarian:

If you haven’t heard about the  Mayan civilzation’s calendar predicting the end of the world on December 21, 2012, then you have been living under a rock.  Personally I believe the Mayans were on to something.  Instead, I believe the end of the world will happen on January 1, 2013.  Why?

As of January 1st NCBI will no longer support Internet Explorer 7 and all the hospitals that haven’t upgraded will begin to have problems searching PubMed. (…)

Read the full article at:

KraftyLibrarian. Internet Explorer, PubMed and the End of the Year. Posted on 12 December 2012, Available from: http://kraftylibrarian.com/?p=2153

 

Written by hbasset

December 12, 2012 at 8:35 pm

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Reading: Is Google Scholar better than PubMed ?!

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According this study, PubMed searches and Google Scholar searches often identify different articles. In this study, Google Scholar articles were more likely to be classified as relevant, had higher numbers of citations and were published in higher impact factor journals.

Nourbakhsh, E., Nugent, R., Wang, H., Cevik, C. and Nugent, K. (2012), Medical literature searches: a comparison of PubMed and Google Scholar. Health Information & Libraries Journal, 29: 214–222.

http://dx.doi.org/10.1111/j.1471-1842.2012.00992.x

Written by hbasset

August 27, 2012 at 4:20 pm

Posted in literature

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PubMed: A few recent changes… (by Intellogist)

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Joelle Mornini, from the great Intellogist webiste, has listed a few recent changes that happened in PubMed.

In a few words, nothing revolutionary… Her conclusion is:

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

See the full article at:

Mornini, Joelle. 5 recent changes to the PubMed interface, Intellogist, 19 June 2012. Available from: http://intellogist.wordpress.com/2012/06/19/5-recent-changes-to-the-pubmed-interface/ [Accessed 20 June 2012]

Personaly, I would rather say that switching to great alternatives such as GoPubMed, PubGet or Biblimed, instead of using this poor PubMed will save precious minutes!!! See my previous post

 

Written by hbasset

June 20, 2012 at 8:48 pm

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iPubSci: an alternative to expensive science journals?

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iPubSci is a new concept for the downloading and purchasing of science articles on a per-article basis.

It could be a real-world solution to the access and affordability problem faced by scientists in both biotech and academia.  iPubSci would meld two already well-designed types of programs in search (PubMed) and the sale of individual pieces of content (iTunes). This concept arose out of numerous brainstorming sessions with Seattle biotech librarian Molly Bernard.

This initiative is developped by Stewart Lyman, a science-for-free activist, that I have already mentioned when he wrote in Nature Biotechnology.

Steward is looking for support of end-users at  biotechnology, pharma, medical devices, and in academia. He hopes to put additional pressure on commercial publishers to low the cost of articles.

http://www.ipubsci.com/support_iPubSci.html

Written by hbasset

December 5, 2011 at 9:23 pm

Posted in Journals

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With a librarian, it is better!!!

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A recent study has has found quantitative evidence of a significant difference in search performance between paediatric residents or interns assisted by a librarian and those searching the literature alone.

Each participant searched PubMed and other online sources, performing pre-determined tasks including the formulation of a clinical question, retrieval and selection of bibliographic records. In the assisted group, participants were supported by a librarian with ≥5 years of experience. The primary outcome was the success of search sessions, scored against a specific assessment tool.

To read in Health information and Libraries Journal:
http://onlinelibrary.wiley.com/doi/10.1111/j.1471-1842.2011.00957.x/abstract

 

Written by hbasset

November 4, 2011 at 7:34 pm

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Semantic MEDLINE: the next PubMed?

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The NLM works on a new interface for PubMed, including latest advances of semantic search (NLP and connected graphs).

Semantic MEDLINE is a prototype Web application that summarizes MEDLINE citations returned by a PubMed search. Natural language processing is used to analyze salient content in titles and abstracts. This information is then presented in a graph that has links to the MEDLINE text processed.

Currently, the results from 35 PubMed searches (including a variety of disorders and drugs) are available to be processed. The 500 most recent citations (from the date of the search) are available for further processing by Semantic MEDLINE”.

The prototype can be tested at:

http://skr3.nlm.nih.gov/SemMedDemo/index.jsp

See also this article:

Rindflesch, T.C., Kilicoglu, H., Fiszman, M., Rosemblat, G., Shin, D. Semantic MEDLINE: An advanced information management application for biomedicine. Information Services and Use,  Volume 31, Issue 1-2, 2011, Pages 15-21

Written by hbasset

September 24, 2011 at 10:01 am

Posted in literature

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Laser medicine: Scopus and Pubmed are the best sources

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Summary
The four most popular search engines PubMed/MEDLINE, ScienceDirect, Scopus and Google Scholar are investigated to assess which search engine is most effective for literature research in laser medicine. Their search features are described and the results of a performance test are compared according to the criteria (1) recall, (2) precision, and (3) importance.
As expected, the search features provided by PubMed/MEDLINE with a comprehensive investigation of medical documents are found to be exceptional compared to the other search engines. 

However the most effective search engine for an overview of a topic is Scopus, followed by ScienceDirect and Google Scholar. 

With regard to the criterion “importance” Scopus and Google Scholar are
clearly more successful than their competitors.

All in all Scopus is the most effective search engine if one requires only an overview of the topic.  For a widespread and in-depth investigation in the area of life science and closely related topics, PubMed/MEDLINE is more  appropriate

Tober, Markus. PubMed, ScienceDirect, Scopus or Google Scholar – Which is the best search engine for an effective literature research in laser medicine? Medical Laser Application. Volume 26, Issue 3, August 2011,
Pages 139-144. Basic Investigations for diagnostic purposes
http://www.sciencedirect.com/science/article/pii/S1615161511000329

Written by hbasset

August 2, 2011 at 4:51 pm

Posted in Tools

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How many Medline platforms on the Web?

Born as the first “open” biomedical database, PubMed is by far the leader platform to search into Medline.

 Despite a very poor evolution since 1996, the NLM’s web site is still the preferred source of millions of physicians, medicine students and academics.

But this huge success (3.5 million searches per day!), is it a “triumph or a disaster”?

Information professionals feel desperate of one day seeing some pieces of semantic search to be introduced into PubMed.

The presentation below covers strengths and flaws of PubMed and presents a selection of the best alternatives available on the market, GoPubMed, PubGet and BibliMed, to name a few.

Written by hbasset

April 27, 2011 at 7:21 pm

Posted in literature

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Clinical queries: Pubmed better than Google Scholar

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Comparison of PubMed and GS results for clinical topics in respiratory care.

Our results suggest that PubMed searches whith the Clinical Queries filter are more precise than with the Advanced Search in Google Scholar for respiratory topics. PubMed appears to be more practical to conduct efficient, valid searches, for informing evidence-based patient-care protocols, for guiding the care of individual patients, and for educational purposes

GS is inappropriate as the sole alternative for clinicians. (…) For now, the optimal application of Google Scholar may be as an adjunct resource, for known authors and articles, or perhaps for initial searches to quickly find a relevant article“.

Anders, Michael E & Evans, Dennis P. Comparison of PubMed and Google Scholar literature searches. Respiratory Care, May 2010, Vol. 55, N°5, pp. 578-583

Written by hbasset

January 27, 2011 at 9:08 pm

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PubMed: a success or a tragedy?

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When celebrating the 20 millions of articles in last july (see my previous post), I missed this excellent review of the famous platform.

PubMed triumphs

  • A central index freely available globally: Many biomedical scientists probably take PubMed for granted, but try to imagine biology and medicine without it – we would struggle to find anything.
  • Twenty million citations: That’s a lot of data and it’s growing at a rate of about one paper per minute (on average).
  • More than a billion searches in 2009: That’s an average of 3.5 million searches per day or 40 searches per second

PubMed tragedies

  • PubMed is too big and full of noise: Theodore Sturgeon’s law states that 90% of everything is rubbish. If correct, this means around 18 million records in PubMed are worthless junk. But that won’t stop them cluttering up the database and your search results making it harder to find what you want when you need it. Many of the papers indexed by PubMed are “salami-sliced” by publication-hungry scientists into the least publishable unit and are of little or no actual scientific value. It can be difficult (or impossible) to find what you need in PubMed. Cameron Neylon calls this discovery deficit, but however you describe it, finding the information you need in PubMed can be frustratingly difficult – despite the redesigns. There is so much in PubMed it is impossible to keep up.
  • PubMed is too small: Some people argue that an overly conservative indexing and editorial policy prevents PubMed from including lots of biomedically relevant literature that is published in physics, chemistry, mathematics, engineering and computer science journals. Currently much of this data is excluded from the database. Actually, what we really need is PubSCIENCE (covering non-medical sciences) but that idea got tragically axed back in 2002.
  • Identity crisis, ambiguous authors:
  • Identity crisis, missing document identifiers: There are over forty million unique document ID’s in the form of DOI’s. They are a useful way to uniquely identify papers on the Web and link directly to their full content wherever they were originally published. But you might have trouble using DOIs in PubMed. Sometimes DOI’s get left out of records (see some random examples here) altogether. When they are included, they can get buried and are not very accessible. For example this record has a DOI but you won’t find it anywhere in the default page served by PubMed, which means you can’t easily click through to the full text of the article which the DOI would take you to. What this means is, PubMed is not as well integrated with other databases as it could and should be.
  • Mostly abstracts only: PubMed has 20 million freely available abstracts rather than 20 million full text papers. Imagine how the rate of scientific discovery and invention might increase (and the cost might decrease) if it was PubMed Central that had 20 million citations instead of just PubMed. Alas, PubMed Central is currently closer to the 2 million mark than the 20 million mark, but it is growing rapidly thanks to deposition mandates and open access publishing.
  • Ranking results: by default PubMed ranks search results by date – but if Google did the same, very few people would bother use it. Ranking results by relevance, by using an algorithm more like PageRank, would be much more useful to many users as demonstrated by Pierre Lindenbaum.
  • Text mining and ontologies: We’ve still a long way to go before fully exploiting the possibilities offered by text-mining and ontologies to allow PubMed users to semantically search and browse the data. MeSH is just the beginning but that’s another story…

PubMed is a substantial fourteen years of work which continues to have significant benefits for many scientists around the world. There is plenty of room for improvement, but it’s hard to imagine Life® without PubMed®.

Duncan Hull. Twenty million papers in PubMed: a triumph or a tragedy?. O’Really, Online, posted on July 27, 2010:
http://duncan.hull.name/2010/07/27/pubmed-20-million/

Written by hbasset

December 17, 2010 at 9:37 pm

Posted in Science 2.0

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