05a_tphcm_sep2005_pubmedoverview_mod4_1.ppt

8/10/2019 05a_TPHCM_Sep2005_PubMedOverview_mod4_1.ppt

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Part 1PubMed 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


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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/


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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


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Main HINARIs 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


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PubMed home page

Welcome to the PubMed Homepage, Part 1 of

the tutorial will look at the Interface, display

options, downloading and emailing results.


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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.


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NCBIOMIM database

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


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PubMed left-hand menu

Down the left-hand side of the

PubMed homepage there are links to

other PubMed resources such as anoverview to PubMed, Help &

Frequently Asked questions, a

Tutorial, and news items.

Down the left-hand side of the

PubMed homepage there are alsolinks to other PubMed utilities such

as the Journals database, MeSH

database, clinical queries, LinkOut

and citation functions.


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PubMed query box

The query box on PubMed is active, type here to

enter your search statement.


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How to Query a Particular Database

(term1[tag delimiter] opterm2[tag delimiter] op)

tag delimiter= Entrez indexing field

op= AND, OR, NOT

Text Word

Journal

MeSH Terms

Author

Bo olean operators MUST be in ALL CAPS!

Examples of

tag del imiters

term1 term2


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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.


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Results - default display

Results of the search are displayed in the mainbody of the page.


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The Details link

To see how PubMed performed the search we

can click on the Details link highlighted belowthe query box.


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Details page

PubMed uses automatic term mapping. Details

shows how the PubMed software breaks down

the search statement. In this example PubMed

searches for Malariaas a text wordand a MeSH

term because of the automatic term mapping.Africaand Infectionsare also searched as a text

words and MeSH terms.


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Resultsdisplay 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.


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Display formats

There are a number of different

formats available to display results.

From the dropdown menu we can seethe 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

Summaryfrom the available options.To change the display click on the

Display button.


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Brief format

From the dropdown menu we can now select the

Brief display option.


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Brief format 2

The brief display shows the name of the first

author, part of the article title, and the PubMed

ID number.


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Abstract format 1

The Abstract Option is now highlighted.


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Abstract formatfull 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.


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Abstract formatAffiliation information

The abstract display also gives affiliation

information. This affiliation information is for the

first author listed on the paper, NOT all authors.


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Citation formatMeSH information

Here we can see the MeSH Terms

assigned to the record duringindexing by the National Library of

Medicine (NLM).


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MEDLINE format 1

The MEDLINE display option is selected here.


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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 formatis best used for downloading

records into reference managing

software.


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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


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Results pages

The results page is now displaying 1-200 of 1599. There

are now only 8 pages of results to view.


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Sorting options

The default ordering of results is by PubMed ID number.

Results can be ordered alphabetically by Author orJournal title, or by publication date. In this example

Journal has been selected from the dropdown menu.

To redisplay by Journal click on Display.


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Selecting references

To select references from the results list you need to

check the box on the left-hand side near the top of eachrecord.


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Selecting references 2

The results page 1-4 have now been selected.


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Send to Text option 1

The results selected can now be formatted for print by

selecting Send To Text from the dropdown menu.


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Send to Text option 2

This option presents a printer friendly

format for output to a printer.


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Send to File 1

To download selected results to a disk drive select

Send To File from the dropdown menu.


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Send to File 2

Select a location to save the file and change the file type

from fcgi documentto all files.


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Send to File 3

Choose a name for your file and give the file a .txtfile

extension. Click on Save


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Send to Email 1

To email selected results choose Send To email from

the dropdown menu.


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Send to Email 2

From this screen you can choose a format

and sorting order, and add text notes.


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Send to Email 3

Type in an email address in the box provided.


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Send to Email 4

Then click on the Mail button


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Send to Clipboard 1

Selected results can also be sent to a clipboard area.

Select Send To Clipboard from the dropdown menu.


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Send to Clipboard 2

An information bar will appear telling you how many

results have been sent to clipboard, the time limit afterwhich they will be lost, and the maximum number of

items allowed on the clipboard.


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Send to Clipboard 3

To retrieve items from Clipboard Click on the link below

the query box.


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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.


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Send to Clipboard 5

To remove an item from clipboard choose Clip Remove

from the dropdown menu.


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Send to Clipboard 6

An information bar will appear saying how many items

were removed from the Clipboard.


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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.

05a_tphcm_sep2005_pubmedoverview_mod4_1.ppt

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