Biblimed: a review by Intellogist

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…

Read Further at:

Mornini, Joelle. The Intuitive Alternative to PubMed: Search MEDLINE on BibliMed. Intellogist, 1st of July 2012. Available from: http://intellogist.wordpress.com/2012/07/01/the-intuitive-alternative-to-pubmed-search-medline-on-biblimed/[Accessed 10th July 2012]

Biblimed, the latest app in SciVerse Scopus

Business news: PubGet acquired by the CCC!

PubGet, one of my favorite PubMed alternatives, has been acquired by the Copyright Clearance Center.

Pubget offers search, retrieval and browse capabilities for content. Its solutions make research more efficient by simplifying the process of finding, managing and analyzing information. Pubget has served more than 5 million researchers and 500 research centers in 2011.
“Blending Pubget’s current and future offerings with CCC’s broad portfolio of licensing products will provide clients with a complete professional information solution,” said Tracey Armstrong, CEO, Copyright Clearance Center. “We’re thrilled to welcome Pubget’s team to CCC and look forward to working together to quickly create market-driven solutions that meet the needs of those who produce content and those who use it.”
“Part of our mission at Pubget is to make access to information seamless. CCC has been making copyright licensing seamless for researchers for decades,” said founder Ramy Arnaout. “We need to work directly with publishers to build this business and CCC has done this while also extending the value of content spend for users. We are all excited about what the future holds with this combination.”
Pubget was founded in 2007 by Arnaout who holds an MD from Harvard, a PhD in mathematical biology from Oxford, and an SB in biology from MIT. Arnaout will join the CCC team as a Senior Advisor.

Press release:

http://www.copyright.com/content/cc3/en/toolbar/aboutUs/newsRoom/pressReleases/press_2012/press-release-12-01-09.html

    

 

 

 

Semantic MEDLINE: the next PubMed?

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

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.

Find science papers fast

PubGet is an amazing tool, to retrieve free and legal PDF once you have a reference. It is not new, but that I didn’t know it, so far.

Of course, the coverage is limited to Medline content, and the full-text document is not always provided. Anyway, it could be a great tool to help end-users when they want to know when an article is freely available somewhere.

Moreover, what is disruptive, is that the search experience  is based on documents availability and not only on relevance and completness.

http://pubget.com/search 

(optimized with an institution subscription)

Follow them at: http://blog.pubget.com/ 

Drug literature: Scopus would be a better choice than WoS and Medline

According a recent study…

Findings:

- Based on the results from this limited (atorvastatin (Lipitor) and olanzapine) but by no means atypical study of comparative strengths and degree of coverage, the best option for retrieving the largest numbers of articles on a particular drug in the literature would be to use both Scopus and Web of Science, as these two databases complement each other with respect to the journal coverage. MEDLINE retrieved much smaller numbers of documents in all searches and should be used only when the other two databases are not available

- The comparison of the total and annual output of documents obtained from the databases showed that Scopus performed better than the other two databases in these respects

-  This article shows that significant differences existed not only in the journal titles but also in the number of documents that the databases retrieved from the same journals. Scopus and WoS complemented well each other in terms of journal coverage, which makes using both of them the best option for comprehensive retrieval of the drug literature

Conclusions:

- Since the introduction of Scopus in 2004, many users and librarians have been trying to evaluate and compare it to WoS. The much easier to navigate interface and the possibility of viewing immediately, on the same screen, the results from analyzing the search results make Scopus a very attractive option for searching the drug literature.

- Based on the results from this study, the best option for comprehensive retrieval of the drug literature would be to use both Scopus and WoS, as these databases complement each other well with respect to the journal coverage. If an institution has to make a decision to choose between Scopus and WoS, Scopus would be a better choice for this kind of literature. Since  MEDLINE has found significantly fewer documents than the other two databases, it should be used only when these two databases are not available

Baykoucheva, Svetla(2010) ‘Selecting a Database for Drug Literature Retrieval: A Comparison of MEDLINE, Scopus, and Web of Science’, Science & Technology Libraries, 29: 4, 276-288

http://dx.doi.org/10.1080/0194262X.2010.522946

PubMed: a success or a tragedy?

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/

Health education: Scopus has a better coverage than Medline

Scopus provided the most thorough coverage of the cited journals, followed by MEDLINE, Social Sciences Citation Index (available at Web of Knowledge)…

Burtis, A.M. & Taylor, M.K..  Mapping the literature of health education, 2006-2008.  J Med Libr Assoc. 2010 October; 98(4): 293–299.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2947136/?tool=pubmed

Quertle: A great new semantic search for Medline

Find meaningful results in context, not just long lists of documents

Quertle is a free search engine for the biomedical literature, providing linguistic approaches to get much more relevant results, returning documents where the author has stated a relationship between the search terms, not just simply throwing back long lists of documents where the terms have been found scattered throughout.

Currently it provides access to all of PubMed, open access full-text articles from PubMed Central and BioMed Central, FierceMarkets news articles, whitepapers, Toxline, and the NIH RePorter database, and is adding more databases all the time.

Because we find and report to the user the specific facts of interest from those articles (nicely highlighted in context), the searcher has a much better idea of whether the article contains information not in the abstract that is worth buying from the publisher.

Why Quertle is different:

It’s easy – Quertle’s friendly interface makes it simple to search and refine results. It’s powerful – Using advanced semantics, Quertle finds quality results, not just long lists. It’s inclusive – All of PubMed, a growing number of full-text documents, news, and more. What’s good: ease of use types of publications: literature + news + whitepapers What’s bad: ads on the middle of results only based on PubMed (hope they will sign with STM publishers) http://www.quertle.info/v2/ 30 seconds to understand what is semantic search in science: http://www.quertle.info/training/Why_Traditional_Search_Engines_Fail.pdf