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SOARING BEAR Ph.D. Pharmacology

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Scientific advisor to the health professions & herbal industry
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Pubmed (Medline) search strategy sharpening for 'difficult' searches - better and faster.

Many (perhaps 80%) pubmed searches are easy, providing what you want in a few minutes, so not requiring these tips.  But some are difficult.

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AMBIGUITY situation with alkylamides layer 1

"Alkylamides from Echinacea Are a New Class of Cannabinomimetics"    ----  If you miss a headline like this then you are busy, and so have even greater need for the following tips.  A title like this would certainly merit wide interest, so you search Pubmed.gov on Alkylamides and get 200 hits, which at first blush seems like enough to get a sense of the topic.

FIRST ALWAYS check Search Details box of the pubmed search results to see how you were interpreted by the Pubmed system - that can explain any odd results. We see:  Alkylamides[All Fields] which means no MeSH term was triggered, which is not unusual but tips you off that your term failed to be recognized.  Trying shorter stems of the search term Alkylamid* doesn't help. 

SECOND step is change Format (just below searchbox) to abstract, and under any useful citations that have been indexed click Mesh Terms to see terms that might help expand your search, which might tip you off to the
Polyunsaturated Alkylamides term that will more surely be found in the next step.

THIRD step to sharpen results is looking in MeSH browser for where your term fits in the huge tree of chemical terms.   MeSH browser doesn't find that exact term but instead is called Polyunsaturated Alkylamides, and when put into pubmed gives 13,000 hits. Just like 200 was too few, 13,000 is too many.

Looking closer at the MeSH tree structure you see under Polyunsaturated Alkylamides is capsaicin, that you know has tons of lit, so tell medline not to explode the tree with searchterm[MH:noexp]  gives you 3300 hits.

So in this short exercise of just a minute or two we started with 200, exploded to 13,000 and sharpened to 3300. That general strategy of first word, widen and then sharpen will always favor you.

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AMBIGUITY situation with alkylamides layer 2

Then there is the spelling issue - Which is proper spelling?

      Alkamides                  Alkylamides

Medline literature by scientists shows roughly equal use of the two spellings:  alkamides[tiab]  = 122    alkylamides[tiab] = 199. 
Yet one is recognized by the Pubmed system better than the other. Alkamides     3420         Alkylamides 199
  this kind of thing can change any time by how pubmed works in the background

    This is why a widening strategy to use anytime you can is chaining together synonyms:  Alkamides OR Alkylamides  giving 3600 hits

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AMBIGUITY situation with receptors - referring either to cells or proteins

Proteins are named and classified by perceived function, substrate, pathway, location, coding genes, interactions, structure, disease, deficiency, excess, processing.  Lots of ambiguities with cell and protein names which are simply a reflection of the complexity of nature and inherently difficult for any classification scheme to 'organize'.  We do the best we can and need to be flexible with context and changing views and perspectives.  There is always a balancing act in search strategies of widening and then sharpening. 

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AMBIGUITY situation with NSAIDS

Warnings were widespread about stomach irritation by NSAIDS but COX-2 that changed the game after discovery 1991 (chronology) - there are inherent problems with any term starting with 'non'.  do we call the new non-NSAIDS generation-2, or non-non, or call the old ones historical? .... or just leave it all together intermixed and leave it to you the searcher to know this field? No easy answers and makes for what I call difficult searches.  MeSH helps as much as it can but there are limits to any scheme when applying language to nature.

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AMBIGUITY situation with resin - historically referring one type of plant secretion (not including sap, latex, mucilage) and more recently broadened to any viscous substance

Language continues to evolve with new discoveries, so new synthetic substances were named for having sticky viscous properties like plant secretions even if very different in chemistry.  Any categorization scheme or search strategy struggles with this kind of dilemma.  One must have awareness of new collisions coming from the sides. MeSH in 2003 fudged by distinguishing with Resins, Plant under biopolymers and Resins, Synthetic under plastics.  That is about as reasonable as one can do but not immediately intuitively obvious until you poke around the system some.

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AMBIGUITY situation with parent outgrowing the child

Strictosidine derivatives are a subgroup of indoles, which is becoming a tail wagging the dog (the child outgrowing the parent) because of greater complexity and range of activities. The indole part of strictosidines is easily noticed so often simply called indoles, so that searching on strictosidin* misses substantial parts of the literature that is mis-categorized in the smaller parent group.

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AMBIGUITY situation with multimeaning words like pulse - meaning either rhythmic wave or beans

Find consistently associated words so
  bean meaning literature found by - pulse[tiab] & (plants OR fabaceae OR beans)
  rhythm meaning found by - rhythm[tiab] & (heartbeat OR wave NOT beans)

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AMBIGUITY situation with




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