Every educational and scientific work begins with literature
search on the problem of interest. In the age of development
of information and computer technologies a possibility to make
this search significantly faster, easier and more comfortable
has emerged. The wealth of biomedical information generated
during the long years has been accumulated in a number of
major scientific centers and is stored in computer databases.
Taking into consideration the great interest towards such
services and significant expenses on collection and maintenance
of such information databases, many organizations allow access
to their services on a commercial basis. Along with these there
are centers that offer their services free of charge and without
substantial limitations, which is achieved through government
support directed at development of science.
MedLine is the largest bibliographic database that covers
over 75% of the world’s biomedical periodicals, a project of the
American National Library of Medicine . It holds leadership
among alike databases on the amount and quality of information
offered, the service being free of charge and convenient.
At the moment this article was written, MedLine database
contained citations from articles in 5835 world’s journals. The latter
includes the vast number of journals of urological and andrological
subjects, including such periodicals as Andrologia, BJU International,
British Journal of Urology, European Urology, International Journal
of Andrology, The Journal of Sexual Medicine, The Journal of
Urology, Urologiia (Moscow, Russia), and many others.
The MedLine database is represented by several sections.
The MedLine itself comprises nearly 12 million citations (a
citation is a short information on a publication) and article
abstracts, published in international biomedical journal since
1966. OldMedLine contains 1,7 million citations and article
abstracts, published between 1950 and 1965. PreMedline
contains bibliographic information and abstracts of publications
not yet entered to Medline, which is refreshed on daily basis.
Approximately half a million of new citations and abstracts are
added to MedLine annually.
In order to create the system of information search the
database itself is not enough, an access interface is required.
The most convenient is Internet-based access. That was the
purpose of the PubMed system, which, in turn, is a bibliographic
component of Entrez search system .
PubMed is not the only service allowing for search in
the MedLine database. Among the most known search
engines the following should be noted: Ovid, Scopus, CDL
MEDLINE (earlier - MELVYL MEDLINE). Each of the systems
mentioned has its own peculiarities, which open multiple
opportunities of scientific work with the aggregated
PubMed is a free resource. It was created and supported
by the NCBI (National Center for Biotechnology Information)
and NLM (U.S. National Library of Medicine), both being the
components of the National Institutes of Health, USA.
The PubMed search system gives the ability to search not
only in the bibliographic database of MedLine, but also in the
number of other resources: e-books, clinical trial materials and
other periodicals adjacent to the medical specialty.
The PubMed search service is represented by two types
of interface. The main interface is available at http://www.
ncbi.nlm.nih.gov/sites/entrez?db=pubmed, and also at http://
www.pubmed.com/ (both links referring to the same web-site.
The light interface (plain text), which is accessible at the link
«Text Version» from the main interface, or by typing the path
in your browser: http://www.ncbi.nlm.nih.gov/entrez/queryd.
On entrance to the PubMed web-site you will instantly get
to the main window of the program, from which queries to
MedLine database can be placed:
The PubMed system provides the following possibilities:
- Forming of simple queries to MedLine database
- Forming of complex queries with multiple instruments,
which allow for fine regulation of parameters.
- Creation of queries based on key words using the
controlled thesaurus MeSH®
- Creation of personal page that provides certain additional
options: saving queries and search results, additional search
options, additional service settings, creation of automated
search with results sent to your e-mail (monitoring of MedLine
- Obtaining of search results in the form of citations or
abstracts in different electronic formats, which later can be sent
to an e-mail.
- Transitions at the offered links to the web-pages of
electronic representations of the journals, where full-text copies
of articles can be obtained. Some publishing houses offer such
an opportunity free of charge, but in most cases you will have
to pay for a full-text article.
- Document delivery services
- Help system with convenient video-clips showing the
main stages of working with PubMed.
All the above mentioned services are provided free of
In order to form a simple query to MedLine database it is
enough to enter a search word to the window “query” and,
without changing anything in the other options of the web-site,
click the «Go» button. In case of simple search conditions the latter
should be enough, but complex tasks call for a more detailed study
of the query language used in the PubMed system.
The basis for this language is the Boolean logic, which
is a mathematical system called in honor of the English
mathematician George Boole. This logic connects terms by
means of several language constructions – logical operators :
AND, OR, NOT.
By default, if you typed a query that consists of several
words, the system breaks it into individual words and inserts
AND operator before each word. For instance, if you typed
«cancer penis» in the query string, the search engine will
present your query as «cancer AND penis» before requesting
a search, which is translated from the machine language as
«search the database for the information on cancer AND penis,
contained in the same article».
The AND operator, placed between the words, means that
in the returned query there must be the citation of the article,
where all words from query, connected with AND will be
The OR operator means that the user is searching for
information, where one or the other word will be found, but
it is not required that they should be all in the same article.
For example, if you want to find all articles on penile cancer
or urethral cancer, you must place OR operator among these,
The NOT operator gives a command to the system to return
information, where the term located on the right in the query
string will not be present. For example, the objective is to find
articles on the ultrasound study of the prostate gland, which do
not involve the cancer thereof. The query in that case will look
the following way: «prostate AND ultrasound NOT cancer».
Queries can be grouped using brackets. For instance, the
previous query may look the following way: «(prostate AND
ultrasound) NOT cancer». Queries can be very complex due to
combinations of operators, coupling of words into groups and
insertion of groups into each other.
If you want the words in the search results to be strictly
following each other and in the very sequence you entered
them in the query, you have to place them in quotation marks
“prostate cancer”. If a part of the word is unknown or you want
to find all lexical forms of the term, you can use the asterisk
operator «*» instead the changeable part of the word, for
example «uro*» will stand for all words beginning with “uro-”.
The system provides a useful opportunity to indicate where
to search the required words in the article citation. There are
several instruments for that.
In intuitively understandable is the use of search limitation
(the «Limits» tab on the search page). On this additional page
you can indicate the exact authors, whose materials you look
for; the name of the journal; the contents of terms in the
abstract; the date and the language of the publication; the type
of the article and special limiting tags, which will be described
later on. After you determine the margins of the search, you
can click the «Go» button in order for the system to start the
database search with new parameters.
Another instrument allowing to narrow the search margins is
the search tags. These are the strictly defined letter abbreviations
for search commands, placed in square brackets. For example,
[AU] – is a tag, which is an abbreviated name of the «Author»
field in the article citation. The tags are placed on the right from
the word entered to the query and determine the belonging of
this word to a certain category. The word «Debruyne[AU]» with
a tag [AU] will mean that we want Debruyne to be one of the
authors of the article in the query.
A very flexible search system is the controlled dictionary of
terms MeSH . This dictionary is a hierarchical dictionary of 16
main branches, such as Anatomy; Organisms; Diseases; Chemical
Substances and Drugs; Diagnostics, Treatment, Therapeutic
Technique and Equipment; Healthcare; Geography terms and
certain others. This dictionary contains 25 thousand main terms,
172 thousand additional terms and around 100 thousand accessory
terms. The higher ‘branches’ in the hierarchy of the dictionary
diverge into smaller ones, which clarify a certain definition. Thus,
for example, the term ‘prostatitis’ belongs to the branch “diseases
› male urogenital diseases › prostatic diseases › prostatitis”.
Every citation after being placed to MedLine database is
matched to the terms, contained in this dictionary, or in other
words the article is classified. From the database point of view
this process is called indexation of articles. The article, as a rule,
is not matched to one term, but too many. Usually it is 5-25
terms per one article.
There is a «MeSH Database» link at the main PubMed page
at the search page using MeSH database. At this page you can
enter a keyword or key phrase, which, in your understanding is
the key one for information search. The system will then display
all connected terms from the MeSH dictionary and you will be
able to perform a more thorough review of possible search
options, while moving through dictionary branches. This will
allow you to either narrow or expand your query.
On the right from each MeSH term there is an active link
«Links». As you click it, you’ll get a drop-down menu where you
can choose the source of the search and proceed to the results
page. On this page you will see the citations of the articles
connected to this term.
A vast team of computer engineers works on the creation of
the dictionary with specific knowledge in the field of medicine,
indexation of articles performed with technologies of artificial
intellect . For this reason searching with MeSH is probably the
most effective method of searching for information in MedLine
After composing and executing a query, the PubMed system
will display on the main page the search results as a list of
article citations found. In the upper part of this page there are
instruments, which allow managing citations. You can perform
the following actions with this panel:
- Change display format of citations. Information can be
given in a short form, an abstract can be shown, search results
can be presented in the XML format, a number of other useful
options is available.
- Chang the number of citations viewed on one page.
- Sort results by date, by authors, by journal name.
- Send the article to the printer, save it as text file, copy it to
clipboard, send it via e-mail, broadcast it via RSS channel.
- One can perform navigation through pages by clicking
the «Next» link ()(next page) or by entering the number of pages
to the window and clicking the «Page» button.
Below the navigation menu there is a page, containing the
found citations. By default, (the «Summary» display mode) an
individual citation is represented by a pictograph, which gives a
visual display of whether the found citation contains an abstract
and whether links to free full-text material are available in the
Internet. The system labels every quotation with a reference
number in the row. The citation contains the following fields
that are highlighted on Fig. 4:
the authors of the article, as an active link. By clicking
this link one can get to the page containing all citations of the
articles of a given author available in MedLine;
the name of the article;
the short name of the journal where the article was
the date the article was published;
the issue number where the article was published.
Additional options are placed on this page in tabs. At the
tab «Limits» there is a possibility to narrow the search results,
what we described above.
At the tab «Preview/Index» you can add extra limiting terms
and indexes to your query, including tags and logical search
operators . As you press the «Preview» button, you can get
a preliminary number of citations that will be found by the
query you created. While transferring via the active link to the
number of citations found, one can study the obtained results
in more detail. Thus, this instrument allows to promptly form
the tactics and strategy of the search without overloading the
page by citations. Different variants of the queries remain seen
on one page.
The «History» tab saves the results of the recent queries you
made in the Pubmed system. By clicking the «Clear History»
button you can clear that list.
The «Clipboard» tab is a convenient instrument for temporary
storage of queries that works as an analogy of clipboard in the
Windows operating system. By selecting the required citations
on the search results page one can place them to the clipboard
for temporary storage.
In order to do this, select the «Clipboard» option in the
«Send to» drop-down menu. Then the citations will be placed
for temporary storage and will be available in this tab even
eight hours after you log out from the system. Clipboard can
contain not more than 500 citations. Citations of the articles
placed there remain highlighted with green color both in the
very clipboard and in the search results.
The «Details» tab allows detailed viewing of queries to the
database and editing these queries in the event of complex and
The «Authority Index» tab is the place where you can
enter a searched word and see the found authors by the
indexes thereof, created in the system. By clicking the name
of the author in the link one can proceed to the page with a
bibliographic list of citations of the articles.
In order to get to the page with detailed description of one
of the articles one has to click a pictograph with a detailed
description of one of the articles which looks as a small sheet,
which stands for a journal.
If a citation contains an abstract, one can view its description
on this page (Fig. 5). In this very place, on the right from the
abstract, there is a link to the full-text version and thematic
links which the developers of the search engine considered
semantically connected to the article.
On the single citation page there is also a set of options that
are similar to those on the general page of search results. Using
that page one can change the display of the citations and save
it, place citations to the clipboard or send them by e-mail .
The additional opportunities are opened with the launch of
a personal page with the PubMed system (it is referred to on the
web-site as «My NCBI»). In order to do this one has to complete a
simple registration process by clicking the «Register» link, located
in the top right corner of the PubMed main page. After that you
will get your login (username) and password that will allow you
to authorize on the WEB-site using the «Sign In» link (Fig. 6).
Registration is optional on that web-site, but it can make
frequent information searches in MedLine easier.
After logging to the personal page (point A on Figure 7)
one has an option to save search results. To do so, complete the
search and click the «Save Search» link (point B on Figure 7).
In a separate window the system will prompt one to enter
the name of the search being saved to allow subsequent
identification thereof (Fig. 8). In the same window one can
set up automatic delivery of new query results to one’s e-mail
After saving search results there will a number of accumulated
queries that will be stored on the personal page. You can
re-access the found materials by clicking the “Query” link (point
A on Figure 9), check the date of the last update (point B on
Figure 9), customize automatic e-mail delivery (point C on Figure
9) or check manually what new has appeared in the MedLine
database by checking the boxes near query and clicking the
button «What’s New for Selected» (point D on Figure 9).
Despite all the variety and the powerful abilities of PubMed
the required information is often not so easy to find. In many
cases it results from poor knowledge of the English language
by many urologists and andrologists. However, there are
certain problems that cannot be overcome given the current
state of information technologies. This is primarily related
to accumulation of an immense bulk of information, which
is often poorly structured, lacking uniformity and imprecise
[5,6,7]. A few articles that a researcher actually needs can be
drowned in a vast ocean of information, especially if the studied
issue is highly specific.
In order to solve such problems the whole flow of
information must be organized and structured, and, which is
the most important and the most difficult – a mutual semantic
connection of individual fragments of knowledge must be
That is the way the development of MedLine database
consistently follows. The creation of managed vocabulary
of terms MeSH and indexation of citations according to the
created structure will allow for subsequent self-description of
stored data with possible programmed analysis. The National
Library of Medicine of the United States has united the efforts
of many scientific trends by creating the UMLS (Unified Medical
Language System) which is the basis for medical knowledge
databases that are different in principle from conventional
The practical value of creating databases is the ability of the
user to post questions to the system in a convenient language.
This will generate a response adequate to the expectations of
the researcher, no matter complex the subjects is.