Hospital Library · Web viewIt was developed in conjunction with publishers of biomedical literature as a search tool for accessing literature citations and linking to full-text journals

MEDLINE via PubMed

Handout Topics

Find references on a specific topic, by a specific author or in a specific journal Use textwords or MeSH Browser (Medical Subject Headings ) for searching Apply limits such as language, age groups or publication type to search results Use Single Citation Matcher to verify a reference Use Cubby to save search strategies

PubMed Overview

PubMed is a search interface developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM), located at the National Institutes of Health (NIH). It was developed in conjunction with publishers of biomedical literature as a search tool for accessing literature citations and linking to full-text journals at web sites of participating publishers.

Databases available for searching via PubMed are shown on the black menu bar across the top of the page. Your choices are: PubMed, Nucleotide, Protein, Genome, Structure, PopSet, Taxonomy and OMIM.

MEDLINE Overview

MEDLINE is the NLM's premier bibliographic database covering the fields of medicine, nursing, dentistry, veterinary medicine, the health care system, and the preclinical sciences. MEDLINE contains bibliographic citations and author abstracts from more than 4,000 biomedical journals published in the United States and 70 other countries. The file contains over 11 million citations dating back to the mid-1960's. Coverage is worldwide but with a bias towards western medical practices. Most records are from English-language sources or have English abstracts.

Searching on MEDLINE via PubMed

You can search MEDLINE by using the MeSH terminology or by using a textword approach.

MeSH (Medical Subject Headings)

The MeSH controlled vocabulary is a distinctive feature of MEDLINE. It imposes uniformity and consistency to the indexing of biomedical literature. The terms are used to describe the subject of each journal article in MEDLINE. MeSH contains more than 19,000 terms and is updated annually to reflect changes in medicine and medical terminology. MeSH terms are arranged hierarchically by subject categories with more specific terms arranged beneath broader terms. PubMed allows you to view this hierarchy in the MeSH Browser.

Skilled subject analysts examine journal articles and assign to each the most specific MeSH terms applicable -- typically ten to twelve. Applying the MeSH vocabulary ensures that articles are indexed uniformly by subject. Preference is given to describing the disease state.

MEDLINE via PubMed 1

Textword

Textword searching (also known as Keyword Searching) is another way to search MEDLINE without the use of the controlled subject headings (MeSH). Textword searches look for the word or words in the Title and/or Abstract fields of the MEDLINE record. Textword searching works best when there is not an appropriate subject heading that describes your specific search concept. Textword searches only find matches on the exact word(s) you type in; so you will want to truncate the word as appropriate to broaden your possible retrieval.

MeSH - Advantages/Disadvantages Textword- Advantages/DisadvantagesFinds all MEDLINEreferences indexed with a specific heading - will not find relevant references that have yet to be fully indexed (PreMEDLINE)

Can find in-process records (Pre-MEDLINE) that do not yet have MeSH terms assigned as well as publisher supplied citations

Consistent vocabulary - you do not need to use of all variations in word endings or spellings when searching

Finds references with specific word in title or abstract - use truncation symbol (*) to account for variations in word endings (ie staph*)

May take a few years for an index heading to be created for a new topic

Can use 'buzzwords' to find references - works if the author has written them in title or abstract

Index headings may change - check scope note to see when term was introduced

How to search MEDLINE using Textwords1. Enter search terms in the query box. Press the Enter key, or click on the Go key.

You may enter one or more terms (e.g. asthma drug therapy). Search terms that are entered in the query box are matched (in this order) against a MeSH (Medical Subject Headings) Translation Table, a Journals Translation Table, a Phrase List, and an Author Index. PubMed ignores stopwords from search queries.

If you enter more than one search term, PubMed automatically combines (ANDs) significant terms together using automatic term mapping. The terms are searched in various fields of the citation.

If you search includes Boolean operators AND, OR, NOT, they must be in upper case, e.g. asthma AND drug therapy.

2. Click on Details to verify how your concepts are translated for searching. In the example, asthma is translated to the MeSH term 'asthma' and the textword 'asthma', and drug therapy is translated to the subheading 'drug therapy' as well as the MeSH term 'drug therapy' and the textword phrase 'drug therapy'


How to Search MEDLINE on PubMed Using the MeSH Browser1. Click on MeSH Database (see left hand column). Enter a search term and click on Go. Note:

if your search term does not map directly to a MeSH term, you will be presented with a list of possible choices. Highlight the term you think is most appropriate and click on Select Term.

2. To see a definition of the MeSH term, and a list of subheadings, click on the term itself


On the next screen, you can find more information about a MeSH term (i.e. the year it was first used [if created after 1966], related terms, etc.) You also can add additional search limits including: Subheadings, MeSH Major Topic, or turn off MeSH explosions.

You may restrict the MeSH term to one or more specific Subheadings.

You may limit the MeSH term to a MeSH Major Topic, select:

[ ] Restrict Search to Major Topic headings only

You may turn off the MeSH explosion for this term, select

[ ] Do Not Explode this term (i.e., do not include MeSH terms found below this term in the MeSH tree).

3. To enter your term into a PubMed query, select the term then click on "Send to" to add the term the Search using operator: AND You may add the term using the following Boolean operators: AND, OR, NOT. The browser will open a PubMed query box with the selected term(s).

4. To display another MeSH term enter the term in the MeSH 'Search for' query box and press enter or click Go.

5. Repeat steps 1 to 4 as often as required to create your search strategy.

6. When you are finished adding the MeSH term(s) to your query, you may return to PubMed by clicking the Search PubMed button. Your search will automatically run in PubMed.

Note: Write out your search terms beforehand and think about how you want to combine the concepts. The order in which you enter concepts will affect your search results since PubMed processes boolean connectors in a left-to-right sequence. See example below to understand how the order in which you enter terms affects your search results

"asthma"[MESH] AND "drug therapy"[MESH] OR "Therapeutics"[MESH:NOEXP]

is equal to the following search strategy - parentheses show which terms are combined first

("asthma"[MESH] AND "drug therapy"[MESH]) OR "Therapeutics"[MESH:NOEXP]

With the above strategy, you will retrieve articles discussing drug therapy for asthma PLUS all references on therapeutics that may or may not be related to asthma.

To find all articles discussing drug therapy or other therapies for asthma, use the following search strategy - note the order of the search concepts - terms to be combined with boolean OR are placed first in the sequence

"drug therapy"[MESH] OR "Therapeutics"[MESH:NOEXP] AND "asthma"[MESH]

or modify your search strategy with parentheses, once you have clicked on PubMed search

"asthma"[MESH] AND ("drug therapy"[MESH] OR "Therapeutics"[MESH:NOEXP])


Searches by Author, Journal Name, Field CodesAuthor Name

To search by an author's name enter the name in the format of last name plus initials (no punctuation), e.g., smith ja, jones k. PubMed automatically truncates the author's name to account for varying initials and designations such as Jr. or 2nd. A name entered using this format will search in the author field. If only the author's last name is entered, PubMed searches the name in All Fields, except when the author name is found in the MeSH (National Library of Medicine's Medical Subject Headings) Translation table (e.g., Yang will search as Yin-Yang [MeSH] or Yang [Text Word].)

Journal Name

You may search by the full journal title, e.g., molecular biology of the cell; the MEDLINE abbreviation, e.g., mol biol cell; or the ISSN number (standardized international code), e.g., 1059-1524. See the Journals Database (http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=journals) for the full journal titles.

Field Searching (Commonly searched fields)

Author [AU] Various limits on the number of authors included in the MEDLINE citation have existed over the years (see NLM policy on author names). MEDLINE does not list the full name. The format to search for an author is: last name followed by a space and up to the first two initials followed by a space and a suffix abbreviation, if applicable, all without periods or a comma after the last name (e.g., fauci as or o'brien jc jr)

Journal Title [TA] The journal title abbreviation, full journal title, or ISSN number (e.g., J Biol Chem, Journal of Biological Chemistry, 0021-9258).

Language [LA] The language in which the article was published. Note that many non-English articles have English language abstracts. You can either enter the language or enter just the first three characters of most languages, e.g., chi [la] retrieves the same as chinese [la]

MeSH Major Topic [MAJR] A MeSH term that is one of the main topics discussed in the article. See MeSH Terms below.

MeSH Terms [MH] NLM's Medical Subject Headings controlled vocabulary of biomedical terms which is used to describe the subject of each journal article in MEDLINE.

Text Words [TW] Includes all words and numbers in the title and abstract, and MeSH terms, MeSH Subheadings, chemical substance names, personal name as subject, and MEDLINE Secondary Source (SI) field. The Personal Name of Subject field can also be searched directly using the search field tag [ps], e.g., nightingale f [ps].

Title [TI] Words and numbers included in the title of a citation.

Unique Identifiers [UID] PubMed Unique Identifier PMID. To search for the PMID type in the number with or without the search field tag [uid]. You can search for several ID numbers by entering each number in the query box separated by a space (e.g., 95091318 97465762), PubMed will OR the terms together.


http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=journals

Features bar The Features bar directly beneath the query box provides access to additional search options. The PubMed query box and Features bar are available from every screen: you do not need to return to the homepage to enter a new search.

Limits

Click on Limits in the Features Bar under the Query Box to limit your search to specific age groups or gender or language or publication type. Note: only the most common languages and publication types are presented in the Limits listing. See Help for complete list of publication types.

Note: If you select a limit and either run a search or move to another screen, a check will appear in a box next to Limits on the Features bar to indicate that limits have been selected. If you then run a search, the limits in effect will appear in the yellow bar above the Display button. To turn off the limits before you run your next search, click on the box to remove the check.

To limit search to pediatrics: DO NOT USE THE MeSH TERM PEDIATRICS. The MeSH term 'pediatrics' retrieves references on the medical sub-specialty of pediatrics. Use the Ages limit and select the age group of interest. You cannot select more than one age group at a time.

To limit search to references recently added to the database - limit search by Entrez date

To limit search to articles published between certain dates: limit search by Publication date


Preview/Index

Use the Preview feature to: Preview the number of search results before displaying the citations. Refine search strategies by adding one or more terms one at a time. Add terms to a strategy from specific search fields. View and select terms from the Index to develop search strategies.

Use the Index feature to: Select from a list of terms within a search field: Select a search field from the All Fields pull-down menu, enter a term in the box, and click

Index. PubMed displays an alphabetic list of terms in the Index for the selected search field. The number of citations that contain the term appears in parentheses to the right of the term. Scroll up or down the list, or click Up or Down to move along in the Index.

History

PubMed holds all your search strategies and results in History. You can see your search History by clicking on History from the Features bar. History is only available after you run your first search. History lists and numbers your searches in the order in which they were run. History


displays the search number, your search query, the time of search, and the number of citations in your results. To view the results from a search, click on the number of results.

You can combine searches or add additional terms to an existing search by using the pound sign (#) before the search number, e.g., #2 AND #6, or #3 AND (drug therapy OR diet therapy). Once you have entered a revised search strategy in the query box, click Go to view the search results. Click Clear History to remove all searches from the History screen and the Preview/Index screen.

Clipboard

The Clipboard gives you a place to collect selected citations from one search or several searches. After you add citations to the Clipboard you may then want to use the print, save, or order buttons. The maximum number of items that can be placed in the Clipboard is 500. Once you have added items to the Clipboard, you can click on Clipboard from the Features bar to view your selections.

Send to Clipboard To place an item in the Clipboard, click on the check box to the left of the citation. At 'Send to', select Clipboard. Click on 'Send to'. Once you have added a citation to the Clipboard, the record number color will change to green.

Notes:If you click on 'Send to' without selecting citations using the check box, PubMed will add all (up to 500 citations) of your search results to the Clipboard.

The Clipboard will be lost after one hour of inactivity on PubMed or any of the other Entrez databases.


Related References, Books, LinkOut

Related References

Each citation in PubMed has a link that will retrieve a pre-calculated set of PubMed citations that are closely related to the selected article. Click on Related Articles to the right of each citation to display the related set of articles. PubMed creates this set by comparing words from the title, abstract, and MeSH terms using a powerful word-weighted algorithm. Citations are displayed in rank order from most to least relevant with the linked from citation displayed first.

Books

In collaboration with book publishers, NCBI is adapting textbooks for the web and linking them to PubMed to provide background so users can explore unfamiliar concepts found in search results. The Books link displays a facsimile of the abstract, in which some phrases are hypertext links. These phrases correspond to terms that are also found in the books available at NCBI. Clicking on a hypertext links you to a list of book pages in which the phrase is found.

You can search the Books database. Select Books from the Search pull-down menu, enter a search in the query box and click Go.

LinkOut

LinkOut allows publishers, aggregators, libraries, biological databases, sequence centers, andother Web resources to display links to their sites on items from the Entrez databases. These links can take you to the provider's site to obtain the full-text of articles or related resources, e.g., consumer health information. There may be a charge to access the text or information. The current list of LinkOut providers is available.

Saving references for importing into reference management software (EndNote, Reference Manager, ProCite)

1. Run a search. 2. You can save all references, or mark a subset of references to be saved. To save a subset of

references, mark them and send them to your clipboard. Go to Clipboard to save the references.3. Set ‘Display’ to MEDLINE format. (Click on down arrow button to see list of formats.)

4. At 'Send to', select File. Click on ‘Send to’ to save references to your hard drive or disk. Be sure to give the file name the extension ‘.txt’ (e.g. medlineref.txt)

5. Consult your reference management software on how to import the saved file of references into your library or database.


Odds and Ends

To view more than 20 items per page, click on the down arrow next to the Show and select a new number. Click on 'Text' to create a page that can be easily printed.

To change the display format from the Summary default, click on the down arrow next to Summary and select another Display format. Click on 'Send To' to create a text page that can be easily printed.

Abstract displays citation plus abstract (if available)Citation displays citation, abstract (if available) MeSH termsMEDLINE displays tagged record (format for reference management software)

To mark records, click in the box to the left of the title. You can use 'Send to' to save records at 'Clipboard' or as a file, or you can click on 'Send to' to create a text page that can be easily printed.

To jump to another page of references, click on 'Next' or type the number of a page in the Page box and click on 'Page' to jump to that page.

If you have a Loansome Doc account, select 'Order' at Send to and click on 'Send to' to request copies of items that you have marked. (See http://hscweb/library/services.asp for information about LoanSome Doc registration.)


http://hscweb/library/services.asp

Other PubMed Services

Journals DatabaseUse the Entrez Journals database to search for a journal and then link to records for that journal in the database. The Journals database can be searched using the journal title, MEDLINE abbreviation, NLM ID, ISO abbreviation, or ISSN. The database includes the journals in all Entrez databases, e.g., PubMed, Nucleotide, Protein.

Single Citation Matcher The Citation Matcher options allow you to find the citation or the PubMed ID of any article in the PubMed database using bibliographic information. Use the Single Citation Matcher to look for a single citation. This feature is a fill-in-the-blank form that lets you enter journal citation information to locate a single citation, or items from a particular volume or issue of a journal.

Hint: Use less rather than more information when filling in the blanks. Common errors include misspelling of the author's name, wrong year of publication.

Clinical QueriesThis specialized search query with built-in search research methodology filters is intended for clinicians. Four study categories or filters are provided: therapy, diagnosis, etiology and prognosis. Two emphasis categories or filters are provided: sensitivity (includes relevant articles but probably some less relevant) and specificity (more precise articles, with less retrieval).

CubbyThe Cubby stores search strategies that may be updated at any time. In order for you to use this feature your web browser must be set to accept cookies. To register for the Cubby, click on Cubby from the PubMed sidebar then click "I Want to Register for Cubby."


Resources

MEDLINE Fact Sheethttp://www.nlm.nih.gov/pubs/factsheets/medline.html

MeSH Fact Sheethttp://www.nlm.nih.gov/pubs/factsheets/mesh.html

MeSH Informationhttp://www.nlm.nih.gov/mesh/meshhome.html

MeSH Browserhttp://www.nlm.nih.gov/mesh/2002/MBrowser.html

PubMedhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi

PubMed Guide (PDF)http://www.nlm.nih.gov/pubs/manuals/pubmed.pdf


Documents

Hospital Library · Web viewIt was developed in conjunction with publishers of biomedical literature as a search tool for accessing literature citations and linking to full-text journals