Indexing of biomedical literature

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

Articles
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 Articles
Autobiography
Bibliography
Biography
Case Reports
Classical Article
Clinical Conference
Clinical Trial
Clinical Trial, Phase I
Clinical Trial, Phase II
Clinical Trial, Phase III
Clinical Trial, Phase IV
Comment
Comparative Study
Congresses
Consensus Development Conference
Consensus Development Conference, NIH
Controlled Clinical Trial
Editorial
Electronic Supplementary Materials
English Abstract
Evaluation Studies
Government Publications
Guideline
Historical Article
Interactive Tutorial
Interview
Introductory Journal Article
Journal Article
Lectures
Legal Cases
Legislation
Letter
Meta-Analysis
Multicenter Study
News
Newspaper Article
Patient Education Handout
Periodical Index
Personal Narratives
Portraits
Practice Guideline
Randomized Controlled Trial
Review
Scientific Integrity Review
Systematic Reviews
Technical Report
Twin Study
Validation Studies
Video-Audio Media
Webcasts
What is a scholarly article or journal 
includes articles or journals that are research
oriented, and are either written or reviewed by
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

Publication
• Print media
(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 - definition
1. 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 It is a reference to a published or unpublished source (not always the original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
1. 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

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
Sri Lanka Journal of Venereology Vol.3(1) 2012 pp.47-51D
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
PMID: 23417685 [PubMed - in process]
Examples of unique identifiers
DOI
DOI
PMID

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
• AMA Manual of Style
• AP Stylebook
• The ASA Style Guide
• Bluebook
• The Chicago Manual of Style
• The Elements of Style
• The Elements of
Typographic Style
• ISO 690
• MHRA Style Guide
• The Microsoft Manual of
Style
• MLA Handbook
• MLA Style Manual
• The New York Times Manual
• The Oxford Guide to
Style/New Hart's Rules
• 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

Citing Contributions to Books

Citing Contributions to Books on the Internet

Citing Entire Dissertations and Theses-entire
dissertation

Citing Entire Dissertations and Theses-
entire masters thesis

Citing Papers and Poster Sessions Presented at
Meetings-for a poster session

Citing Parts of Reports

Citing Parts of Journal Articles

Citing Parts of Books on the Internet

Citing Parts of Books

Referencing
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/NBK7265/

• 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
http://tilt.library.skagit.edu/modu
le4/plagiarism.htm

Now you will be able to
describe the following
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

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 Access
Catalog (OPAC)
The card catalog was a 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)

Indexing
(noun-Index, plural-Indexes/Indices)
Articles are usually indexed using the
following elements in combination
• Author name/s
• Title
• Journal name
• Journal volume
• Journal issue
• Abstract
• Keywords
• Publisher
• Publication type
• Pagination etc
Depending on the type of databases
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)

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 Lanka
Health Literature 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

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

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

Indexing of biomedical literature

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