Indexing of biomedical literature
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    Indexing of biomedical literature Indexing of biomedical literature Presentation Transcript

    • 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 It is a reference to a published or unpublished source (not always the original source) 3.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 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/
    • 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
    • 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 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)
    • Pubmed/MEDLINE
    • 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
    • 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