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PubMed User Guide

Last update: September 13, 2019

FAQs

Search PubMed

How do I search PubMed?

  1. Identify the key concepts for your search. 
  2. Enter the terms (or key concepts) in the search box.
  3. Press the Enter key or click Search.

For many searches, it is not necessary to use special tags or syntax. PubMed uses multiple tools to help you find relevent results:

To limit the number of search results: 

Find a specific citation

Paste the article title into the search box, or enter citation details such as the author, journal name and the year the article was published in the search box and the PubMed citation sensor will automatically analyze your query for citation information to return the correct citation. The citation sensor incorporates a fuzzy matching algorithm and will retrieve the best match even if a search includes an incorrect term. You do not need to use field tags or Boolean operators.

Enter the author’s last name and initials without punctuation in the search box, and click Search. 

If you only know the author’s last name, use the author search field tag [au], e.g., brody[au]. 

Names entered using either the lastname+initials format (e.g., smith ja) or the full name format (john a smith) and no search tag are searched as authors as well as collaborators, if they exist in PubMed.

Enter a full author name in natural or inverted order, e.g., julia s wong or wong julia s.

Omit periods after initials and put all suffixes at the end, e.g., vollmer charles jr

Initials and suffixes are not required. If you include a middle initial or suffix, you will only retrieve citations for articles that were published using the middle initial or suffix.

More information about author searching:

For additional information on author names in PubMed, please see the journal article, “Author Name Disambiguation for PubMed.”

Enter one of the following in the search box:

More information about journal searching: 

A list of journals included in PubMed is available by FTP.

Searching by date

Using the results timeline

Click and drag the sliders on the Results by Year timeline to change the date range for your search.

Note: The Results by Year timeline uses only the primary publication date for a citation as supplied by the publisher: the print date or the electronic date. In contrast, the Publication Date filters and search tag [dp] incorporate both print and electronic publication dates for a citation, which may span more than one year; for example, an article that was published online in November 2018, and published in a print issue in January 2019. Therefore, results may differ slightly when filtering using the timeline vs. by Publication Date.

Using the search builder

  1. Click Advanced search and use the search builder.
  2. Select a date field from the All Fields menu, e.g., Date – Publication, and enter a single date or a date range in the fill-in-the-blank boxes. Month and day are optional. If you want to search for a date range up to the current date, do not edit the ‘Present’ date box.
  3. Click Search.

Searching by a single date in the search box

Enter dates using the format yyyy/mm/dd [date field]. The available date fields are:

The month and day are optional. 

Searching for a date range in the search box

Enter date ranges using a colon (:) between each date followed by a [date field].

Comprehensive searches for a full year should be entered as 2000:2000[dp] rather than 2000[dp] to retrieve citations with a different print and electronic year of publication.

Date range searching includes both print and electronic dates of publication.

Searching for a relative date range

Use the following format to search for a relative date range:

where X is the number of days, months or years immediately preceding today’s date and [date field] is the date field tag: [dp], [edat] or [crdt].

Filters

You can use filters to narrow your search results by article type, text availability, publication date, species, language, sex, subject, journal category, and age.

To apply a filter:

  1. Run a search in PubMed.
  2. Click the filter you would like to activate from the sidebar. A check mark will appear next to the activated filter(s). 
  3. Subsequent searches will be filtered until the selected filters are cleared, or until 8 hours of inactivity.

The most popular filters are included on the sidebar by default. To display additional filters on the sidebar:

  1. Click the “Additional filters” button.
  2. A pop-up menu will appear showing the available filters for each category: article type, species, language, sex, subject, journal, and age.
  3. Choose a category from the list of options on the left side of the menu: Article Type, Species, etc.
  4. Within each category, select the filters you would like to add to the sidebar.
  5. Click Apply. This will close the pop-up menu and display your selections on the sidebar with the other filters.
  6. If you would like to cancel your selections, click Cancel or click on the X in the upper right corner to close the pop-up and return to your search results.
  7. To apply the filter(s) to your search, click the filter(s) on the sidebar. 

More information about filters:

Article type

Select article types to narrow your results based on the type of material the article represents, such as: Clinical Trial or Review.

You can add more article types to the sidebar using the Additional Filters button. The complete list of MEDLINE publication types is available. Systematic review articles are retrieved using a search strategy.

These filters may exclude some citations that have not yet completed the MEDLINE indexing process.

Text availability

To filter your results to only citations that include a link to full text, a link to free full text, or an abstract, click the appropriate selections.

Alternatively, you may search for citations with links to full text, free full text or include an abstract using the values: full text[sb], free full text[sb], or 'hasabstract'. No search field tag is required for hasabstract. You may also search for all MEDLINE citations with a structured abstract with ‘hasstructuredabstract’.

Note: Most citations in PubMed to articles published before 1975 do not include abstracts.

Publication date

To filter your results by Publication Date, click 1 year, 5 years, or 10 years. These filters include both electronic and print publication dates. 

Species

Species selections restrict your results to human or animal studies.

You can add species filters to the sidebar using the Additional Filters button.

These filters may exclude some citations because they have not yet completed the MEDLINE indexing process.

Language

Language selections restrict your search to articles written in that language.

You can add language filters to the sidebar using the Additional Filters button.

Sex

Sex restricts your search results to a specific sex for an animal or human study.

You can add sex filters to the sidebar using the Additional Filters button.

This filter may exclude some citations because they have not yet completed the MEDLINE indexing process.

Subjects

Subject filters restrict retrieval to specific subjects. 

To add subjects to the sidebar, use the Additional Filters button.

Subjects use a specialized search strategy.

Subjects can also be searched using aids[sb] or cancer[sb]. The Systematic Reviews filter is also included with the Article Type filters.

Journal categories & more subsets

Select journal categories can be added to the sidebar using the Additional Filters button:

The Journal/Citation subsets restrict retrieval to specialized journals or articles on specialized topics in other journals. The table below lists the journal subsets, along with the code used for searching. Some subsets are closed and are no longer being assigned to current data.

To search for a Journal/Citation subset, enter in the search box: jsubset?, where ? represents the subset code. The Journal/Citation subset does not require a search tag.

Subset Code Journal/Citation Subset
AIM Abridged Index Medicus is a list created in 1970 of approximately 120 core clinical English language journals that corresponds to "Core clinical journals" journal category selection in filters.
D Dentistry journals
E Citations from bioethics journals or selected bioethics citations from other journals
H Health administration journals, non-Index Medicus
IM Index Medicus journals
K Consumer health journals
N Nursing journals
Q History of medicine journals and selected citations from other journals
QIS Citations from non-Index Medicus journals in the field of history of medicine
S Citations from space life sciences journals and selected space life sciences citations from other journals
T Health technology assessment journals, non-Index Medicus
X AIDS/HIV journals (selected citations from other journals 1980-2000)
PubMed Central Subset

To restrict retrieval to citations that have a free full-text article available in PubMed Central (PMC), search pubmed pmc[sb].

Use the PMID/PMCID/NIHMSID Converter to convert IDs for publications referenced in PubMed and PMC. To retrieve citations that include an NIHMS ID use the query, hasnihmsid.

Citation Status Subsets

The citation status indicates the internal processing stage of an article in the PubMed database (see PubMed Citation Status Subsets).

To search for a particular citation status, enter one of the search terms below followed by the [sb] search tag:

To search for the total number of PubMed citations, enter all[sb] in the search box.

Ahead of Print Citations

Publishers may submit citations for articles that appear on the web prior to their publication in final or print format. To search for these ahead-of-print citations, enter pubstatusaheadofprint.

Ages

Age filters restrict results to a specific age group for a human study.

You can add age filters to the sidebar using the Additional Filters button.

Age filters include:

These filters may exclude some citations because they have not yet completed the MEDLINE indexing process.

Searching for a phrase

PubMed does not perform adjacency searching. However, many phrases are recognized by the subject translation table used in PubMed's Automatic Term Mapping (ATM). For example, if you enter fever of unknown origin, PubMed recognizes this phrase as a MeSH Term.

You can bypass ATM and search for a specific phrase using the following formats:

Phrases may appear in a PubMed record but not be in the phrase index. To browse indexed phrases, use the Show Index feature included in the Advanced Search Builder: select a search field, enter the beginning of a phrase, and then click Show Index.

When you enter search terms as a phrase, PubMed will not perform automatic term mapping that includes the MeSH term and any specific terms indented under that term in the MeSH hierarchy. For example, "health planning" will include citations that are indexed to the MeSH term, Health Planning, but will not include the more specific terms, e.g., Health Care Rationing, Health Care Reform, Health Plan Implementation, that are included in the automatic MeSH mapping.

Truncating search terms

To search for all terms that begin with a word, enter the word followed by an asterisk (*): the wildcard character. 

To search for a phrase including a truncated term, use the following formats:

The truncated term must be the last word in the phrase.

Truncation stops at the end of a term; it does not process beyond a space.

Truncation turns off automatic term mapping and the process that includes the MeSH term and any specific terms indented under that term in the MeSH hierarchy. For example, heart attack* will not map to the MeSH term Myocardial Infarction or include any of the more specific terms, e.g., Myocardial Stunning; Shock, Cardiogenic.

Combining search terms with Boolean operators (AND, OR, NOT)

PubMed applies an AND operator between concepts, e.g., “vitamin c common cold” is translated as vitamin c AND common cold. Enter Boolean operators in uppercase characters to combine or exclude search terms:

PubMed processes searches in a left-to-right sequence. Use parentheses to “nest” concepts that should be processed as a unit and then incorporated into the overall search.

Boolean operators must be used when combining tagged search terms as follows: search term [tag] BOOLEAN OPERATOR search term [tag]. See Search Field Descriptions and Tags.

Display, Sort, and Navigate

Understanding your search results

Citations are initially displayed 10 items per page and sorted by Best Match.

By default, PubMed search results are displayed in a summary format and include snippets from the citation abstract. Snippets and highlighted terms are selected based on relatedness to your query.

To see the abstract for an individual citation, click the title of the citation to go to its abstract page.

PubMed may also include non-English abstracts, if supplied by the publisher. The additional language view links are available on the Abstract display. The abstract text defaults to English when a citation has an accompanying non-English abstract. To retrieve citations with non-English abstracts, use the query hasnonenglishabstract.

You can mouseover a journal’s title abbreviation to display the full journal name.

Display an abstract

Click the title of the citation to go to its abstract page, or change the search results display to Abstract format using the gear icon in the upper right corner of the search results page.

Changing the display format of search results

Results are initially displayed in the summary format, except a single citation result will display the abstract format. You can change the results display by selecting a format from the format menu:

  1. Click the gear icon in the upper right corner of the search results page
  2. Select the display format you would like to use: Summary or Abstract

Showing more results

The results page indicates the total number of citations retrieved.

Ten citations are displayed per page. Click "Show more" to display the next page of results, or click "Jump to page" to navigate directly to a specific page of results. 

Sorting your results

Select an option to sort by:

More information about sorting:

Finding the full-text article

PubMed records contain citation information (e.g., title, authors, journal, publication date) and abstracts of published articles and books. PubMed search results do not include the full text of the journal article, but the abstract view in PubMed includes links to the full text from other sources when available, such as the publisher’s website or the PubMed Central (PMC) database. The full-text journal site may require a fee or subscription, however online journals sometimes provide free access. Access may also be available through your organization, or local medical library.

You may be able to obtain free copies of full-text articles in these ways:

Free full text filter

On the filter sidebar, click "Free full text" to narrow results to resources that are available for free on the web, including PubMed Central, Bookshelf, and publishers' websites. Alternately, include free full text[Filter] in your query.

PubMed Central

When full text is available in PubMed Central (PMC), the "Free in PMC" icon will appear on the citation's abstract display under Full-Text Links. Click the icon to view the article in PMC.

PubMed Central (PMC) is the U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature.

From the publisher

Journal publishers or related organizations may provide access to articles for free, for free after registering as an individual or guest, or for a fee. When provided by the publisher or other organization, icons linking to these sources can be found on the citation's abstract display under the "Full-Text Links" and/or "LinkOut" sections. Icons will often indicate free full text when the article is available for free.

Note: When you click a full text icon or link in PubMed, you leave PubMed and are directed to the full text at an external provider's site. NCBI does not hold the copyright to this material, and cannot give permission for its use. Users should review all copyright restrictions set forth by the full text provider before reproducing, redistributing, or making commercial use of material accessed through LinkOut.

Please see the Copyright and Disclaimers page for additional information.

If you are affiliated with a hospital, university, or other institution

Your local medical library is your best option. If you see icons for your library on the abstract view this indicates that your library provides a link to the article, has the journal in its collection, or may otherwise obtain the article for you through interlibrary loan. If your library does not have access to the article you need, ask a librarian about ordering the article from another institution.

Local library

Some local libraries have copies of medical journals or can get a copy of an article for you. Ask your local librarian about inter-library loan options and fees.

Similar articles

The abstract page for a citation includes links to PubMed citations for similar articles:

See Computation of similar articles for more information.

References

PubMed abstracts include references when available. Reference lists are available for citations to full-text articles included in PMC and for citations where the publisher supplied references in the citation data sent to PubMed.

Cited by

PubMed abstracts include links to other resources citing the current item. "Cited by" is generated using data from NCBI resources and is not a complete list of works citing a particular item.

Find related resources using LinkOut

Most PubMed records include LinkOut resources to a variety of websites including publishers, aggregators, libraries, biological databases, and sequence centers. LinkOut resources link to providers’ sites to obtain the full-text of articles or related information, e.g., consumer health. There may be a charge to access the text or information from a provider's site.

To view LinkOut resources, navigate to the LinkOut section at the end of an individual citation's abstract page.

To find citations with links to free full-text articles, apply the "Free full text" filter to your search results.

To find citations with links to full-text articles, enter search terms followed by AND full text[sb].

More information about Links:

LinkOut links are supplied by the LinkOut providers. Publishers who electronically supply their data to PubMed may include an icon that links to a site providing the full-text. Corrections and changes to links are made by the providers and are their responsibility.

To report problem links or inquire about online journal subscriptions, contact the provider directly. Contact information is typically available at a provider's web site.

Cite, Save, and Share

Save citations temporarily using the Clipboard

The Clipboard provides a place to collect up to 500 items from one or more searches. Items saved to the Clipboard will expire after 8 hours of inactivity on PubMed.

To add items to the Clipboard:

  1. From your search results, use the check boxes to select items. To save all results (up to a maximum of 500), do not tick any check boxes.
  2. Click the ellipses button " ... " to show more actions.
  3. Select Send to: Clipboard.
  4. Selected items will be added to the Clipboard.
    • If no items were selected, a drop-down menu of options will display where you may add selected items, all results on the page, or all results (up to a maximum limit of 500 citations) to the Clipboard.
    • Individual items can also be added to Clipboard from their abstract page using the "More actions" icon.
  5. To view your selections, click the Clipboard link under the Search bar. This link will only appear after one or more items have been added to the Clipboard; the link is not present when the Clipboard is empty.

To delete items from the Clipboard:

More information about the Clipboard:

Save citations as a text file

Use the Save button to download citations to a text file.

  1. Click Save and choose a Selection and Format from the menus that appear.
    • Selection: The citations you would like to save. Use the check boxes to select citations from your search results or Clipboard. You may move to other pages and continue your selections. Alternately, save: all results on this page, or all results (up to a maximum of 10,000 citations)
    • Format: Summary, RIS, PMID list, Abstract, or CSV
  2. Click Create file.
  3. Your web browser will prompt you to save the file on your computer.

More information about saving citations to a file:

Export citations into citation management software

To export citations into a citation management software program such as EndNote, Mendeley, RefWorks, or Citavi, follow the instructions for saving citations as a text file and choose the format: RIS. Import this saved file into your citation management program.

Questions regarding citation management software should be directed to the respective companies.

Email citations

  1. Use the check boxes to select citations from your search results or Clipboard. You may move to other pages and continue your selections. You may also choose to email all citations shown on the page without making any selections.
  2. Click the Email button.
  3. Enter an email address, subject line, and any additional text you would like to include in the body of the email. Select which citations to send and the format.
  4. Click Send email. The system returns you to your results page and displays a confirmation e-mail sent message.

More information about emailing citations:

Create an email alert for a search

Click "Create alert" under the search bar to create an automatic email update for searches. You must sign in to My NCBI to use this feature.

Use the print function of your web browser. To print citations from different searches, save the citations in PubMed’s Clipboard, and then print.

See also:

To get the URL for an individual citation, copy the permalink for the citation under "Share."

To get the URL for your search results, copy the URL from your web browser's address bar or bookmark the URL using your web browser's bookmark function.

More information about PubMed links:

Download PubMed Data

Once a year, NLM releases a complete (baseline) set of PubMed citation records in XML format for download from our FTP servers. Incremental update files are released daily and include new, revised, and deleted citations. The PubMed DTD states any changes to the structure and allowed elements from year to year.

Tools included on the Advanced Search page help users to: search for terms in a specific field, combine searches and build large, complex search strings, see how each query was translated by PubMed, and compare number of results for different queries.

Searching by a specific field

Use the Advanced Search Builder to search for terms in a specific field, such as author or journal. For some fields, an autocomplete feature will provide suggestions as you type.

  1. From the "All Fields" drop-down menu, select the field you would like to search.
  2. Add terms from the builder to the query box to construct your search. The default Boolean operator is AND; if desired, choose OR or NOT from the pull-down menu.
  3. Once you have finished adding terms to the query box, click Search (or Add to History) to run the search.

You may also search a specific field -- and bypass automatic term mapping -- by adding a search tag to a term (see: Search Field Descriptions and Tags).

Browsing the index of terms

The Advanced Search Builder includes the Show Index feature, which provides an alphabetical display of terms appearing in each PubMed search field. You can browse by all fields or within a specific field such as MeSH Subheadings.

  1. Click Advanced to navigate to the Advanced Search page, and use the Builder to select a search field from the All Fields menu.
  2. Enter a term in the search box, then click Show Index.
  3. The index displays an alphabetic list of search terms and the number of citations for each term.
  4. Scroll until you find a term you want to include in your search, and then highlight it to add it to the search box.
  5. Multiple terms may be selected from the list and added to the search box.
  6. Add terms from the builder to the query box to construct your search.
  7. Once you have finished adding terms to the query box, click Search (or Add to History) to run the search.

More information about using the index:

History

Your PubMed search history appears on the Advanced Search page under History. This feature requires your web browser to accept cookies.

Descriptions of each column in the History table appear below:

Previewing the number of search results

  1. Click Advanced to navigate to the Advanced Search page.
  2. Use the builder to add search terms to the query box, or type your search directly into the query box.
  3. Use the split button to toggle the button function from "Search" to "Add to History".
  4. Click Add to History. This will run the search without leaving the Advanced Search page.
  5. See your query including the number of results in the History table.

Combining searches using History

Searches can be combined or used in later searches using your search History.

  1. Click Advanced to navigate to the Advanced Search page.
  2. In the History table, click the More Actions icon " ... " next to your query.
  3. From the available options, select "Add query" to copy the query to the Query box.
  4. After you've added content to the Query box, options to use the Boolean operators AND, OR, or NOT will appear when adding more queries to the Query box.
  5. Edit your query in the Query box if you would like to make any changes before running the search.
  6. Click Search (or Add to History).

More information about combining searches from your History:

Viewing the Search Details

PubMed may modify or add additional search terms to your search to optimize retrieval, such as: MeSH terms, British/American spellings, singular/plural word forms, and other synonyms.

  1. Search Details are included on the Advanced Search page under History.
  2. Click the chevron icon " > " next to a query in History to expand the Search Details. 
  3. When expanded, the details below a query in the History table show the search strategy used to run the search.

Other services

Clinical Queries

PubMed Clinical Queries provides specialized searches for clinicians:

Search by clinical study category

Clinical Study Categories use a specialized search method with built-in search filters that limit retrieval to citations to articles reporting research conducted with specific methodologies, including those that report applied clinical research.

To find citations using the Clinical Study Category:

  1. Click Clinical Queries from the PubMed homepage
  2. Enter your search terms in the search box
  3. Click Search
  4. Select a Category: Therapy, Diagnosis, Etiology, Prognosis, or Clinical prediction guides
  5. Select a Scope: Narrow (specific search) or Broad (sensitive search)
  6. See results in the Clinical Study Categories column

Finding systematic reviews

In PubMed, Systematic Reviews cover a broad set of articles that build consensus on biomedical topics. A list of related sources on this topic is available.

To search for systematic reviews:

  1. Click Clinical Queries from the PubMed homepage
  2. Enter your search terms in the search box
  3. Click Search
  4. See results in the Systematic Reviews column

Alternatively, use the article type filter for systematic reviews, or enter search terms followed by AND systematic[sb] in the search box. For example, lyme disease AND systematic[sb].

To search for citations assigned the Systematic Review publication type, use the publication type search tag[pt], i.e., systematic review[pt].

Medical genetics searches

In PubMed, Medical Genetics finds citations related to various topics in medical genetics.

  1. Click Clinical Queries from the PubMed homepage
  2. Enter your search terms in the search box
  3. Click Search
  4. Choose a specific topic, if applicable
  5. See results in the Medical Genetics column

Finding a citation using the Single Citation Matcher

The Single Citation Matcher has a fill-in-the-blank form for searching for a citation when you have some bibliographic information, such as journal name, volume, page number.

More information about using the Single Citation Matcher:

Search PubMed using the MeSH database

MeSH (Medical Subject Headings) is the NLM controlled vocabulary thesaurus used for indexing PubMed citations.

Use the MeSH database to find MeSH terms, including Subheadings, Publication Types, Supplementary Concepts and Pharmacological Actions, and then build a PubMed search. The MeSH database can be searched by MeSH term, MeSH Entry Term, Subheading, Publication Type, Supplementary Concept, or MeSH Scope Note.

More information about the MeSH database:

Launching PubMed searches from the MeSH database

To build a PubMed search from MeSH:

  1. Run a search in the MeSH database.
  2. Select terms using the check boxes.
  3. Click "Add to search builder" in the PubMed search builder portlet.
  4. You may continue searching and including additional terms to the PubMed search builder using the “Add to search builder” and Boolean pull-down menu.
  5. When you are finished, click “Search PubMed.”

Searching for journal information in the NLM Catalog

The NLM Catalog includes information about the journals in PubMed and the other NCBI databases.

Click Journals in NCBI Databases on the homepage of NLM Catalog or the Journals link on the PubMed homepage to limit your NLM Catalog results to the subset of journals that are referenced in NCBI database records.

See the NLM Catalog help for additional information.

Other journal resources include:

Using the E-Utilities API tools

E-utilities are tools that provide access to data outside of the regular NCBI web search interface. This may be helpful for retrieving search results for use in another environment. If you are interested in large-scale data mining on PubMed data, you may download the data for free from our FTP server. Please see the terms and conditions for data users.

Find PMIDs using the Batch Citation Matcher

Use the Batch Citation Matcher to retrieve PMIDs (PubMed IDs) for multiple citations in batch mode. The Matcher requires you enter the bibliographic information (journal, volume, page, etc.) in a specific citation format.

To retrieve PubMed PMIDs or PubMed Central IDs:

  1. Enter each citation string on a separate line below, or create a file using the following format:
    journal_title|year|volume|first_page|author_name|your_key|
    Fields must be separated by a vertical bar with a final bar at the end of the string.
  2. Enter your email address. Email messages may take several minutes to process and be sent to your email address.
  3. If you created a file, click Browse to select it from your system directory.

If a match is not found the citation string will display one of the following:

Notes:

Example input:

Example output:

Consumer health

The National Library of Medicine cannot provide specific medical advice. NLM urges you to consult a qualified health care professional for answers to your medical questions. NLM does not have pamphlets or other materials to mail.

MedlinePlus and MedlinePlus en español are specifically designed for consumers, containing hundreds of topic pages including NIH-written descriptive information, videos, health check tools, drug, herb and supplement info, links to Fact Sheets from other NIH Institutes, the CDC, etc., and more.

Appendices

Further assistance and training

Contact customer support

Other NLM publications

Search Field Descriptions and Tags

Affiliation may be included for authors, corporate authors and investigators, e.g., cleveland [ad] AND clinic [ad], if submitted by the publisher. Multiple affiliations were added to citations starting from 2014, previously only the first author’s affiliation was included. PubMed includes the note “Contributed equally” in the affiliation field when this information is supplied by publishers.

All Fields [ALL]

Untagged terms and terms tagged with [all fields] are processed using Automatic Term Mapping. Terms that do not map are searched in all search fields except for Place of Publication, Create Date, Completion Date, Entry Date, MeSH Date, and Modification Date. Terms enclosed in double quotes or truncated will be searched in all fields and not processed using automatic term mapping. PubMed ignores stopwords.

Article Identifier [AID]

Includes article identifiers submitted by journal publishers such as DOI (digital object identifier).

Author [AU]

The format to search for this field 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). Initials and suffixes may be omitted when searching.

PubMed automatically truncates a search for an author's name to account for varying initials, e.g., o'brien j [au] will retrieve o'brien ja, o'brien jb, o'brien jc jr, as well as o'brien j.

Searching by full author name for articles published from 2002 forward is also possible, if available. See NLM policy on author names.

Author Identifier [AUID]

The author identifier includes a unique identifier associated with an author, corporate or investigator name, if supplied by a publisher. The field includes the organization authority that established the unique identifier, such as, ORCID, ISNI, VIAF, e.g., orcid 0000-0001-5027-4446 [auid].

Book [BOOK]

The book search field includes book citations, e.g., genereviews [book].

Use the following untagged searches to retrieve all book or book chapters, e.g., ataxia AND pmcbookchapter

Comment Correction Type

The data in these fields are citations to other associated journal publications, e.g., comments or errata. Often these link to the respective citation. Comments/Corrections data can be retrieved by the search term that follows each type:

Completion Date [DCOM]

Used by NLM for internal processing. Completon Date is not included in All Fields retrieval; the [dcom] search tag is required.

Conflict of Interest Statement [COIS]

The conflict of interest statement from the published article. To retrieve all citations that contain conflict of interest statements, use the query hascois.

Corporate Author [CN]

Corporate author identifies the corporate or collective authorship of an article. Corporate names display exactly as they appear in the journal.

Note: Citations indexed pre-2000 and some citations indexed in 2000-2001 retain corporate authors at the end of the title field. For comprehensive searches, consider including terms and/or words searched in the title field [ti].

Create Date [CRDT]

The date the citation record was first created. Create Date is not included in All Fields retrieval; the [crdt] search tag is required.

EC/RN Number [RN]

EC/RN numbers are assigned by:

The EC/RN number search field includes both the Registry Number and the Related Registry Number (available in the NLM MeSH Browser).

Editor [ED]

The editor search field includes the editors for book or chapter citations.

Entry Date [EDAT]

Date the citation was added to the PubMed database. Note: Entry Date was called Entrez Date in the legacy PubMed system (retired in 2020).

Exceptions: As of December 15, 2008, citations added to PubMed more than twelve months after the date of publication have the EDAT set to the date of publication, except for book citations. Prior to this, the Entry Date was set to the Publication Date on citations published before September 1997. Entry Date is not included in All Fields retrieval; the [edat] search tag is required.

Search results are displayed in Entry Date for Most Recent sort order, i.e., last in, first out.

To search for a date range, insert a colon (:) between each date, e.g., 1996:1997 [edat] or 1998/01:1998/04 [edat].

See Searching By Date for additional information.

Filter [FILTER] [SB]

Technical tags used by LinkOut, filters include:

First Author Name [1AU]

The first personal author name in a citation.

Full Author Name [FAU]

The full author name for articles published from 2002 forward, if available. Full author searches can be entered in natural or inverted order, e.g., julia s wong or wong julia s.

Full Investigator Name [FIR]

The index for the article's full investigator or collaborator name, if available. Full investigator searches can be entered in natural or inverted order, e.g., harry janes or janes harry.

Grant Number [GR]

The grant number search field includes research grant numbers, contract numbers, or both that designate financial support by agencies of the US PHS (Public Health Service), and other national or international funding sources. The four parts of the grant data are:

  1. number, e.g., LM05545
  2. PHS 2-character grant abbreviation, e.g., LM
  3. institute acronym, e.g., NLM NIH HHS
  4. country, e.g., United States

Each individual grant part can be searched using [gr], e.g., NIH[gr]

See Grant Number Information Found in the GR Field in MEDLINE/PubMed for the 2-character abbreviations, PHS agency acronyms, and other US and non-US funding organizations.

More information about grant numbers:

Investigator [IR]

Names of principal investigator(s) or collaborators who contributed to the research. Search names following the author field format, e.g., soller b [ir]

ISBN [ISBN]

The ISBN for book or book chapters.

Issue [IP]

The number of the journal issue in which the article was published.

Journal [TA]

The journal search field includes the journal title abbreviation, full journal title, or ISSN number (e.g., J Biol Chem, Journal of Biological Chemistry, 0021-9258). If a journal title contains special characters, e.g., parentheses, brackets, enter the name without these characters, e.g., enter J Hand Surg [Am] as J Hand Surg Am.

Language [LA]

The language search field includes the language in which the article was published. Note that many non-English articles have English language abstracts. You may search using either the language or the first three characters of most languages, e.g., chi [la] retrieves the same results as chinese [la]. The most notable exception is jpn [la] for Japanese.

Last Author Name [LASTAU]

The last personal author name in a citation.

Location ID [LID]

Location ID includes the DOI or publisher ID that serves the role of pagination to locate an online article.

MeSH Date [MHDA]

The date the citation was indexed with MeSH Terms and elevated to MEDLINE for citations with an Entry Date after March 4, 2000. The MeSH Date is initially set to the Entry Date when the citation is added to PubMed. If the MeSH Date and Entry Date on a citation are the same, and the Entry Date is after March 4, 2000, the citation has not yet been indexed. MeSH Date is not included in All Fields retrieval; the [mhda] search tag is required.

Dates must be entered using the format YYYY/MM/DD [mhda], e.g. 2000/03/15 [mhda]. The month and day are optional (e.g., 2000 [mhda] or 2000/03 [mhda]).

To enter a date range, insert a colon (:) between each date, e.g., 1999:2000 [mhda] or 2000/03:2000/04 [mhda].

MeSH Major Topic [MAJR]

A MeSH term that is one of the main topics discussed in the article denoted by an asterisk on the MeSH term or MeSH/Subheading combination, e.g., Cytokines/physiology* See MeSH Terms [MH] below.

MeSH Subheadings [SH]

MeSH Subheadings are used with MeSH terms to help describe more completely a particular aspect of a subject. For example, the drug therapy of asthma is displayed as asthma/drug therapy; see MeSH/Subheading Combinations in MeSH Terms [MH] below.

The MeSH Subheading field allows users to "free float" Subheadings, e.g., hypertension [mh] AND toxicity [sh].

MeSH Subheadings automatically include the more specific Subheading terms under the term in a search. To turn off this automatic feature, use the search syntax [sh:noexp], e.g., therapy [sh:noexp].

In addition, you can enter the two-letter MeSH Subheading abbreviations rather than spelling out the Subheading, e.g., dh [sh] = diet therapy [sh].

MeSH Terms [MH]

The NLM Medical Subject Headings controlled vocabulary of biomedical terms that is used to describe the subject of each journal article in MEDLINE. MeSH 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 and select terms for searching in the MeSH Database.

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 uniformly indexed by subject, whatever the author's words.

More information about MeSH Terms and Major MeSH Topic search fields:

Modification Date [LR]

Modification date is a completed citation’s most recent revision date. Modification Date is not included in All Fields retrieval; the [lr] search tag is required.

NLM Unique ID [JID]

The NLM ID is the alpha-numeric identifier for the cited journal that was assigned by the NLM Integrated Library System LocatorPlus, e.g., 0375267 [jid].

Other Term [OT]

The author keyword field (OT field) is searchable with the text word [tw] and other term [ot] search tags. To retrieve all citations that have keywords, use the query haskeyword. Other term data may display an asterisk to indicate a major concept; however, you cannot search other terms with a major concept tag.

Owner

The owner search field includes the acronym that identifies the organization that supplied the citation data. Search using owner + the owner acronym, e.g., ownernasa.

Pagination [PG]

Enter only the first page number that the article appears on. The citation will display the full pagination of the article but this field is searchable using only the first page number.

Personal Name as Subject [PS]

Use this search field tag to limit retrieval to where the name is the subject of the article, e.g., varmus h[ps]. Search for personal names as subject using the author field format, e.g., varmus h[ps].

Pharmacological Action [PA]

Substances known to have a particular pharmacologic action. Each pharmacologic action term index is created with the drug/substance terms known to have that effect. This includes both MeSH terms and terms for Supplementary Concept Records.

Place of Publication [PL]

Indicates the cited journal's country of publication. Geographic place of publication regions are not searchable. In order to retrieve records for all countries in a region (e.g., North America) it is necessary to OR together the countries of interest. Note: This field is not included in all fields or text word retrieval.

PMCID and MID

Search for PMC or NIH manuscript identifiers using the appropriate prefix followed by the ID number, e.g., PMC2600426. To retrieve all NIH manuscript citations, use the query hasnihmsid.

PMID [PMID]

To search for a PubMed Identifier (PMID), enter the ID with or without the search field tag [pmid]. You can search for several PMIDs by entering each number in the search box separated by a space (e.g., 17170002 16381840); PubMed will OR the PMIDs together.

To search in combination with other terms, you must enter the search field tag, e.g., lipman[au] 16381840[pmid].

PMIDs do not change over time or during processing and are never reused.

Publication Date [DP]

Publication date is the date that the article was published.

Dates or date ranges must be searched using the format yyyy/mm/dd [dp], e.g. 1998/03/06 [dp]. The month and day are optional (e.g., 1998 [dp] or 1998/03 [dp]).

To enter a date range search, insert a colon (:) between each date, e.g., 1996:1998 [dp] or 1998/01:1998/04 [dp].

Use the following format to search X days, months or years immediately preceding today’s date where X = numeric value:

More information about publication dates:

Publication Type [PT]

Describes the type of material the article represents (e.g., Review, Clinical Trial, Retracted Publication, Letter); see the PubMed Publication Types, e.g., review[pt]. Publication Types are arranged hierarchically with more specific terms arranged beneath broader terms. Publication types automatically include the more specific publication types in a search. To turn off this automatic feature, use the search syntax [pt:noexp], e.g., review [pt:noexp].

Publisher [PUBN]

Includes publisher names for Bookshelf citations.

Secondary Source ID [SI]

The SI field identifies secondary source databanks and accession numbers, e.g., GenBank, GEO, PubChem, ClinicalTrials.gov, ISRCTN. The field is composed of the source followed by a slash followed by an accession number and can be searched with one or both components, e.g., genbank [si], AF001892 [si], genbank/AF001892 [si]. To retrieve all citations with an SI value, search hasdatabanklist.

Subset [SB]

The subset field is a method of restricting retrieval by subject, citation status and journal category, with the search tag [SB]. See also filters and Finding Related Links for a Citation Using LinkOut.

Supplementary Concept [NM]

Includes chemical, protocol, disease or organism terms. Synonyms to the supplementary concepts will automatically map when tagged with [nm]. This field was implemented in mid-1980; however, many chemical names are searchable as MeSH terms before that date.

Text Words [TW]

Includes all words and numbers in the title, abstract, other abstract, MeSH terms, MeSH Subheadings, Publication Types, Substance Names, Personal Name as Subject, Corporate Author, Secondary Source, Comment/Correction Notes, and Other Terms (see Other Term [OT] above) typically non-MeSH subject terms (keywords), including NASA Space Flight Mission, assigned by an organization other than NLM.

Title [TI]

Words and numbers included in the title of a citation, as well as the collection title for book citations.

Title/Abstract [TIAB]

Words and numbers included in a citation's title, collection title, abstract, other abstract and keywords. English language abstracts are taken directly from the published article. If an article does not have a published abstract, NLM does not create one.

Transliterated Title [TT]

Words and numbers in title originally published in a non-English language, in that language. Non-Roman alphabet language titles are transliterated. Transliterated title is not included in Text Word [TW] retrieval.

Volume [VI]

The number of the journal volume in which an article is published.

How PubMed works: Automatic Term Mapping (ATM)

Untagged terms that are entered in the search box are matched (in this order) against a Subject translation table (including MeSH (Medical Subject Headings) , a Journals translation table, the Author index, and an Investigator (Collaborator) index.

When a match is found for a term or phrase in a translation table the mapping process is complete and does not continue on to the next translation table.

To see how your terms were translated, check the Search Details available on the Advanced Search page for each query under History. If you want to report a translation that does not seem accurate for your search topic, please e-mail the information to the NLM Help Desk.

1. Subject translation table

The Subject Translation Table contains:

If a match is found in this translation table, the term will be searched as MeSH (that includes the MeSH term and any specific terms indented under that term in the MeSH hierarchy), and in all fields.

For example, if you enter child rearing in the search box, PubMed will translate this search to: "child rearing"[MeSH Terms] OR ("child"[All Fields] AND "rearing"[All Fields]) OR "child rearing"[All Fields]

If you enter a MeSH Term that is also a Pharmacologic Action PubMed will search the term as [MeSH Terms], [Pharmacologic Action], and [All Fields].

If you enter an entry term for a MeSH term the translation will also include an all fields search for the MeSH term associated with the entry term. For example, a search for odontalgia will translate to: "toothache"[MeSH Terms] OR "toothache"[All Fields] OR "odontalgia"[All Fields] OR "odontalgias"[All Fields] because Odontalgia is an entry term for the MeSH term toothache.

Substance name mappings do not include a mapping for individual terms in a phrase, e.g., IL-22 will not include IL[All Fields AND 22[All Fields].

MeSH term mappings that include a standalone number or single character do not include a mapping for individual terms in a phrase, e.g., Protein C will not include Protein[All Fields] or C[All Fields].

2. Journals translation table

The Journals translation table contains the:

These will automatically map to the journal abbreviation that is used to search journals in PubMed and in all fields. For example, a search for endocrine pathology will translate to: "Endocr Pathol"[Journal] OR ("endocrine"[All Fields] AND "pathology"[All Fields]) OR "endocrine pathology"[All Fields]

3. Author index

If the term is not found in the above tables, and is not a single term, PubMed checks the author index for a match. The author index includes author names and initials, as well as full author names for articles published from 2002 forward, if available.

More information about author searching:

4. Investigator (Collaborator) index

If the term is not found in the above tables, except for Author, and is not a single term, the investigator index is consulted for a match. The investigator (collaborator) index includes full names, if available. Enter a full investigator name in natural or inverted order, e.g., harry janes or janes harry.

5. If no match is found?

PubMed breaks apart the phrase and repeats the above automatic term mapping process until a match is found. PubMed ignores stopwords in searches.

If there is no match, the individual terms will be combined (ANDed) together and searched in all fields.

When a search includes terms that were tagged with a search field during the automatic term mapping process and retrieves zero results, the system triggers a subsequent search using “Schema: all .” “Schema: all” modifies the search by removing the automatically added search field tags, and then searches each term in all fields.

Algorithm for finding best matching citations in PubMed

The learned ranking algorithm combines over 150 signals that are helpful for finding best matching results. Most of these signals are computed from the query-document term pairs (e.g. number of term matches between the query and the document) while others are either specific to a document (e.g. publication type; publication year) or query (e.g. query length). The new ranking model was built on relevance data extracted from the anonymous and aggregated PubMed search logs over an extended period of time.

For more information about the Best Match algorithm, please see Best Match: New relevance search for PubMed .

PubMed coverage

PubMed provides access to bibliographic information that includes MEDLINE, as well as:

For additional information, please see the NLM Fact Sheet: Medline, PubMed, and PMC (PubMed Central): How are they different ?

MEDLINE

MEDLINE is the NLM premier bibliographic database that contains references to journal articles in the life sciences with a concentration on biomedicine. MEDLINE records are indexed with NLM Medical Subject Headings (MeSH). The database contains citations from the late 1940s to the present , with some older material. New citations that have been indexed with MeSH terms, publication types, GenBank accession numbers, and other indexing data are available daily. To limit your search to MEDLINE citations, add medline[sb] to your search.

Publisher-supplied citations

Citations are received electronically from publishers and appear in PubMed daily. Most citations progress to in-process, and then to indexed for MEDLINE. However, not all citations will be indexed for MEDLINE. Publishers may submit citations for articles that appear on the web in advance of the journal issue's release. These ahead-of-print citations display the tag [Online ahead of print].

NLM author indexing policy

NLM author indexing policy is as follows:

More information:

Error messages

System error messages

Please provide your IT staff with the technical browser advice for NCBI web pages to ensure your browser, firewall, and servers are enabled for JavaScript, cookies, pop-ups, and HTTP 1.1. Antivirus software may affect page caching which can result in unexpected page expired messages. Also, nlm.nih.gov should be added as a browser exception and be considered a trusted site by your system and network. You may have to delete your browser's cache (temporary files) before trying to access PubMed again.

Typographical errors

Please contact the journal publisher directly to report an error and initiate a correction to PubMed citations for content other than MeSH.

To report a MeSH error in a PubMed citation, please contact the NLM Help Desk and include the PMID number (e.g., PMID: 12345678), and an indication of the incorrect and correct information.

NLM provides data to vendors around the world. Other products and services will not necessarily immediately reflect corrections made to PubMed records. If you search through a vendor's system, please contact your vendor about their maintenance schedules.

Cookies

A "cookie" is information stored by a web site server on your computer. See the NLM Privacy Policy for additional information.

In the case of PubMed, cookies store information about your interactions that may be needed later to perform a function. Cookies placed by PubMed are removed from your computer after a set time period unless you choose to use a persistent cookie with the My NCBI automatic sign in function.

To use these interactive features you need to enable cookies on your computer. Consult your browser's help for information on enabling cookies.

If you have problems using cookie-dependent features of PubMed, even after enabling cookies, possible reasons may include:

MeSH Subheadings

See the MeSH Subheadings table below and scope notes and allowable categories on the NLM website.

Abbreviation MeSH Subheading Abbreviation MeSH Subheading
AB Abnormalities IR Innervation
AD Administration and Dosage IS Instrumentation
AE Adverse Effects IP Isolation and Purification
AG Agonists LJ Legislation and Jurisprudence
AA Analogs and Derivatives ME Metabolism
AN Analysis MT Methods
AH Anatomy and Histology MI Microbiology
AI Antagonists and Inhibitors MO Mortality
BI Biosynthesis NU Nursing
BS Blood Supply OG Organization and Administration
BL Blood PS Parasitology
CF Cerebrospinal Fluid PY Pathogenicity
CS Chemical Synthesis PA Pathology
CI Chemically Induced PK Pharmacokinetics
CH Chemistry PD Pharmacology
CL Classification PH Physiology
CO Complications PP Physiopathology
CN Congenital PO Poisoning
CY Cytology PC Prevention and Control
DF Deficiency PX Psychology
DI Diagnosis RE Radiation Effects
DH Diet Therapy RT Radiotherapy
DG Diagnostic Imaging RH Rehabilitation
DE Drug Effects SC Secondary
DT Drug Therapy ST Standards
EC Economics SN Statistics and Numerical Data
ED Education SD Supply and Distribution
EM Embryology SU Surgery
EN Enzymology TU Therapeutic Use
EP Epidemiology TH Therapy
ES Ethics TO Toxicity
EH Ethnology TM Transmission
ET Etiology TR Transplantation
GE Genetics TD Trends
GD Growth and Development UL Ultrastructure
HI History UR Urine
IM Immunology VE Veterinary
IN Injuries VI Virology

Stopwords

Stopwords
A a, about, again, all, almost, also, although, always, among, an, and, another, any, are, as, at
B be, because, been, before, being, between, both, but, by
C can, could
D did, do, does, done, due, during
E each, either, enough, especially, etc
F for, found, from, further
H had, has, have, having, here, how, however
I i, if, in, into, is, it, its, itself
J just
K kg, km
M made, mainly, make, may, mg, might, ml, mm, most, mostly, must
N nearly, neither, no, nor
O obtained, of, often, on, our, overall
P perhaps, pmid
Q quite
R rather, really, regarding
S seem, seen, several, should, show, showed, shown, shows, significantly, since, so, some, such
T than, that, the, their, theirs, them, then, there, therefore, these, they, this, those, through, thus, to
U upon
V various, very
W was, we, were, what, when, which, while, with, within, without, would

PubMed character conversions

Certain characters have special meaning in searches, others are converted to spaces.

Searches that include the following characters are translated as follows:

Characters converted to spaces in search queries:

Some characters have special meaning in MeSH fields:

Publication Types

See the complete list of Publication Types. Publication types found in PubMed are listed below.

Status Subsets

How to Search Citation Status
publisher[sb] NOT pubstatusnihms NOT pubstatuspmcsd NOT pmcbook Citations recently added to PubMed via electronic submission from a publisher, and are soon to proceed to the next stage, PubMed - in process (see below). Also for citations received before late 2003 if they are from journals not indexed for MEDLINE, or from a journal that was accepted for MEDLINE after the citations' publication date. These citations bibliographic data have not been reviewed.
inprocess[sb] MeSH terms will be assigned if the subject of the article is within the scope of MEDLINE.
medline[sb] Citations that have been indexed with MeSH terms, Publication Types, Substance Names, etc.
pubstatusnihms AND publisher[sb] Author manuscripts submitted to PMC that fall under the NIH Public Access Policy.
pubstatuspmcsd AND publisher[sb] Records for selective deposit articles in PMC. These are articles published in non-MEDLINE journals where the publisher has chosen to deposit in PMC only those articles that fall under the NIH Public Access Policy.
pmcbook Book and book chapter citations available on the NCBI Bookshelf.
pubmednotmedline[sb] Citations that will not receive MEDLINE indexing because they are for articles in non-MEDLINE journals, or they are for articles in MEDLINE journals but the articles are out of scope, or they are from issues published prior to the date the journal was selected for indexing, or citations to articles from journals that deposit their full text articles in PMC but have not yet been recommended for indexing in MEDLINE.

Clinical Queries filters

Systematic reviews search filter

Clinical Queries using research methodology filters

The Clinical Queries search filters are based on the work of Haynes RB et al.

Category Optimized For Sensitive/ Specific PubMed Equivalent
therapy sensitive/broad 99%/70% ((clinical[Title/Abstract] AND trial[Title/Abstract]) OR clinical trials as topic[MeSH Terms] OR clinical trial[Publication Type] OR random*[Title/Abstract] OR random allocation[MeSH Terms] OR therapeutic use[MeSH Subheading])
specific/narrow 93%/97% (randomized controlled trial[Publication Type] OR (randomized[Title/Abstract] AND controlled[Title/Abstract] AND trial[Title/Abstract]))
diagnosis sensitive/broad 98%/74% (sensitiv*[Title/Abstract] OR sensitivity and specificity[MeSH Terms] OR diagnose[Title/Abstract] OR diagnosed[Title/Abstract] OR diagnoses[Title/Abstract] OR diagnosing[Title/Abstract] OR diagnosis[Title/Abstract] OR diagnostic[Title/Abstract] OR diagnosis[MeSH:noexp] OR diagnostic * [MeSH:noexp] OR diagnosis,differential[MeSH:noexp] OR diagnosis[Subheading:noexp])
specific/narrow 64%/98% (specificity[Title/Abstract])
etiology sensitive/broad 93%/63% (risk*[Title/Abstract] OR risk*[MeSH:noexp] OR risk *[MeSH:noexp] OR cohort studies[MeSH Terms] OR group[Text Word] OR groups[Text Word] OR grouped [Text Word])
specific/narrow 51%/95% ((relative[Title/Abstract] AND risk*[Title/Abstract]) OR (relative risk[Text Word]) OR risks[Text Word] OR cohort studies[MeSH:noexp] OR (cohort[Title/Abstract] AND study[Title/Abstract]) OR (cohort[Title/Abstract] AND studies[Title/Abstract]))
prognosis sensitive/broad 90%/80% (incidence[MeSH:noexp] OR mortality[MeSH Terms] OR follow up studies[MeSH:noexp] OR prognos*[Text Word] OR predict*[Text Word] OR course*[Text Word])
specific/narrow 52%/94% (prognos*[Title/Abstract] OR (first[Title/Abstract] AND episode[Title/Abstract]) OR cohort[Title/Abstract])
clinical prediction guides sensitive/broad 96%/79% (predict*[tiab] OR predictive value of tests[mh] OR score[tiab] OR scores[tiab] OR scoring system[tiab] OR scoring systems[tiab] OR observ*[tiab] OR observer variation[mh])
specific/narrow 54%/99% (validation[tiab] OR validate[tiab])

Medical genetics search filters

The genetics searches were developed in conjunction with the staff of GeneReviews: Genetic Disease Online Reviews at GeneTests, University of Washington, Seattle.

Category PubMed Equivalent
Diagnosis (Diagnosis AND Genetics)
Differential Diagnosis (Differential Diagnosis[MeSH] OR Differential Diagnosis[Text Word] AND Genetics)
Clinical Description (Natural History OR Mortality OR Phenotype OR Prevalence OR Penetrance AND Genetics)
Management (therapy[Subheading] OR treatment[Text Word] OR treatment outcome OR investigational therapies AND Genetics)
Genetic Counseling (Genetic Counseling OR Inheritance pattern AND genetics)
Molecular Genetics (Medical Genetics OR genotype OR genetics[Subheading] AND genetics)
Genetic Testing (DNA Mutational Analysis OR Laboratory techniques and procedures OR Genetic Markers OR diagnosis OR testing OR test OR screening OR mutagenicity tests OR genetic techniques OR molecular diagnostic techniques AND genetics)
All ((Diagnosis AND genetics) OR (Differential Diagnosis[MeSH] OR Differential Diagnosis[Text Word] AND genetics) OR (Natural History OR Mortality OR Phenotype OR Prevalence OR Penetrance AND genetics) OR (therapy[Subheading] OR treatment[Text Word] OR treatment outcome OR investigational therapies AND genetics) OR (Genetic Counseling OR Inheritance pattern AND genetics) OR (Medical Genetics OR genotype OR genetics[Subheading] AND genetics) OR (DNA Mutational Analysis OR Laboratory techniques and procedures OR Genetic Markers OR diagnosis OR testing OR test OR screening OR mutagenicity tests OR genetic techniques OR molecular diagnostic techniques AND genetics))

Computation of similar articles

The neighbors of a document are those documents in the database that are the most similar to it. The similarity between documents is measured by the words they have in common, with some adjustment for document lengths. To carry out such a program, one must first define what a word is. For us, a word is basically an unbroken string of letters and numerals with at least one letter of the alphabet in it. Words end at hyphens, spaces, new lines, and punctuation. The 132 common, but uninformative, words (also known as stopwords) are eliminated from processing at this stage. Next, a limited amount of stemming of words is done, but no thesaurus is used in processing. Words from the abstract of a document are classified as text words. Words from titles are also classified as text words, but words from titles are added in a second time to give them a small advantage in the local weighting scheme. MeSH terms are placed in a third category, and a MeSH term with a subheading qualifier is entered twice, once without the qualifier and once with it. If a MeSH term is starred (indicating a major concept in a document), the star is ignored. These three categories of words (or phrases in the case of MeSH) comprise the representation of a document. No other fields, such as Author or Journal, enter into the calculations.

Having obtained the set of terms that represent each document, the next step is to recognize that not all words are of equal value. Each time a word is used, it is assigned a numerical weight. This numerical weight is based on information that the computer can obtain by automatic processing. Automatic processing is important because the number of different terms that have to be assigned weights is close to two million for this system. The weight or value of a term is dependent on three types of information: 1) the number of different documents in the database that contain the term; 2) the number of times the term occurs in a particular document; and 3) the number of term occurrences in the document. The first of these pieces of information is used to produce a number called the global weight of the term. The global weight is used in weighting the term throughout the database. The second and third pieces of information pertain only to a particular document and are used to produce a number called the local weight of the term in that specific document. When a word occurs in two documents, its weight is computed as the product of the global weight times the two local weights (one pertaining to each of the documents).

The global weight of a term is greater for the less frequent terms. This is reasonable because the presence of a term that occurred in most of the documents would really tell one very little about a document. On the other hand, a term that occurred in only 100 documents of one million would be very helpful in limiting the set of documents of interest. A word that occurred in only 10 documents is likely to be even more informative and will receive an even higher weight.

The local weight of a term is the measure of its importance in a particular document. Generally, the more frequent a term is within a document, the more important it is in representing the content of that document. However, this relationship is saturating, i.e., as the frequency continues to go up, the importance of the word increases less rapidly and finally comes to a finite limit. In addition, we do not want a longer document to be considered more important just because it is longer; therefore, a length correction is applied. This local weight computation is based on the Poisson distribution and the formula can be found in Lin J and Wilbur WJ.

The similarity between two documents is computed by adding up the weights (local wt1 × local wt2 × global wt) of all of the terms the two documents have in common. This provides an indication of how related two documents are. The resultant score is an example of a vector score. Vector scoring was originated by Gerard Salton and has a long history in text retrieval. The interested reader is referred to Salton, Automatic Text Processing, Reading, MA: Addison-Wesley, 1989 for further information on this topic. Our approach differs from other approaches in the way we calculate the local weights for the individual terms. Once the similarity score of a document in relation to each of the other documents in the database has been computed, that document's neighbors are identified as the most similar (highest scoring) documents found. These closely related documents are pre-computed for each document in PubMed so that when you select Similar articles, the system has only to retrieve this list. This enables a fast response time for such queries.

Journal lists

PubMed journals

NCBI molecular biology database journals

PubMed and NCBI molecular biology database journals

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