upon reflection I have changed my approach to PubMed ‘Alternatives’: as the NLM make their PubMed data available for free, it created a free playground for all kind of PubMed search options, 3rd-party add-ons, semantic searching etc. There are e.g. Medsum, Anne O’Tate’ and others which help to identify search terms [MeSH) for further searching. Medsum can even distinguish between major (starred) MeSH terms with subheadings and other MeSH terms allocated to a set of PubMed records on a given subject. Excellent!

Reinhard

Ranking results by relevance, by using an algorithm more like [Google’s] PageRank, would be much more useful to many users…”

Indeed, but the meantime, one can use the Google algorithm by using Google itself. Try some site-restricted searches in this form:

site:ncbi.nlm.nih.gov/pubmed

I usually use Google Scholar (scholar.google.com) instead, however: Scholar searches not only PubMed, but the broader literature of science as a whole, and it links to full-text articles found anywhere on the Web, including those posted only on private and university websites.

Highly recommended.

Thank you for your comments.

PubMed provides the best map / representation of a complex reality (here: the literature of biomedicine) we have and, just like other curated databases (WoS, Embase, Scopus, Chemical Abstracts, Cinahl etc.) requires some effort to use properly for complex investigations. That *some* people find this difficult is irrelevant: map reading requires some skills* if you want to use them for more than a Sunday afternoon stroll. Natural curiosity and intuition to find out what a map symbol means would help, but these two qualities are perhaps in short supply in some digital natives who want everything effortlessly and *now*.

I do agree of course with your original suggestion (I paraphrase) that “PubMed’s strengths far outweigh its weaknesses”.

Reinhard

*As does playing chess, reading music, sailing, differential calculus, or determining the ppv of an ELISA test.

Thanks for your feedback on this post…

My point about difficulty of use was really that PubMed could be much easier to use than it currently is. How easy/difficult pubmed is to use depends on who you ask of course, but there is always room for improvement. Some (probably not all) users *do* find it difficult to use, not just the conventional interface at http://pubmed.gov but the http://eutils.ncbi.nlm.nih.gov could be improved as well.

I can’t see the NCBI would be likely to pull all the funding for PubMed in the near future, there would be an international uproar if they did. As for the fulltext issue, thankfully this is being addressed by the work of PubMedCentral and its mirrors like http://ukpmc.ac.uk here in the UK

Finally, I see your point about the signal to noise ratio being “quite good” but do we currently accept similar noisy results from the likes of Google?

Duncan,

Your blog item ‘PubMed: Triumph or Tragedy’ provides some thoughtful questions but misses several points:

PubMed’s real tragedy (which may eventually kill it) is that among the big professionally-curated databases (WoS, Scopus, Chemical Abstracts, Engineering Index, Cinahl, Embase) it is the only one which is accessible freely AND makes its data available on licence, but again for free, to any institution which wishes to provide an ‘alternative’ interface and access route. As some of these ‘alternative’ PubMed providers are profit-driven they have an interest in proclaiming that they are easier to use and provide access to e.g. full-text articles faster than ‘PubMed original’. These alternative PubMed resources suggest, quite wrongly, that PubMed is difficult to use. They attract large chunks of the PubMed user-base and may eventually lead to funding reductions of PubMed via the NCBI. What then?

PubMed is easy to use; it accepts Google-like, focused questions with ease. No knowledge of MeSH terms, subheadings, Boolean operators, or Venn diagrams, nesting of search elements is required. Search results ca be easily manipulated for sensitivity and specificity, or if required, arranged by relevance (in an easy, very sophisticated fashion). PubMed’s search formulation translation algorithm, working quietly in the background is highly developed and used by most ‘alternative’ interfaces, usually without attribution.

The perception that PubMed is difficult to use is also encouraged by medical librarians, who, to show their mettle, point at manuals, help-sheets, explanatory videos: none are necessary for a casual (or regular?) user.

Some subjects may be difficult to search: this is not PubMed’s fault but a reflection of biomedicine’s complexity, which doesn’t let itself to simple yes-no answers. A PubMed search can be compared to a screening test which always (and by definition) produces a false-positive and, sometimes, false-negative results. A screening test with 100% sensitivity AND 100% precision does not exist; why expect it of a PubMed search?

The limitations of PubMed you mention, e.g. no full-text for all articles, author ambiguity, salami-publication tactic, is inherent to all databases (incl. Google) and can’t be put a PubMed’s feet. Your suggestion that PubMed is both too big and too small indicates that it gets it ‘about right’. If you say that it is impossible to ‘find what you need’ you should give examples of focused, biomedical question which do not provide some answers on PubMed.

Your quote of Sturgeon’s law that 90% of everything is rubbish may be correct, but is not helpful. Apart from the fact that a noise-to-signal ratio of 9/1 is quite good, I am reminded of the suggestion ’50% of what we learn at medical school is obsolete by the time we start practicing: unfortunately we don’t know which 50%’ which is more indicative of the problem. PubMed, used intelligently and with realistic expectations (not something Anna Kushnir seems able to do) can help to manage this problem.

Long may it prosper! Thank you, American taxpayers, for making this excellent, unique, powerful resource available for free!

Reinhard