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Advanced PubMed Searching

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Robert Wright

on 22 October 2018

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Transcript of Advanced PubMed Searching

Search the
MeSH Database
with one of your concepts
this process
for all of your
other concepts
the key
Rob Wright, Basic Science Informationist
Getting from
"visualizing signaling activities using FRET in live cells, with a focus on kinases and phosphatases"
((("2010/01/01"[PDat] : "2013/12/31"[PDat])) AND (("Protein Kinases"[Mesh] OR Protein Kinase*[tw] OR "Phosphoric Monoester Hydrolases"[Mesh] OR Phosphoric monoester hydrolase*[tw] OR Phosphomonoesterase*[tw] OR Phosphatase*[tw] OR Phosphohydrolase*[tw])) AND (("Fluorescence Resonance Energy Transfer"[Mesh] OR "Fluorescence Resonance Energy Transfer"[tw] OR "Forster Resonance Energy Transfer"[tw] OR "FRET"[tw] OR "FRET-BASED BIOSENSORS"[tw] OR "fluorescence lifetime imaging microscopy"[tw] OR "RESONANCE ENERGY-TRANSFER"[tw] OR "FLIM"[tw] OR "N(epsilon)-(7-diethylaminocoumarin-3-carboxyl)-9-fluorenylmethoxycarbonyllysine"[Supplementary Concept] OR "N(epsilon)-(7-diethylaminocoumarin-3-carboxyl)-L-Fmoc-lysine"[tw] OR "Fmoc-Lys(DAC)"[tw] OR "N(epsilon)-(7-methoxycoumarin-3-carboxyl)-9-fluorenylmethoxycarbonyllysine"[Supplementary Concept] OR "N(epsilon)-(7-methoxycoumarin-3-carboxyl)-L-Fmoc-lysine"[tw] OR "Fmoc-Lys(MC)"[tw] OR "fluorescein-cystamine-methyl red"[Supplementary Concept] OR "FL-S-S-MR cpd"[tw] OR "FRET imaging"[tw])) AND (("Signal Transduction"[Mesh] OR “signaling”[tw] OR “signalling”[tw] OR Signal Transduction*[tw] OR Signal Transduction System*[tw] OR Signal Transduction Pathway*[tw] OR Receptor-Mediated Signal Transduction*[tw] OR Signal Pathway*[tw] OR "Intracellular Signaling Peptides and Proteins"[Mesh] OR “Intracellular Signaling Peptides”[tw] OR “Intracellular Signaling Proteins”[tw] OR “Intracellular Signalling Peptides”[tw] OR “Intracellular Signalling Proteins”[tw])))
embedded in your research question
"visualizing signaling activities using FRET in live cells, with a focus on kinases and phosphatases"
Concept #1A - kinase
Concept #3 - signaling
Concept #2 - FRET
When identifying key concepts, attempt to
simplify as much as possible. For instance, the
terms "visual(izing)" and "live cells" do not need
to be included in our list of concepts, because "visual(izing)" is implicit in the concept "FRET" and "live cells" may be too restrictive.
Start a Word document as a place to build your search as you go. This will be the place you can record concepts and their synonyms and make revisions.
Use the link to PubMed from the Welch Medical Library homepage - http://welch.jhmi.edu/welchone/
Concept #1B - phosphotase
Concept #1A -
Use the auto-fill feature to identify exact matches in MeSH or to suggest variations.
MeSH stands for Medical Subject Headings.
MeSH terms are uniformly applied to articles in PubMed by human indexers.
Using MeSH terms ensures precision.
Only articles with these terms as
important concepts will appear in your results.
Using MeSH also ensures comprehensiveness.
All the variations of a concept
will map to the same MeSH term.
The MeSH database is also an important source of synonyms for searching.
Why use MeSH?
The MeSH Database is a specialized tool available from the PubMed homepage.
For our search, we want the most general result. So, scroll down ...
This is general.
Scroll down the page to
see the MeSH hierarchy
and pick a more specific
Copy and paste this code
into your Word document.
Use entry terms in your search with the code [tw], for text word (e.g. "Protein Kinase"[tw]). Add entry terms as synonyms on your Word document.
Use text words (keywords) derived from entry terms in the MeSH database (or from article titles or abstracts) in addition to MeSH terms. Do so to ensure that your search is comprehensive. Text words catch errors in indexing. They also pull very new articles into your search results that haven't been assigned MeSH terms yet.
This is the format copied from the search builder in the MeSH Database.
Use the Boolean operator "OR" (in all caps to distinguish it from the other text), because these two terms are synonyms.
The asterisk searches for all variations of the root word. It's a time saver. In this case we'll search for "kinase" and "kinases."
[tw] is a field tag. Field tags in PubMed are always represented in brackets. The "tw" stands for "text word," which is like a keyword.
Use PubMed's
Advanced search
to run concept searches
and combine them.
Run individual searches for each of the other concepts.
Contact me!
Run separate searches for each concept as a way to test that you have the proper syntax for each search and as a way to test the predicted scope of each search. This also cuts down on syntax errors when you combine these large strings of terms.
Click on "Add" to add the three searches to the search builder.
Filter your search results if needed - in this case to a specific date range.
Click on the JHU
FULL-TEXT button
for direct access to full-text.
Click on the FIND IT @ JH button to see all possible options for full-text access.
If the FIND IT page indicates no online access, click on the Welch link to get the article through inter-library loan.
The JHU FULL-TEXT and FIND IT @ JH buttons only appear in the version of PubMed accessible from the Welch Medical Library homepage.
Click on the search number on the PubMed Advanced search page, then choose "Save in My NCBI."
If you already have a My NCBI account, then log in. Otherwise register for an account.
Rename your search,
then click "Save."
Set up automatic e-mail alerts for newly-published articles that meet the criteria of your search.
Welch Medical Library
Johns Hopkins University School of Medicine
This version of PubMed has links to the full-text available to you from Hopkins.
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