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Scope
The PubMed database covers the biomedical literature and,
to some extent, life sciences in general. You will find almost
all articles published on Schizophrenia or ADHD. You have
a good chance to find some articles on evolution. Unfortunately,
PubMed is not so great in ecology, animal behaviour or botany.
As a first practice, check whether your favorite journal is
covered by PubMed. Go to NCBI mainpage,
hit PubMed in the deep blue navigation bar, which should lead
you to PubMed main
page. Check the options on the left side bar. There are
several "PubMed Services" listed.
Journal
Browser
Click at "Journal Browser". Please, recognise,
that the page header on top has changed to "Journal Browser",
meaning that you would search now in that database. It is
useful to have a glance at the page header so that you would
always know what options you have.
Type the word "Behaviour" in the querry box (on
the right of Search... for....). At the present time (2001-06-29)
there are only four hits (journals). Now, americanise yourself,
and type "Behavior" with American spelling. Surprise,
we have far more hits now. Words in Journal Browser, are matched
letter by letter. So let us outsmart Journal Browser by typing
"Behavio*" in the querry box. Success, this time
we have most journals related to behaviour, like the ones
containing "behavioural" in their titles. Search
can be narrowed by using Boolean operators, for example by
typing "AND" (in capitals) between words ("behavio*
AND evolution).
To restrict a search to a given journal find the journal
in the Journal Browser. Click at Journal abbreviaton, and
you get back to PubMed main window with the journal name +
[Jour] in brackets. If you leave the journal name in the search
bar, all searches will be restricted to that journal.
PubMed does not cover all life sciences.
Before you make a novel search in PubMed, check whether major
journals of your field are covered.
MeSH
Browser
MeSH, Medical Subject Headings, are basically key words listed
in PubMed records. MeSH terms are listed in a hierarchical
manner. Terms are professionaly defined and explained. Open
MeSH browser here.
Let's say, we want to find papers related to molecular phylogeny.
Please, type or paste "molecular phylogeny" in the
SEARCH bar. In the window below you see a list of terms related
to the querry words. Mark "Phylogeny" and hit Browse.
You get a definition of Phylogeny, and a list of terms. Click
at "Evolution" and find Evolution, Molecular as
a MeSH term.
Even though it takes time, it is a good idea to check MeSH
terms for your topics. Once you find appropriate MeSH terms,
you can always use them to focus your search. To warn Entrez,
that the word should be searched as a MeSH term, simply type
[mh] right AFTER the term. The search can be focused even
more by coding your term as major topic. For that, type [majr]
after your term.
MeSH terms should be looked up, because they are not obvious.
If you are interested in the evolution of birds, you can search
with BIRD, or BIRDS or AVIAN or AVES, However, only one of
these words is a MeSH term. Check it out yourself.
To see how using MeSH terms would reduce noise, open PubMed,
and type BIRDS, EVOLUTION in the Search bar. You should get
more than 3,000 hits, all the papers containing the words
birds and evolution. Now type "evolution [majr], birds",
making evolution a major term. Focus your search even more
by using "birds" as a major term as well. Please,
note, that using MeSH terms can focus your search very effectively,
because what you loose is marginal information. By searching
with the word "birds" you get all kind of papers,
even papers authored by Somebody Birds.
Using MeSH terms can focus your search.
Before making a search in a field new to you, find out what
the appropriate MeSH term is for your querry. Put [mh] or
[majr] after the word you want to use as MeSH term.
Single
Citation Matcher
Finding a specific article of known author, title, journal
is easy in Single
Citation Matcher. Type in any information you know (journal,
author etc.) and hit Search. (if you do not have any author
in mind, type Kabai as author, chick* as title). You will
get a few papers. Please note, that in the PubMed search bar,
the label [auth] will appear right after the author's name.
Fields
Words in your querry can be searched against certain fields
in the database. One such example is typing [mh] after a word,
indicating that the word is a MeSH term. Another example is
to type [auth] after a name, so that the search will be restricted
to authors. You can restrict the search to a certain year,
1996, by typing 1996[dp] or to journals by [Jour].
Again, field abbrevitaions and field terms are not obvious.
The best way to find MeSH terms relevant to your interest
is to find a relevant citation, and check it for terms. To
do that, go to PubMed, search with some words (neandertal
AND gene, or birds AND evolution), and click at the most relevant
citation in the querry result list. Now you get the abstract.
Set the DISPLAY bar to MedLine and hit Display. This way you
get a list of field abbreviations on the left, with the actual
field terms on the right. You can now use those terms with
the field abbreviation to focus your next search.
Feature Bar
There are a few services listed in the Feature Bar (right
under Search bar) in PubMed.
Click at LIMITS in Feature Bar. Setting the limits
is similar to adding [field names] after the words. Use Limits
carefuly, becuse all your querry words will be limited. It
is convenient to set limits to publication date (for example
articles published since 1999) or language (for example English).
In HISTORY you can check and combine all your previous
searches.
DETAILS give you all fields of your last search in
a window. With some practice you can rewrite your terms in
that window, and make a new search. Remember to click at Search
BELOW the window, and not in the main window.
Links
Most hits have links within and between databeses. They are
extremely useful.
Related Articles: articles similar to your hit will
be shown. Do not get discouraged, if similarity is not always
defined in a way you like it. Would be nice to narrow the
search within similar articles, unfortunately, we are not
aware of any trick to do it.
Nucleotide: link to nucleotide sequences used in
the study.
PopSet: link to aligned nucleotide sequences used
in the study.
Taxonomy: link to the taxa under study. Very convenient,
because youg get the pylogeny used by GenBank, and number
of sequences and links to such sequences for any species in
the databank.
Practice: open PubMed,
and find an article according to PubMed identification number
PMID: 10220421. Simply pasting "PMID: 10220421"
in the SEARCH bar will not work. Paste the number only "10220421",
or paste the number and PMID in brackets "10220421[PMID]"
will show you an abstract on a Neanderthalensis study. Spend
some time with following the link the original publication,
to nucleotide sequences and PopSet. You will recognise, that
at any nucleotide sequence there is a link back to the article.
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