Indexing of the

Biomedical
Literature
Ajith Karawita
MBBS, Pg Dip Ven, MD
 A. BACKGROUND
Background information to understand the
concept of indexing of the biomedical
literature
 1. What is an
Article
A piece of writing on a specific topic or subject
Article
s
A piece of writing on a specific topic or
subject found in
• journal
• periodical
• magazine
• newspaper
• encyclopaedia or
• edited book
• Full text online databases
 Types of
Autobiograph Articles
Interactive Tutorial Portraits
y Bibliography Interview Practice Guideline
Biography
Introductory Journal Article Randomized Controlled Trial
Case Reports Review
Classical Article
Journal Article Scientific Integrity Review
Clinical Conference Lectures Systematic Reviews
Clinical Trial Legal Cases Technical Report
Clinical Trial, Phase I Legislation Twin Study
Clinical Trial, Phase II Letter Validation Studies
Clinical Trial, Phase III Video-Audio Media
Meta-Analysis Webcasts
Clinical Trial, Phase
IV Comment
Multicenter Study
Comparative Study News
Congresses Newspaper
Consensus Development Conference Article
Consensus Development Conference, NIH Patient Education Handout
Controlled Clinical Trial Periodical Index
Editorial
Personal Narratives
Electronic Supplementary Materials
English Abstract What is a scholarly article or journal 
Evaluation Studies
Government Publications
includes articles or journals that are research
Guideline oriented, and are either written or reviewed by
Historical Article experts in the field.
Millions of articles are written by
authors
 2. What is
“Publishing”
Publishing is the process of production
and dissemination of literature, music, or information
OR
The activity of making information available
to the general public
 Publicatio
• Print media
n
(Books, Newspapers, Magazines, Journals etc)
• Electronic media
(electronic versions of books (eBooks), Audio
books, magazines, Newspapers, Journals, web
sites, Blogs etc)
3. What is the meaning of
“citation”
1. Unique description of an article (common meaning)

2. Other meanings - Sometimes referred to the extracted

or quoted part of an article in your writing
 3.1. Citation -
1.
definition
Unique description of an article
2. It is a reference to a published or unpublished source (not always the original
source)
3. Details of an item, such as a book or journal article, that can be used to
identify
it.
4. The bibliographic details of a work which enable it to be identified, for example:
title, author, date of publication, the publisher’s name, place of publication,
volume, issue and page numbers.

Citations have

5. Elements (Author
name, title etc)
2. Punctuations (, ; . :)
3. Spaces
 3.2. Citation
content
• Citation content can vary depending on the type
of source and may include
1. Book -author(s), book title, publisher, date of
publication, and page number(s)
2. Journal -author(s), article title, journal title, date of
publication, and page number(s)
3. Web site -author(s), article and publication
title where appropriate, as well as a URL, and a
date when the site was accessed
4. Other Resources (news paper articles, Video
recordings, Dictionary, encyclopaedia, play, poem)
5. Personal communications – Personal
letters, conversations, emails, interviews
etc)
 3.3. Citation Unique
identifiers
• Alone with the basic citation formats sometimes include unique
identifiers

– ISBN- International Standard Book Number

– SICI – Serial Item and Contribution identifier
– DOI – Digital Object Identifier (in electronic documents)
– PMID – Biomedical research articles may have a PubMed
Identifier
 Examples of unique
identifiers
Effectiveness of gentamicin for gonorrhoea treatment: systematic review and
meta- analysis.
Dowell D, Kirkcaldy RD
Postgrad Med J. 2013 Mar;89(1049):142-7.
doi: 10.1136/postgradmedj-2012-050604rep DO
PMID: 23417685 [PubMed - in process] I

PMI
D
Mapping and size estimation of female sex workers and men who have sex with
men in Sri Lanka
DA Karawita, S Moses, I Emmanuel, I Shajy, N Edirisinghe, KAM Ariyaratne, D Ranatunga, R
Chawla, K Navaratne
DOI: http://dx.doi.org/10.4038/sljv.v3i1.5413 DOI
Sri Lanka Journal of Venereology Vol.3(1) 2012 pp.47-51D
 3.4. Common Citation Styles (and Style
Manuals)
• The following style manuals are the most commonly used citation
guides for research.

• Vancouver Citation Style – used by most biomedical journals and

many scientific journals.
• APA -Publication Manual of the American Psychological
Association, 6th ed., 2010.
• CSE - Scientific style and format : the CSE manual for
authors,
editors, and publishers
• Chicago -The Chicago Manual of Style, 15th ed., 2003.
• MLA -MLA Handbook for Writers of Research Papers,
7th ed., 2009.
• Turabian -A Manual for Writers of Term Papers, Theses,
and
Dissertations, 7th ed., 2007.
• NLM Style – NLM Style guide
3.4.1. Citation styles in Ms Word
2007
 Citation styles in Ms Word
2007
• ACS Style Guide • ISO 690
• • MHRA Style Guide
AMA Manual of Style
• The Microsoft Manual of
• AP Stylebook Style
• The ASA Style Guide • MLA Handbook
• Bluebook • MLA Style Manual
• • The New York Times
The Chicago Manual of Style
Manual
• The Elements of Style • The Oxford Guide to
• The Elements of Style/New Hart's Rules
Typographic Style • The Publication Manual of
the APA
• Turabian
 3.5. Selection of Citation styles in your
work depend on

• Field of your work (Humanities, Law, Science,

mathematics, engineering, physiology and medicine,
Social sciences etc)
• Your professor or supervisors preference
• Publishers preference
• Publication guidelines
Examples of citations of
different publications
Patrias K, author; Wendling D, editor. Citing Medicine: The NLM Style Guide
for Authors, Editors, and Publishers [Internet]. 2nd edition. Bethesda (MD):
National Library of Medicine (US); 2007-. Available from:
http://www.ncbi.nlm.nih.gov/books/NBK7256/
 Citing Journal
Articles

Patrias K, author; Wendling D, editor. Citing Medicine: The NLM Style Guide for Authors, Editors, and
Publishers [Internet]. 2nd edition. Bethesda (MD): National Library of Medicine (US); 2007-. Available
from: http://www.ncbi.nlm.nih.gov/books/NBK7256/
 Citing Articles on the
Internet

Patrias K, author; Wendling D, editor. Citing Medicine: The NLM Style Guide for Authors, Editors, and
Publishers [Internet]. 2nd edition. Bethesda (MD): National Library of Medicine (US); 2007-. Available
from: http://www.ncbi.nlm.nih.gov/books/NBK7256/
 Citing Contributions to
Books

Patrias K, author; Wendling D, editor. Citing Medicine: The NLM Style Guide for Authors, Editors, and
Publishers [Internet]. 2nd edition. Bethesda (MD): National Library of Medicine (US); 2007-. Available
from: http://www.ncbi.nlm.nih.gov/books/NBK7256/
 Citing Contributions to Books on the
Internet

Patrias K, author; Wendling D, editor. Citing Medicine: The NLM Style Guide for Authors, Editors, and
Publishers [Internet]. 2nd edition. Bethesda (MD): National Library of Medicine (US); 2007-. Available
from: http://www.ncbi.nlm.nih.gov/books/NBK7256/
 Citing Entire Dissertations and Theses-entire
dissertation

Patrias K, author; Wendling D, editor. Citing Medicine: The NLM Style Guide for Authors, Editors, and
Publishers [Internet]. 2nd edition. Bethesda (MD): National Library of Medicine (US); 2007-. Available
from: http://www.ncbi.nlm.nih.gov/books/NBK7256/
 Citing Entire Dissertations and
Theses- entire masters
thesis

Patrias K, author; Wendling D, editor. Citing Medicine: The NLM Style Guide for Authors, Editors, and
Publishers [Internet]. 2nd edition. Bethesda (MD): National Library of Medicine (US); 2007-. Available
from: http://www.ncbi.nlm.nih.gov/books/NBK7256/
 Citing Papers and Poster Sessions Presented
at Meetings-for a poster session

Patrias K, author; Wendling D, editor. Citing Medicine: The NLM Style Guide for Authors, Editors, and
Publishers [Internet]. 2nd edition. Bethesda (MD): National Library of Medicine (US); 2007-. Available
from: http://www.ncbi.nlm.nih.gov/books/NBK7256/
 Citing Parts of
Reports

Patrias K, author; Wendling D, editor. Citing Medicine: The NLM Style Guide for Authors, Editors, and
Publishers [Internet]. 2nd edition. Bethesda (MD): National Library of Medicine (US); 2007-. Available
from: http://www.ncbi.nlm.nih.gov/books/NBK7256/
 Citing Parts of Journal
Articles

Patrias K, author; Wendling D, editor. Citing Medicine: The NLM Style Guide for Authors, Editors, and
Publishers [Internet]. 2nd edition. Bethesda (MD): National Library of Medicine (US); 2007-. Available
from: http://www.ncbi.nlm.nih.gov/books/NBK7256/
 Citing Parts of Books on the
Internet

Patrias K, author; Wendling D, editor. Citing Medicine: The NLM Style Guide for Authors, Editors, and
Publishers [Internet]. 2nd edition. Bethesda (MD): National Library of Medicine (US); 2007-. Available
from: http://www.ncbi.nlm.nih.gov/books/NBK7256/
 Citing Parts of
Books

Patrias K, author; Wendling D, editor. Citing Medicine: The NLM Style Guide for Authors, Editors, and
Publishers [Internet]. 2nd edition. Bethesda (MD): National Library of Medicine (US); 2007-. Available
from: http://www.ncbi.nlm.nih.gov/books/NBK7256/
 Referencin
g
Relation between objects

The first object in this relation is said to refer

to the second object (the referent)
 References - Reference Lists Vs In-Text References

• References are presented in two ways in medical

publications
• 1. Reference list (all of the references that
contributed to the work are presented in a list called
references, end references, literature cited, or
bibliography.)
• 2. In-Text References (Within the text of an article,
individual references are presented in an abbreviated
format that refers back to the list. These abbreviated
references within the text are called "in-text
references.“)
 In-text
• references
Three major systems of in-text references are used by
medical publishers:
– Citation-sequence system (Vancouver Referencing) - numbers
are used to refer to the reference list. References are numbered
in the list in the order they first appear in the text.
– Citation-name system - numbers are also used in the text to
refer to the reference list. However, the references in the list are
numbered in alphabetical order by author. Thus a reference
authored by Adam would be number 1, by Baker number 2, etc.
These numbers are used in the text regardless of the order in
which they appear.
– Name-year system (Harvard referencing, Parenthetical
referencing) - in-text references consist of the surname
of the author and the year of publication, usually enclosed in
parentheses, such as (Smith 2006). The list of references is
ordered first by author, then by year

http://www.ncbi.nlm.nih.gov/books/NBK72
65/
 http://tilt.library.skagit.edu/m
odu le4/plagiarism.htm

• As a part of an academic community, it is important that you show

the reader where you have used someone else’s ideas or words.
• Failure to properly reference using a reference system may make
the reader think that you are cheating by claiming someone
else’s work as your own.
• In the academic environment, we call this plagiarism (derived from
Latin word Plagiaries which means “Kidnapper”) and it is seen as a
very serious offence
 Now you will be able to
describe thefollowing

1. What is an article?
2. What do you mean by “publishing”
and publications, and publication
media
3. What is a citation, citation contents, citation styles
and style guidelines, citation unique identifiers
4. Referencing methods (three basic methods)
5. Plagiarism
B. CATALOGING AND
INDEXING
 1. Cataloging (or
• cataloguing)
Is a register of all items
found in a library or
group of libraries such as
network of libraries at
several locations.
• A log or register of all the
owned by a particular
library
• But it has been
effectively replaced by
the Online Public The card catalog was a
Access Catalog (OPAC) familiar sight to library users
for generations
 2.
Indexing
(noun-Index, plural-Indexes/Indices)
• Index - a systematically arranged list of
articles and other data which allows each item
to be located easily.
• These list of articles are arranged according to
key identification tags (citation elements and
key words sometimes abstracts)
 Indexin
g
(noun-Index, plural-Indexes/Indices)
Articles are usually indexed using the
following elements in combination
• Author name/s • Keywords
• Title • Publisher
• Journal name • Publication type
• Journal volume • Pagination etc
• Journal issue Depending on the type of databases
• Abstract and sophistication  number of
indexing elements vary
Providers of Indexing Services
and access to biomedical
databases
The indexing services and most important
databases are located in famous
university/academic centres
 1. US National library of Medicine (NLM)
Index Medicus (IM)

• Index Medicus (IM) is a comprehensive index

of medical scientific journal articles, published since
1879.
• It was initiated by John Shaw Billings, head of
the Library of the Surgeon General's Office, United
States Army.
• This library later evolved into the United States
National Library of Medicine (NLM), which continues
publication of the Index

http://en.wikipedia.org/wiki/Index_Medicus
 US National Library of Medicine
(NLM)
• Index medicus (IM) print
• Index medicus CDROM with
search facility
• Pubmed/MEDLINE (online
access to article index
http://www.nlm.nih.gov/
How pages look like in Index medicus (IM)
Pubmed/MEDLIN
E
 The National Library of Medicine
• (NLM)
The National Library of Medicine (NLM), in Bethesda, Maryland, is a
part of the National Institutes of Health, US Department of Health
and Human Services (HHS)
• Found in 1836
• It is the world's largest biomedical library and the developer of
electronic information services that deliver trillions of bytes of data
to millions of users every day. Scientists, health professionals
• has nearly 19 million books, journals, manuscripts, audiovisuals,
and other forms of medical information on its shelves, making it the
largest health-science library in the world.
• The most frequently consulted online scientific medical resource in
the world is MEDLINE®/PubMed®, a publicly available database of
over 22 million journal citations from 1946 to the present.
• Another important part of NLM's vast online holdings is PubMed
Central® (PMC), a Web-based repository of biomedical journal literature
providing free, unrestricted access to more than 2.5 million full-text
articles.
 2. Index Medicus for the South-East Asian
Region
• Index Medicus for South-East Asia Region
(IMSEAR) is a database of articles published in
selected journals within the WHO South-East
Asia Region.
• It is a collaborative effort of participating
libraries in Health Literature, Library and
Information Services (HELLIS) network in the
region.

http://www.who.int/library/databases/searo/en/
 3. Western Pacific Region Index Medicus
(WPRIM)
• The Western Pacific Region Index Medicus
(WPRIM) is a project of the WHO Western Pacific
Regional Office in collaboration with several
institutions in its Member States.
• This is the Region's contribution to the Global Health
Library (GHL)
• WPRIM will be deployed and hosted, along with the
index medici of other WHO Regions, at the Global
Index Medicus portal

http://www.wprim.org
/
 4. African Index Medicus
(WHO)
• In order to give access to information published
in or related to Africa and to encourage local
publishing, the World Health Organization, in
collaboration with the Association for Health
Information and Libraries in Africa (AHILA), has
produced an international index to African health
literature and information sources.
• This index is called African Index Medicus (AIM).

http://indexmedicus.afro.who.int/
5. Thai Index
Medicus

http://imsear.hellis.org/handle/123456789/127183
 6. HeLLIS Sri
Health LiteratureLanka
Libraries and Information Services network
(is a consortium of Health Libraries in the South-East Asian Region)

http://hellis.srilankahealthrepository.org/handle/123456789/1
7. Sri Lanka Journals Online
(SLJOL)
Sri Lanka Journal of
Venereology
Sri Lanka Journal of
Venereology
Other Biomedical online
databases
 ISI Web of Science
• WoS (WoS)
is an online academic citation index
provided by Thompson Reuters Provide access
to multiple databases
• In-depth exploration (from disciplineto
subfields)
• Useful in cross disciplinary research
• ELSEVIER - One of the leading provider
of science and health information
• EXCERPTA MEDICA/EMBASE – record
coverage-24 million, Coverage of peer
reviewed journals >7600, Time coverage –
1947-present, In-depth indexing (drug
reactions etc)
• SCOPUS – Is the largest abstract and citation
database of peer-reviewed literature with
smart tools to track, analyse and visualize
research,
– record coverage-46 million, Time coverage- some
articles as far as 1823. Publisher coverage – 5000,
Conference paper coverage – 4.6 million. Title
coverage 19,500
• SCIRUS – Is a free web search engine developed
especially for scientists, researchers and students,
Record coverage - 480 million
• EBSCO – Established in 1944, world’s
largest leading information agent
• ULRICH’S PERIODICAL DIRECTORY – Is the
standard libray directory and database providing
information about popular and academic
magazines, scientific journals, newspapers and
other serial publications
• HINARI – Programme set up by WHO together
with major publishers. Journal coverage
8500,e-book coverage- 7000, was established
in January 2002 with some 1500 journals from
six major publishers
• GFMER (Geneva Foundation for
Medical education and Research) –
Established in 2002, WHO collaborating
centre
• CABI
 Some indicators to assess biomedical
databases

• Journal coverage
• Language coverage
• Indexing coverage – (e.g. from the year 1900-the
present)
• Retrospective and prospective coverage
• Cross disciplinary research
• In-depth exploration
• Single discipline/ multiple discipline databases
Indexing information of
a journal
Abstracting and indexing
information
 Abstracting and Indexing
• information
Abstracts on Hygiene and Communicable Diseases, CAB
Abstracts, Caspur, CNKI (China National Knowledge
Infrastructure), DOAJ, EBSCO Publishing’s Electronic
Databases, Excerpta Medica / EMBASE, Expanded
Academic ASAP, Genamics JournalSeek, Global Health,
Google Scholar, Health & Wellness Research Center,
Health Reference Center Academic, Hinari, Index
Copernicus, Indian Science Abstracts, IndMed, MANTIS,
MedInd, National Science Library, OpenJGate,
PrimoCentral, ProQuest, PubMed, Pubmed Central,
Scimago Journal Ranking, SCOLOAR, SCOPUS, SIIC
databases, Summon by Serial Solutions, Tropical
Diseases Bulletin, Ulrich’s International Periodical
Directory
Abstracting and indexing information
Journal of the National Science
Foundation
 Measure of importance of an academic journals
(journal prestige)

• Impact factor (IF) – e.g. 2008 impact factor of BMJ = (total

number of times BMJ articles of 2006 and 2008 appear in all
indexed journals in 2008) divided by (total number of
citable items of BMJ in 2006 and 2007 )
• Immediacy index - the number of citations the articles in
a journal receive in a given year divided by the number of
articles published.
• Cited half-life – read about it
• Aggregate impact factor – read about it
 Measure of importance of an
author

• Authors total number of publications

• Total number of citations for an author
• Age-weighted citation rate (AWCR)
• h-index /h-score– e.g. H-score of 10 means they
have 10 papers with at lease 10 citations each.
 Thank
you
Next Step
Finding articles from databases