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[MUSIC].

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Hello and welcome.

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We'll be looking at searching PubMed
effectively.

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PubMed is a government website, based at
the Natural Library of Medicine.

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It contains over 23 million biomedical and
life science publications.

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Searching it effectively, can be a very
useful strategy.

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And it's also relevant, because the
mechanism for searching Pubmed, is

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remarkably similar to the method for

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searching nucleotide and protein sequence
databases.

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[MUSIC]

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Our objectives include, searching by
author.

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For instance, finding papers written by a
particular individual.

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Either by using the last name format, or
by using one or two initials.

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We will also look at how to search with
field tags.

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In other words, limiting your search, to
very specific fields in PubMed.

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We will search by subject, and combine
searches with subject, and an author name.

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That is a Boolean operation.

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[MUSIC].

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We will look at the MeSH database.

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MeSH, has a controlled vocabulary, that

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allows for more effective searches of
PubMed.

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We will use filters.

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Filters, help narrow down to certain types
of papers.

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We will also examine the truncated
searches, which

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allow for searching for variations of a
particular work.

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[MUSIC]

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First, let's go to PubMed.

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There is an address for PubMed, at the
National Library of Medicine.

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However, pubmed.gov, that is P-U-B-M-E-D
.gov is a working alias.

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So, pubmed.gov will take you to the NIH
website where PubMed is hosted.

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Let's use the word, greider, and search.

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You will see some papers that include

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an author named Greider, which I just
highlighted.

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You will also see some papers, where
Greider, is not listed as an author.

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Carol Greider is a nobel prize winning
researcher of telomeres.

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So perhaps Greider was mentioned in
[SOUND] that particular paper.

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We'll look at a way to avoid those kinds
of results shortly.

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The last name Greider, finds 223 results
in PubMed.

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If I want to limit further to specific
authors with the last name Greider.

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I can add a first initial.

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So, Greider C, would narrow down to 102
papers.

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You can see that Carol Greider's second
initial is W.

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A one initial search, will find all
variations

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of C, so C followed by any second initial.

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Or just c by itself.

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[BLANK_AUDIO].

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I could further narrow, by adding the
second initial.

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You see, that narrows the search down to
94 papers.

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So basically, last name is the broadest
search.

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One initial is a little more specific, and
two initials are the most specific.

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Some authors use more than two initials.

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However, PubMed limits searches to two
initials, and

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PubMed actually only enters two initials
for any author.

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Okay, now I mentioned, there is a way

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to avoid matching words outside the author
field.

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I'm going to go back to searching for
Greider, last name only.

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If you noticed, the first paper did not
have Greider as an author.

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So I'm going to open that paper now.

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When you open a record it's going to show
the abstract.

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So here's the abstract.

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And you can see that it says that the 2009
Nobel prize

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in medicine was awarded to, there it is,
Blackburn, Stostak, and Greider.

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So her name is in the abstract, and not in
the author field.

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The author field lists only one author,
and that is Wang.

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So, if I want to limit the search to only
the author field.

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The way to do that, would be to type,
greider(author).

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[BLANK_AUDIO].

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Now, I only see those papers, where
greider is in the author field.

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I eliminated that result, and others,
where greider was in the abstract.

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Basically, by putting brackets around the
field name, I

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can limit a specific term, to a particular
field.

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There are acceptable abbreviations.

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For instance, if I had typed, bracket au.

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Au, is an accepted abbreviation for
author, I would get the same result.

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There are a list of fields available

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that are searchable, including the author
field.

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Now, suppose I wanted to search by
subject.

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There are several ways to do it.

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And usually one of the easiest ways to do
it, is to simply type in the subject.

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So I am going to type in, RNAi.

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RNA interference, is a very, very popular
search topic.

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And, a very important topic in life
science.

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RNAi, was famously studied by Craig Mello
and Andrew Fire.

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So, let's say that I want to get papers on
RNAi, by Craig Mello.

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I can type in,

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RNAi And,

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mello(author).

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Now, what you might notice, is that and is
capitalized

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and for all searches, you should
capitalize the Boolean operators.

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Boolean operators are, and, not, and or.

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This gets me papers that are about RNAi,
and are

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written by an author named Mello, which
gives me 27 papers.

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Some of them have, RNAi in the title.

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Some of them don't.

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So, if I want to further limit RNAi to the
title field.

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After RNAi, I would type (title), and
you'd see the list

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is now narrowed to ten papers that have
RNAi in the title.

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You can see RNAi bolded in the title field
of each paper.

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Okay.

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So we can see, how to limit to very
specific fields.

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We can also see how to use the and
operator.

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Be sure to use all capital letters for all
Boolean operators.

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So that it doesn't look for the word, and
as a search term.

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There is another way to search PubMed by
subject.

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That involves, using the MeSH database.

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MeSH which stands for medical subheadings,
uses a controlled vocabulary.

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It allows for more consistent complete
searches.

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Some writers, use different words to
describe the same phenomenon.

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The controlled vocabulary is used to index
each specific paper consistently.

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There is a very good video on

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YouTube, provided by the National Library
of Medicine.

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And it is available at this address, and
you can view that

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video called, using MeSH to build a better
PubMed query, for more information.

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[BLANK_AUDIO].

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Quickly though, if I want to search RNAi,
instead

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of PubMed, I would now search the MeSH
database.

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And you see, that the preferred term,
again, this

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is a controlled vocabulary, is RNA, column
small interfering.

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If I want to search PubMed, I would simply
add it to the search builder.

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And it may be even add.

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And, Mello (author) and then click search
PubMed, I actually

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got 25 papers, some different from the
ones I got using the same

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search, with just RNAi, that's because
sometimes the term

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RNAi, might not have been used in those
particular papers.

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But those papers are about RNA
interference.

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Therefore, I get those additional papers,
using the control vocabulary.

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You might also notice that on the left
menu, are a series of filters.

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Those filters include article type, so if
I want only review

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papers, I would click Review, and that
would narrow it down further.

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A popular one is text availability.

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Most papers, when you open the record, it
only shows the abstract.

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But most papers have a link to full text.

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And sometimes the full text, comes at a
cost from the publisher.

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Sometimes it's free, and very often, you
would want free full text, why not?

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If I click the, free full text available

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filter, then I narrowed it down to 16
papers.

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Now, when I click that first paper.

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I know that there is a link that reads,
cell

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press, and it says, free NPMC in the upper
right corner.

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When I click that link, I am going to be
able to download the

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entire paper for no cost, because I chose
that filter of free full text.

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That's very useful, if you are not at an
institution that subscribes to

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a bunch of specific journals that will
allow you to have access to them.

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The truncated search could be very useful
if there are variations of a word, for

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instance, if you're unsure of spelling, or
if there is a singular plural issue.

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An asterisk can represent the rest of the
word.

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The asterisk can only come at the end of

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the word, and not at the beginning or the
middle.

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Immunoglo asterisk, will hit both the

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singular immunoglobulin, and the plural
immunoglobulins.

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You don't need to search twice.

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[BLANK_AUDIO].

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It's also very useful for an author name,
if you don't know the spelling.

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However, there is a limitation.

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It only shows the first 600 alphabetic
variants.

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For instance, if you are using the name
McDonald, and,

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you're not quite sure if it's McDonald or
McDonald's son.

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Then it is better to type, M-C-D-O-N star
than just,

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M-C-D star, put in as much of the spelling
as possible.

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An example of that particular type of
search

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is to type, immunoglo star and smith (au).

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I now get papers on immunoglobulin, and
immunoglobulins.

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The last topic to cover, involved the date
fields.

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Both EDAT for entry date, meaning the date
that that paper was entered into PubMed.

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Or PDAT, publication date, meaning the
date on the journal itself.

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For instance, the January 9th issue of
Science.

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Ways to limit to specific dates, include
year.

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2014, will limit you to the entire year
2014.

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Or 1998 for the entire year 1998.

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Year/month, so, 2014/03,

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will give you, all of March 2014.

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Finally, the specific date.

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2014/03/17, gives you March 17, 2014.

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It's most commonly used in a range,

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in a range of dates, 1998/02:

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the colon indicates a range.

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2013/09/27.

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That translates to February 1st.

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Since it's at the beginning of the range,
you get the whole month of February.

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February 1st, 1998 through September 27th,
2013.

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An alternative type of dates search is,
"last 19 days"(edat).

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Of course, the number can vary.

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So, for example, if I had heard about a
paper that was submitted to nature

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within the last ten days, I would type,
"last ten days"(edat).

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I know that it was submitted within the
last ten days.

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Not with a publication date within the
last ten days.

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And, nature(journal).

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That limits the search, to the journal
nature.

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[BLANK_AUDIO]

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Well, here's a good lesson.

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I still have a filter activated.

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The filter, is free full text available,
and nature

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doesn't have free full text, so there are
no results.

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I have to clear that filter, because those
filters persist.

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So, if you use those filters, be very,
very careful.

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They stay on in subsequent searches unless
you turn them off.

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Now, if I want to limit to a particular
date range, let's say we know that

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it was toward the end of 2011 or

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was the beginning of 2012, somewhere
around that time-frame.

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So let's go for all of November 11.

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Two, well let's get all of February 2012.

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So, let's type, 2011/

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11: 2012/02[edat].

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Let's say it's a

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science paper.

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So, capital AND science(journal).

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And, it was something about DNA, so I'll
put in DNA.

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I found, 37 papers, that were in the
journal Science, that were

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about DNA, and sort of toward the end of
2011 or beginning of 2012.

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Maybe I could now sort through, and find
the paper I was thinking about.

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[MUSIC].

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This concludes our exercise on PubMed, and
I think the best

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way to really learn it, is to go to PubMed
and

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play around a little bit with some of
these field tags

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and Boolean operators, and see what you
come up with, good luck.

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[MUSIC]

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[BLANK_AUDIO]