Part 1 – PubMed Interface, Display options, Saving, Printing, and Emailing results.

Instructions

This part of the course is a PowerPoint demonstration intended to show a guided tour of the PubMed interface.

This part of the module is off-line and intended as an information resource for reference use.

This part of the module should be taken before using the live tutorial on the PubMed and does not require a HINARI training password.

MODULE 4 How to use PubMed

HINARI Log-In 1

Before logging into PubMed we can Log In to the HINARI website using the URL http://www.who.int/hinari/en/

HINARI Log-In 2

You will need to insert your HINARI User ID and password in the Log In box and click on the “Sign On” Icon

Main HINARI’s Journal webpage

From the main HINARI webpage you can access PubMed from the “Find articles” link in the body of the webpage. Click on Search for articles through PubMed (Medline).

Special Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=hinari

PubMed home page

Welcome to the PubMed Homepage, Part 1 of the tutorial will look at the Interface, display options, downloading and emailing results.

NCBI databases bar

The black bar above the query box contains links to the other NCBI databases, highlighted above are the links to PROTEIN, OMIM, and the PubMed Journals database. To move between databases Click on the database name.

NCBI – OMIM database

Here is the OMIM database, to return to PubMed click on the link on the database bar.

PubMed left-hand menu

Down the left-hand side of the PubMed homepage there are links to other PubMed resources such as an overview to PubMed, Help & Frequently Asked questions, a Tutorial, and news items.

Down the left-hand side of the PubMed homepage there are also links to other PubMed utilities such as the Journals database, MeSH database, clinical queries, LinkOut and citation functions.

PubMed query box

The query box on PubMed is active, type here to enter your search statement.

How to Query a Particular Database

(term1[tag delimiter] op term2[tag delimiter] op …)

tag delimiter = Entrez indexing field

op = AND, OR, NOT

Text WordJournalMeSH TermsAuthor

Boolean operators MUST be in ALL CAPS!

Examples oftag delimiters

term1 term2

PubMed simple search

In this example we will enter a search for “malaria infections in Africa” into the query box. To execute the query click on the “Go” Icon.

Results - default display

Results of the search are displayed in the main body of the page.

The Details link

To see how PubMed performed the search we can click on the “Details” link highlighted below the query box.

Details page

PubMed uses automatic term mapping. Details shows how the PubMed software breaks down the search statement. In this example PubMed searches for Malaria as a text word and a MeSH term because of the automatic term mapping. Africa and Infections are also searched as a text words and MeSH terms.

Results – display options

Highlighted below the query box are the default display options. Records are displayed in Summary format, records 1-20 out of 1599 are displayed and the Sort order is by PubMed ID number.

Display formats

There are a number of different formats available to display results. From the dropdown menu we can see the possible choices. When using PubMed we will use either Summary, Brief, Abstract, Citation, and Medline. The other formats are for other NCBI databases. We have selected Summary from the available options. To change the display click on the “Display” button.

Summary format

The Summary format displays the authors names, the title of the article, the title of the source publication with citation details, and the PubMed ID number.

Brief format

From the dropdown menu we can now select the “Brief” display option.

Brief format 2

The brief display shows the name of the first author, part of the article title, and the PubMed ID number.

Abstract format 1

The “Abstract” Option is now highlighted.

Abstract format – full text links

The abstract display option will show any links to publishers websites which may have full text available. In this example we have a link to Elsevier Science and next to this is the HINARI Icon which identifies access rights for HINARI registered institutions.

Abstract format – Affiliation information

The abstract display also gives affiliation information. This affiliation information is for the first author listed on the paper, NOT all authors.

Citation format 1

The “Citation” display option is similar to the abstract display but has some extra information such as MeSH terms and substances listed.

Citation format – MeSH information

Here we can see the MeSH Terms assigned to the record during indexing by the National Library of Medicine (NLM).

MEDLINE format 1

The “MEDLINE” display option is selected here.

MEDLINE field identifiers

The “MEDLINE” display option shows all the fields in the MEDLINE record with field identifiers at the beginning of each line. This format is best used for downloading records into reference managing software.

Number of records displayed

There are a number of different options for displaying the number of references per page. These range from 5 to 500. It is advisable to download as many references per page as possible as this will save time when viewing results by eliminating the need to scroll through numerous pages. From the dropdown menu “200” has been selected, to re-display the results Click on “Display”

Results pages

The results page is now displaying 1-200 of 1599. There are now only 8 pages of results to view.

Sorting options

The default ordering of results is by PubMed ID number. Results can be ordered alphabetically by Author or Journal title, or by publication date. In this example “Journal” has been selected from the dropdown menu. To redisplay by Journal click on “Display”.

Sorting by journal title

The results 1-200 are now displayed alphabetically by journal title.

Selecting references

To select references from the results list you need to check the box on the left-hand side near the top of each record.

Selecting references 2

The results page 1-4 have now been selected.

Send to Text option 1

The results selected can now be formatted for print by selecting “Send To Text” from the dropdown menu.

Send to Text option 2

This option presents a printer friendly format for output to a printer.

Send to File 1

To download selected results to a disk drive select “Send To File” from the dropdown menu.

Send to File 2

Select a location to save the file and change the file type from fcgi document to all files.

Send to File 3

Choose a name for your file and give the file a .txt file extension. Click on Save

Send to Email 1

To email selected results choose “Send To email” from the dropdown menu.

Send to Email 2

From this screen you can choose a format and sorting order, and add text notes.

Send to Email 3

Type in an email address in the box provided.

Send to Email 4

Then click on the “Mail” button

Send to Email 5

When you return to the main results screen a message bar appears to inform that an email has been sent from the PubMed server to the client address.

Send to Clipboard 1

Selected results can also be sent to a clipboard area. Select “Send To Clipboard” from the dropdown menu.

Send to Clipboard 2

An information bar will appear telling you how many results have been sent to clipboard, the time limit after which they will be lost, and the maximum number of items allowed on the clipboard.

Send to Clipboard 3

To retrieve items from Clipboard Click on the link below the query box.

Send to Clipboard 4

From within Clipboard you can re-format and display results in the same way as you can from the main results page.

Send to Clipboard 5

To remove an item from clipboard choose “Clip Remove” from the dropdown menu.

Send to Clipboard 6

An information bar will appear saying how many items were removed from the Clipboard”.

This is the end of Module 4 Part 1

This is the end of Module 4 Part 1.

There is a Work Book to accompany this part of the module. The workbook will take you through a live session covering the topics included in this demonstration with working examples.