HOW TO SEARCH THE LITERATURE -BASIC SEARCH -ADVANCED SEARCH National Library of Medicine(PUBMED): ncbi.nlm.nih/pubmed - PowerPoint PPT Presentation

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HOW TO SEARCH THE LITERATURE -BASIC SEARCH -ADVANCED SEARCH National Library of Medicine(PUBMED): www.ncbi.nlm.nih.gov/pubmed Workshop on Research Methodology and Proposal Development, Conference Hall, National TB Control Programme Islamabad, 18-27 June, 2004. BASIC SEARCH STRATEGY.

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HOW TO SEARCH THE LITERATURE -BASIC SEARCH -ADVANCED SEARCH National Library of Medicine(PUBMED): ncbi.nlm.nih/pubmed

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HOW TO SEARCH THE LITERATURE

-BASIC SEARCH

-ADVANCED SEARCH

National Library of Medicine(PUBMED): www.ncbi.nlm.nih.gov/pubmed

Workshop on Research Methodology and Proposal Development, Conference Hall,

National TB Control Programme

Islamabad, 18-27 June, 2004

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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BASIC SEARCH STRATEGY

  • Pick a search topic: for example, previous PPM studies in the literature?

  • Divide topic into concepts

  • Find words (keywords) or subject headings (MeSH) to represent these concepts

  • Combine concepts with AND, OR, or NOT

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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FIRST CONCEPT

    ____________

OR____________

OR____________

SECOND CONCEPT

AND _____________

OR______________

OR______________

THIRD CONCEPT

AND ___________

OR___________

OR____________

RESEARCH TOPIC SEARCH

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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When to Use Boolean Operators

  • In a Basic Search

  • In an Advanced Search

  • AND is assumed each time you add another step to the Query.

  • Scroll down to Modify Current Query to change the Boolean Operator to OR or NOT

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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Glossary

  • Boolean Operators (named for George Boole, 1815-1864, a mathematician) - combining terms such as AND, OR, and NOT used in building a search statement or in putting several sets together.

  • Citation a bibliographic representation of a journal article or a book chapter, etc; one unit in a bibliographic database. It includes many fields, such as the author, article title, journal title, year, volume, issue and page numbers and is the information you need to locate the article or book. Synonym of Record.

  • Entrez date the date that a record is entered into the Entrez database

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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Glossary

  • Field one of many units in a record (or citation) in a database. In PubMed, fields include author, title, source (journal name, year, volume, pages), abstract, publication type, language, etc.

  • Indexed chosen for inclusion in a particular database.

  • ISSN International Standard Serial Number - a unique number assigned to represent a journal title.

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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Glossary

  • Journal a periodical (or magazine) published on a regular basis.

  • Major MeSH a controlled vocabulary term that is one of the most important concepts covered in the article represented in the record.

  • Major Topic Terms Some MeSH terms are assigned as Major Topic terms, meaning that the indexer has determined that these terms represent the major thrust of the document. Using the Major Topic field in the MeSH Browser can help you discard documents that are less relevant to your search.

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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Glossary

  • MEDLINE Medline is the National Library of Medicine's (NLM) premier bibliographic database covering the fields of medicine, nursing, dentistry, veterinary medicine, the health care system, and the preclinical sciences as far back as 1966.

  • MeSH a Medical Subject Heading. A controlled vocabulary term used by all the indexers in an organization to ensure consistency in assigning terms to articles (or records) on the same topic. They are also used in searching to avoid having to think of all the possible words that various authors could have used to express the same concept. For example, the MeSH heading AGED is assigned instead of aging, older, elderly, senior citizen, geriatric person, etc. that might appear in the title or abstract of the article.

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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Glossary

  • Premedline - is the NLM database that provides basic citation information and abstracts before the full records are prepared and added to MEDLINE.

  • Query box a box in which you enter a search term before clicking on [search] or [enter].

  • Record a collection of data about a single unit in a database; in PubMed, each record represents one journal article. Synonym of Citation. Each record or citation is composed of many fields.

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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Glossary

  • Serial a publication that is issued on a regular basis

  • Set all the records meeting your search criteria. Sets are combined with AND, OR, or NOT depending on whether you require the search terms from both sets to be included, you want either or both of the terms included, or you want only the terms from one set and NOT the ones from the other set.

  • Subheading - A term used with MeSH headings to help focus on a specific aspect of the subject. For example, subheadings for a disease could be, complications, drug-therapy, diagnosis, etc.

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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When should I Use Basic or Advanced Search Mode?

  • Here are some general rules to go by:

  • Basic

  • Use the Basic Search when you have only a single term to search.

  • Use the Basic Search when you are only searching by the author.

  • Advanced

  • Use the Advanced Search when you have more than one concept to search.

  • Use the Advanced Search when you want to search in a specific field.

  • Use the Advanced Search when you want to limit search by language or publication type

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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BASIC SEARCH

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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  • Enter your search term(s) in the query box. You may use "OR", "AND", or "NOT"; PubMed will automatically combine terms with "AND" using automatic term mapping. Terms are matched against a MeSH translation table, a Journals translation table, a phrase list, and an Author index -- in that order.

  • PubMed will display your results as brief citations in batches of 20 per page, by default. To change the "Number of documents to display per page:", select a higher number from the pull-down menu below the query box.

  • The Entrez Date is the date the citation was added to the PubMed database, which differs from the Date of Publication. Use the "Entrez Date limit" pull-down menu to select a range of days or years.

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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Author names should be entered in the form Smith JB, but initials are optional. PubMed automatically truncates the author's last name to allow for varying initials and designations such as Jr. or 2nd. If only the author's last name is entered (no initials), PubMed will search that name in All Fields not just the Author field.

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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  • Journal titles may be entered in full:

  • as valid MEDLINE abbreviations:

  • or as ISSN numbers:

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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Citation display format displays the source, title, author and affiliation, abstract, MeSH and unique identifier

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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  • Searching in the different fields

    • In Advanced search, you now have the option to search in the different Medline fields

    • Just click on the arrow in the “Search field” box to see the list

    • Highlight the one you want and click once

Advanced Search

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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How to combine search terms

  • Advanced search’s main feature is the ability to do a search with 2 or more terms

  • The first step is to select the search terms that apply to your question using MeSH Browser

  • Example: Are there any articles on the diagnosis and chemoprevention of TB?

  • The search terms for this query would be:

  • tuberculosis

  • Diagnosis

  • prevention

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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How to Combine Search Terms

  • Using MeSH Browser, see which term will best match diagnosis, PubMed has now found citations “diagnosis”

  • now you want to add “prevention” to the search

  • Using the MeSH Browser again, you would see that the best term for this is “chemoprevention”

  • Add “chemoprevention” to your search as a MeSH term and click on search

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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The Journal Browser

The Journal Browser allows you to look up a journal by title, ISSN, or by the MEDLINE journal abbreviation to search for citations from that journal.

To do this, from the Journal Browser page, enter either the full journal title or MEDLINE abbreviation in the query box and click on the "Start..." button.

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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The Journal Browser will display a listing of possible matches each with the full journal title, ISSN number, and MEDLINE abbreviation. Click on the MEDLINE abbreviation to retrieve all of the citations for that journal that are available in PubMed

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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Journal Browser then runs a MEDLINE search for citations from that journal and displays the results in the regular searching mode.

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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  • Journal Browser also provides links to online journals via MEDLINE Journals With Links to Publisher Web Sites

  • This is a list of the journals in MEDLINE for which publishers have provided links to their journal Web sites, sorted alphabetically by journal title .

  • A list sorted by publisher is also available.

  • Web-based journals usually contain the full-text of the original article, but this is not always the case.

  • User registration, a subscription fee, or some other type of fee may be required to access the full text of articles in some journals.

  • Follow access instructions provided on the journal's Web page.

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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Journal Browser Worksheet

  • How can I find out if a journal is indexed for MEDLINE?

  • a. Scrolling through the list of MEDLINE Journals With Links to Publisher Web Sites

  • b. Reading the list of Journals Indexed for MEDLINE

  • c. Searching the Journal Browser

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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MeSH Browser

Each citation in the PubMed database is indexed by Medical Subject Headings (or MeSH) that describe the subject content of the article. The PubMed MeSH Browser allows you to look up articles by the MeSH term.

We are doing a search on types of drug and diet therapy for skin cancer. When we do a simple search on the terms "skin, "cancer," "drug," and "therapy" we come up with 4140 results, most of which do not relate to our search. We can use the MeSH browser to refine our search.

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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  • To enter the MeSH Browser click on the link on the left hand column of the PubMed screen.

  • To look up the correct MeSH heading enter your first search term in the MeSH browser form.

  • Since Cancer is not a MeSH term, PubMed will give you the closest related term to search under. PubMed will also show you where the term falls in its subject tree and broader and narrower definitions of the term.

  • Add to Query allows you to use this term as it is, choosing all subheadings.

  • The Detailed Display will allow you to refine your search term and select subheadings.

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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  • The Detailed Display will allow you to refine your search term and select subheadings.

  • Choose "drug therapy" and "diet therapy" and click on "Add."

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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  • PubMed will show you the search strategy for your search so far. From here we can return to PubMed and view the results of our search, or we can choose to add to our search.

  • For our search we will click on "Enter Another MeSH term to browse."

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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  • From here we are able to choose subheadings. We are are not going to limit to any specific subheadings for this search.

  • Some MeSH terms are assigned as Major Topic terms, meaning that the indexer has determined that these terms represent the major thrust of the document. Using the Major Topic field in the MeSH Browser can help you discard documents that are less relevant to your search. For this search click on the "Restrict Search to Major Topic headings only."

  • Click on "Add" to add this term to our search

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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  • This will bring the search string of the search we have done so far. From here we can continue our search or return to the PubMed Advanced search screen to refine our search and see the results.

  • Click on "Return to PubMed."

Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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Workshop on Research Methods and Proposal Development, NTP, Islamabad, Pakistan


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